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+<tr id="row_0_0_0_0_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html" target="_self">AccumulatorAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html" target="_self">AnalysisAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_2_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html" target="_self">AnalysisCtrlRuleAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_3_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html" target="_self">AnalysisDataAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_4_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html" target="_self">AnalysisJobAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_5_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html" target="_self">AnalysisStatsAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_6_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html" target="_self">BaseAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_7_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html" target="_self">DataflowRuleAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_8_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html" target="_self">DBAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_9_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html" target="_self">DBConnection</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_10_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html" target="_self">LogMessageAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_11_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html" target="_self">MetaAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_12_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html" target="_self">MetaContainer</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_13_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html" target="_self">NakedTableAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_14_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html" target="_self">ObjectAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_15_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html" target="_self">ResourceClassAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_16_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html" target="_self">ResourceDescriptionAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_0_17_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html" target="_self">SqlSchemaAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img id="arr_0_0_0_1_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_0_0_1_')"/><img src="ftv2ns.png" alt="N" width="24" height="22" /><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html" target="_self">Meadow</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_1_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html" target="_self">LOCAL</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_1_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html" target="_self">LSF</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img id="arr_0_0_0_2_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_0_0_2_')"/><img src="ftv2ns.png" alt="N" width="24" height="22" /><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html" target="_self">PipeConfig</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_any_commands__conf.html" target="_self">AnyCommands_conf</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_apply_to_databases__conf.html" target="_self">ApplyToDatabases_conf</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_2_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html" target="_self">CompressFiles_conf</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_3_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html" target="_self">FailureTest_conf</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_4_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html" target="_self">FastaSplitter_conf</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_5_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html" target="_self">HiveGeneric_conf</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_6_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html" target="_self">LongMult_conf</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_7_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html" target="_self">LongMultSt_conf</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_8_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html" target="_self">MemlimitTest_conf</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_9_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html" target="_self">RunListOfCommandsOnFarm_conf</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_2_10_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html" target="_self">TableDumperZipper_conf</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img id="arr_0_0_0_3_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_0_0_3_')"/><img src="ftv2ns.png" alt="N" width="24" height="22" /><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html" target="_self">RunnableDB</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_0_0_0_3_0_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_0_0_3_0_')"/><img src="ftv2ns.png" alt="N" width="24" height="22" /><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult.html" target="_self">LongMult</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_0_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html" target="_self">AddTogether</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_0_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html" target="_self">DigitFactory</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_0_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html" target="_self">PartMultiply</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html" target="_self">DatabaseDumper</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html" target="_self">Dummy</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_3_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html" target="_self">FailureTest</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_4_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html" target="_self">FastaFactory</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_5_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html" target="_self">JobFactory</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_6_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html" target="_self">MySQLTransfer</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_7_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html" target="_self">NotifyByEmail</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_8_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html" target="_self">SqlCmd</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_9_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html" target="_self">SqlHealthcheck</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_3_10_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html" target="_self">SystemCmd</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_4_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img id="arr_0_0_0_4_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('0_0_0_4_')"/><img src="ftv2ns.png" alt="N" width="24" height="22" /><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html" target="_self">Utils</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_4_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html" target="_self">Config</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_4_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html" target="_self">Graph</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_4_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html" target="_self">GraphViz</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_4_3_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html" target="_self">RedirectStack</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_4_4_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html" target="_self">Stopwatch</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_4_5_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l.html" target="_self">URL</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_5_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html" target="_self">Accumulator</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_6_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html" target="_self">Analysis</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_7_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html" target="_self">AnalysisCtrlRule</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_8_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html" target="_self">AnalysisJob</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_9_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html" target="_self">AnalysisStats</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_10_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html" target="_self">Configurable</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_11_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html" target="_self">DataflowRule</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_12_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html" target="_self">DependentOptions</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_13_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html" target="_self">Limiter</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_14_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html" target="_self">Meadow</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_15_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html" target="_self">NakedTable</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_16_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html" target="_self">Params</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_17_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html" target="_self">Process</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_18_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html" target="_self">Queen</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_19_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html" target="_self">ResourceClass</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_20_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html" target="_self">ResourceDescription</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_21_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html" target="_self">Scheduler</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_22_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html" target="_self">URLFactory</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_23_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html" target="_self">Utils</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_24_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html" target="_self">Valley</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_25_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_version.html" target="_self">Version</a></td><td class="desc"></td></tr>
+<tr id="row_0_0_0_26_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html" target="_self">Worker</a></td><td class="desc"></td></tr>
+<tr id="row_1_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_mini_pecan_multi__conf.html" target="_self">MiniPecanMulti_conf</a></td><td class="desc"></td></tr>
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+</table>
+</div><!-- directory -->
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: scripts/beekeeper.pl File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="dynsections.js"></script>
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+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
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+<!-- end header part -->
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li><a href="annotated.html"><span>Classes</span></a></li>
+ <li class="current"><a href="files.html"><span>Files</span></a></li>
+ <li>
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+ <li><a href="files.html"><span>File List</span></a></li>
+ <li><a href="globals.html"><span>File Members</span></a></li>
+ </ul>
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+</div><!-- top -->
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+ onmouseout="return searchBox.OnSearchSelectHide()"
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+
+<!-- iframe showing the search results (closed by default) -->
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+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="summary">
+<a href="#func-members">Functions</a> </div>
+ <div class="headertitle">
+<div class="title">beekeeper.pl File Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:a3ce8b237b3bdb2817dac6f769e5768c2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">main</a> ()</td></tr>
+<tr class="separator:a3ce8b237b3bdb2817dac6f769e5768c2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad7de8680eb8b39e160cee04957ccd668"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="beekeeper_8pl.html#ad7de8680eb8b39e160cee04957ccd668">generate_worker_cmd</a> ()</td></tr>
+<tr class="separator:ad7de8680eb8b39e160cee04957ccd668"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:af314298b28a69538fb25aa7eb1327c98"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="beekeeper_8pl.html#af314298b28a69538fb25aa7eb1327c98">run_autonomously</a> ()</td></tr>
+<tr class="separator:af314298b28a69538fb25aa7eb1327c98"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<h2 class="groupheader">Function Documentation</h2>
+<a class="anchor" id="ad7de8680eb8b39e160cee04957ccd668"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public generate_worker_cmd </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-generate_worker_cmd" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-generate_worker_cmd-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-generate_worker_cmd-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-generate_worker_cmd-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="beekeeper_8pl.html#ad7de8680eb8b39e160cee04957ccd668">generate_worker_cmd</a> {</div>
+<div class="line"> my ($self, $run_analysis, $run_job_id, $force) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $worker_cmd = $ENV{<span class="stringliteral">'EHIVE_ROOT_DIR'</span>}.<span class="stringliteral">'/scripts/runWorker.pl'</span>;</div>
+<div class="line"></div>
+<div class="line"> unless(-x $worker_cmd) {</div>
+<div class="line"> print(<span class="stringliteral">"Can't run '$worker_cmd' script for some reason, please investigate.\n"</span>);</div>
+<div class="line"> exit(1);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $worker_option (<span class="stringliteral">'url'</span>, <span class="stringliteral">'reg_conf'</span>, <span class="stringliteral">'reg_type'</span>, <span class="stringliteral">'reg_alias'</span>, <span class="stringliteral">'nosqlvc'</span>, <span class="stringliteral">'job_limit'</span>, <span class="stringliteral">'life_span'</span>, <span class="stringliteral">'retry_throwing_jobs'</span>, <span class="stringliteral">'can_respecialize'</span>, <span class="stringliteral">'hive_log_dir'</span>, <span class="stringliteral">'debug'</span>) {</div>
+<div class="line"> <span class="keywordflow">if</span>(defined(my $value = $self->{$worker_option})) {</div>
+<div class="line"> $worker_cmd .= <span class="stringliteral">" -${worker_option} $value"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # special task:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span> ($run_job_id) {</div>
+<div class="line"> $worker_cmd .= <span class="stringliteral">" -job_id $run_job_id"</span>;</div>
+<div class="line"> } elsif ($run_analysis) {</div>
+<div class="line"> $worker_cmd .= <span class="stringliteral">" -logic_name "</span>.$run_analysis->logic_name;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span> (defined($force)) {</div>
+<div class="line"> $worker_cmd .= <span class="stringliteral">" -force $force"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $worker_cmd;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3ce8b237b3bdb2817dac6f769e5768c2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public main </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-main" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-main-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-main-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-main-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">main</a> {</div>
+<div class="line"> $| = 1;</div>
+<div class="line"> Bio::EnsEMBL::Registry->no_version_check(1);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # ok this is a hack, but I'm going to pretend I've got an object here</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # by creating a hash ref and passing it around like an object</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # this is to avoid using global variables in functions, and to consolidate</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # the globals into a nice '$self' package</span></div>
+<div class="line"><span class="preprocessor"></span> my $self = {};</div>
+<div class="line"></div>
+<div class="line"> my $help = 0;</div>
+<div class="line"> my $report_versions = 0;</div>
+<div class="line"> my $loopit = 0;</div>
+<div class="line"> my $sync = 0;</div>
+<div class="line"> my $local = 0;</div>
+<div class="line"> my $show_failed_jobs = 0;</div>
+<div class="line"> my $default_meadow_type = undef;</div>
+<div class="line"> my $submit_workers_max = undef;</div>
+<div class="line"> my $total_running_workers_max = undef;</div>
+<div class="line"> my $submission_options = undef;</div>
+<div class="line"> my $run = 0;</div>
+<div class="line"> my $max_loops = 0; # not running by <span class="keywordflow">default</span></div>
+<div class="line"> my $run_job_id = undef;</div>
+<div class="line"> my $force = undef;</div>
+<div class="line"> my $keep_alive = 0; # ==1 means run even when there is nothing to <span class="keywordflow">do</span></div>
+<div class="line"> my $check_for_dead = 0;</div>
+<div class="line"> my $all_dead = 0;</div>
+<div class="line"> my $balance_semaphores = 0;</div>
+<div class="line"> my $job_id_for_output = 0;</div>
+<div class="line"> my $show_worker_stats = 0;</div>
+<div class="line"> my $kill_worker_id = 0;</div>
+<div class="line"> my $reset_job_id = 0;</div>
+<div class="line"> my $reset_all_jobs_for_analysis = 0;</div>
+<div class="line"> my $reset_failed_jobs_for_analysis = 0;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'url'</span>} = undef;</div>
+<div class="line"> $self->{<span class="stringliteral">'reg_conf'</span>} = undef;</div>
+<div class="line"> $self->{<span class="stringliteral">'reg_type'</span>} = undef;</div>
+<div class="line"> $self->{<span class="stringliteral">'reg_alias'</span>} = undef;</div>
+<div class="line"> $self->{<span class="stringliteral">'nosqlvc'</span>} = undef;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'sleep_minutes'</span>} = 1;</div>
+<div class="line"> $self->{<span class="stringliteral">'retry_throwing_jobs'</span>} = undef;</div>
+<div class="line"> $self->{<span class="stringliteral">'can_respecialize'</span>} = undef;</div>
+<div class="line"> $self->{<span class="stringliteral">'hive_log_dir'</span>} = undef;</div>
+<div class="line"> $self->{<span class="stringliteral">'submit_stdout_file'</span>} = undef;</div>
+<div class="line"> $self->{<span class="stringliteral">'submit_stderr_file'</span>} = undef;</div>
+<div class="line"> $self->{<span class="stringliteral">'submit_log_dir'</span>} = undef;</div>
+<div class="line"></div>
+<div class="line"> GetOptions(</div>
+<div class="line"> # connection parameters</div>
+<div class="line"> <span class="stringliteral">'url=s'</span> => \$self->{<span class="stringliteral">'url'</span>},</div>
+<div class="line"> <span class="stringliteral">'reg_conf|regfile=s'</span> => \$self->{<span class="stringliteral">'reg_conf'</span>},</div>
+<div class="line"> <span class="stringliteral">'reg_type=s'</span> => \$self->{<span class="stringliteral">'reg_type'</span>},</div>
+<div class="line"> <span class="stringliteral">'reg_alias|regname=s'</span>=> \$self->{<span class="stringliteral">'reg_alias'</span>},</div>
+<div class="line"> <span class="stringliteral">'nosqlvc=i'</span> => \$self->{<span class="stringliteral">'nosqlvc'</span>}, # can<span class="stringliteral">'t use the binary "!" as it is a propagated option</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # loop control</span></div>
+<div class="line"><span class="stringliteral"> '</span>run<span class="stringliteral">' => \$run,</span></div>
+<div class="line"><span class="stringliteral"> '</span>loop<span class="stringliteral">' => \$loopit,</span></div>
+<div class="line"><span class="stringliteral"> '</span>max_loops=i<span class="stringliteral">' => \$max_loops,</span></div>
+<div class="line"><span class="stringliteral"> '</span>keep_alive<span class="stringliteral">' => \$keep_alive,</span></div>
+<div class="line"><span class="stringliteral"> '</span>job_id|run_job_id=i<span class="stringliteral">'=> \$run_job_id,</span></div>
+<div class="line"><span class="stringliteral"> '</span>force=i<span class="stringliteral">' => \$force,</span></div>
+<div class="line"><span class="stringliteral"> '</span>sleep=f<span class="stringliteral">' => \$self->{'</span>sleep_minutes<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # meadow control</span></div>
+<div class="line"><span class="stringliteral"> '</span>local!<span class="stringliteral">' => \$local,</span></div>
+<div class="line"><span class="stringliteral"> '</span>meadow_type=s<span class="stringliteral">' => \$default_meadow_type,</span></div>
+<div class="line"><span class="stringliteral"> '</span>total_running_workers_max=i<span class="stringliteral">' => \$total_running_workers_max,</span></div>
+<div class="line"><span class="stringliteral"> '</span>submit_workers_max=i<span class="stringliteral">' => \$submit_workers_max,</span></div>
+<div class="line"><span class="stringliteral"> '</span>submission_options=s<span class="stringliteral">' => \$submission_options,</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # worker control</span></div>
+<div class="line"><span class="stringliteral"> '</span>job_limit=i<span class="stringliteral">' => \$self->{'</span>job_limit<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> '</span>life_span|lifespan=i<span class="stringliteral">' => \$self->{'</span>life_span<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> '</span>logic_name=s<span class="stringliteral">' => \$self->{'</span>logic_name<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> '</span>hive_log_dir|hive_output_dir=s<span class="stringliteral">' => \$self->{'</span>hive_log_dir<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> '</span>retry_throwing_jobs=i<span class="stringliteral">' => \$self->{'</span>retry_throwing_jobs<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> '</span>can_respecialize=i<span class="stringliteral">' => \$self->{'</span>can_respecialize<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> '</span>debug=i<span class="stringliteral">' => \$self->{'</span>debug<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> '</span>submit_stdout_file=s<span class="stringliteral">' => \$self->{'</span>submit_stdout_file<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> '</span>submit_stderr_file=s<span class="stringliteral">' => \$self->{'</span>submit_stderr_file<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> '</span>submit_log_dir=s<span class="stringliteral">' => \$self->{'</span>submit_log_dir<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # other commands/options</span></div>
+<div class="line"><span class="stringliteral"> '</span>h|help!<span class="stringliteral">' => \$help,</span></div>
+<div class="line"><span class="stringliteral"> '</span>v|versions!<span class="stringliteral">' => \$report_versions,</span></div>
+<div class="line"><span class="stringliteral"> '</span>sync!<span class="stringliteral">' => \$sync,</span></div>
+<div class="line"><span class="stringliteral"> '</span>dead!<span class="stringliteral">' => \$check_for_dead,</span></div>
+<div class="line"><span class="stringliteral"> '</span>killworker=i<span class="stringliteral">' => \$kill_worker_id,</span></div>
+<div class="line"><span class="stringliteral"> '</span>alldead!<span class="stringliteral">' => \$all_dead,</span></div>
+<div class="line"><span class="stringliteral"> '</span>balance_semaphores<span class="stringliteral">'=> \$balance_semaphores,</span></div>
+<div class="line"><span class="stringliteral"> '</span>no_analysis_stats<span class="stringliteral">' => \$self->{'</span>no_analysis_stats<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> '</span>worker_stats<span class="stringliteral">' => \$show_worker_stats,</span></div>
+<div class="line"><span class="stringliteral"> '</span>failed_jobs<span class="stringliteral">' => \$show_failed_jobs,</span></div>
+<div class="line"><span class="stringliteral"> '</span>reset_job_id=i<span class="stringliteral">' => \$reset_job_id,</span></div>
+<div class="line"><span class="stringliteral"> '</span>reset_failed|reset_failed_jobs_for_analysis=s<span class="stringliteral">' => \$reset_failed_jobs_for_analysis,</span></div>
+<div class="line"><span class="stringliteral"> '</span>reset_all|reset_all_jobs_for_analysis=s<span class="stringliteral">' => \$reset_all_jobs_for_analysis,</span></div>
+<div class="line"><span class="stringliteral"> '</span>job_output=i<span class="stringliteral">' => \$job_id_for_output,</span></div>
+<div class="line"><span class="stringliteral"> '</span>monitor!<span class="stringliteral">' => \$self->{'</span>monitor<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if ($help) { script_usage(0); }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($report_versions) {</span></div>
+<div class="line"><span class="stringliteral"> report_versions();</span></div>
+<div class="line"><span class="stringliteral"> exit(0);</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $config = Bio::EnsEMBL::Hive::Utils::Config->new(); # will probably add a config_file option later</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($run or $run_job_id) {</span></div>
+<div class="line"><span class="stringliteral"> $max_loops = 1;</span></div>
+<div class="line"><span class="stringliteral"> } elsif ($loopit or $keep_alive) {</span></div>
+<div class="line"><span class="stringliteral"> unless($max_loops) {</span></div>
+<div class="line"><span class="stringliteral"> $max_loops = -1; # unlimited</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> unless(defined($self->{'</span>monitor<span class="stringliteral">'})) {</span></div>
+<div class="line"><span class="stringliteral"> $self->{'</span>monitor<span class="stringliteral">'} = 1;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($self->{'</span>url<span class="stringliteral">'} or $self->{'</span>reg_alias<span class="stringliteral">'}) {</span></div>
+<div class="line"><span class="stringliteral"> $self->{'</span>dba<span class="stringliteral">'} = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new(</span></div>
+<div class="line"><span class="stringliteral"> -url => $self->{'</span>url<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> -reg_conf => $self->{'</span>reg_conf<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> -reg_type => $self->{'</span>reg_type<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> -reg_alias => $self->{'</span>reg_alias<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> -no_sql_schema_version_check => $self->{'</span>nosqlvc<span class="stringliteral">'},</span></div>
+<div class="line"><span class="stringliteral"> );</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> print "\nERROR : Connection parameters (url or reg_conf+reg_alias) need to be specified\n\n";</span></div>
+<div class="line"><span class="stringliteral"> script_usage(1);</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $self->{'</span>safe_url<span class="stringliteral">'} = $self->{'</span>dba<span class="stringliteral">'}->dbc->url('</span>WORKER_PASSWORD<span class="stringliteral">');</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $queen = $self->{'</span>dba<span class="stringliteral">'}->get_Queen;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $pipeline_name = $self->{'</span>dba<span class="stringliteral">'}->get_MetaAdaptor->fetch_value_by_key( '</span>hive_pipeline_name<span class="stringliteral">' );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($pipeline_name) {</span></div>
+<div class="line"><span class="stringliteral"> warn "Pipeline name: $pipeline_name\n";</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> print STDERR "+---------------------------------------------------------------------+\n";</span></div>
+<div class="line"><span class="stringliteral"> print STDERR "! !\n";</span></div>
+<div class="line"><span class="stringliteral"> print STDERR "! WARNING: !\n";</span></div>
+<div class="line"><span class="stringliteral"> print STDERR "! !\n";</span></div>
+<div class="line"><span class="stringliteral"> print STDERR "! At the moment your pipeline doesn'</span>t have <span class="stringliteral">'pipeline_name'</span> defined. !\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> print STDERR "</span>! This may seriously impair your beekeeping experience unless you are !\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> print STDERR "</span>! the only farm user. The name should be set in your PipeConfig file, !\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> print STDERR "</span>! or <span class="keywordflow">if</span> you are running an old pipeline you can just set it by hand !\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> print STDERR "</span>! in the <span class="stringliteral">'meta'</span> table. !\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> print STDERR "</span>! !\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> print STDERR "</span>+---------------------------------------------------------------------+\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($run_job_id) {</span></div>
+<div class="line"><span class="stringliteral"> $submit_workers_max = 1;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $default_meadow_type = 'LOCAL' if($local);</span></div>
+<div class="line"><span class="stringliteral"> my $valley = Bio::EnsEMBL::Hive::Valley->new( $config, $default_meadow_type, $pipeline_name );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my ($beekeeper_meadow_type, $beekeeper_meadow_name) = $valley->whereami();</span></div>
+<div class="line"><span class="stringliteral"> unless($beekeeper_meadow_type eq 'LOCAL') {</span></div>
+<div class="line"><span class="stringliteral"> die "</span>beekeeper.pl detected it has been itself submitted to <span class="stringliteral">'$beekeeper_meadow_type/$beekeeper_meadow_name'</span>, but <span class="keyword">this</span> mode of operation is not supported.\n<span class="stringliteral">"</span></div>
+<div class="line"><span class="stringliteral"> ."</span>Please just run beekeeper.pl on a farm head node, preferably from under a <span class="stringliteral">'screen'</span> session.\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $valley->config_set('SubmitWorkersMax', $submit_workers_max) if(defined $submit_workers_max);</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $default_meadow = $valley->get_default_meadow();</span></div>
+<div class="line"><span class="stringliteral"> warn "</span>Default meadow: <span class="stringliteral">".$default_meadow->signature."</span>\n\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $default_meadow->config_set('TotalRunningWorkersMax', $total_running_workers_max) if(defined $total_running_workers_max);</span></div>
+<div class="line"><span class="stringliteral"> $default_meadow->config_set('SubmissionOptions', $submission_options) if(defined $submission_options);</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($reset_job_id) { $queen->reset_job_by_dbID_and_sync($reset_job_id); }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($job_id_for_output) {</span></div>
+<div class="line"><span class="stringliteral"> printf("</span>===== job output\n<span class="stringliteral">");</span></div>
+<div class="line"><span class="stringliteral"> my $job = $self->{'dba'}->get_AnalysisJobAdaptor->fetch_by_dbID($job_id_for_output);</span></div>
+<div class="line"><span class="stringliteral"> $job->print_job();</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if(my $reset_logic_name = $reset_all_jobs_for_analysis || $reset_failed_jobs_for_analysis) {</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $reset_analysis = $self->{'dba'}->get_AnalysisAdaptor->fetch_by_logic_name($reset_logic_name)</span></div>
+<div class="line"><span class="stringliteral"> || die( "</span>Cannot AnalysisAdaptor->fetch_by_logic_name($reset_logic_name)<span class="stringliteral">"); </span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $self->{'dba'}->get_AnalysisJobAdaptor->reset_jobs_for_analysis_id($reset_analysis->dbID, $reset_all_jobs_for_analysis); </span></div>
+<div class="line"><span class="stringliteral"> $self->{'dba'}->get_Queen->synchronize_AnalysisStats($reset_analysis->stats);</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if ($kill_worker_id) {</span></div>
+<div class="line"><span class="stringliteral"> my $kill_worker = $queen->fetch_by_dbID($kill_worker_id);</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> unless( $kill_worker->cause_of_death() ) {</span></div>
+<div class="line"><span class="stringliteral"> if( my $meadow = $valley->find_available_meadow_responsible_for_worker( $kill_worker ) ) {</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if( $meadow->check_worker_is_alive_and_mine ) {</span></div>
+<div class="line"><span class="stringliteral"> printf("</span>Killing worker: %10d %35s %15s %20s(%d) : <span class="stringliteral">", </span></div>
+<div class="line"><span class="stringliteral"> $kill_worker->dbID, $kill_worker->host, $kill_worker->process_id, </span></div>
+<div class="line"><span class="stringliteral"> $kill_worker->analysis->logic_name, $kill_worker->analysis_id);</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $meadow->kill_worker($kill_worker);</span></div>
+<div class="line"><span class="stringliteral"> $kill_worker->cause_of_death('KILLED_BY_USER');</span></div>
+<div class="line"><span class="stringliteral"> $queen->register_worker_death($kill_worker);</span></div>
+<div class="line"><span class="stringliteral"> # what about clean-up? Should we do it here or not?</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> die "</span>According to the Meadow, the Worker (dbID=$kill_worker_id) is not running, so cannot kill<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> die "</span>Cannot access the Meadow responsible for the Worker (dbID=$kill_worker_id), so cannot kill<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> die "</span>According to the Queen, the Worker (dbID=$kill_worker_id) is not running, so cannot kill<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $analysis = $run_job_id</span></div>
+<div class="line"><span class="stringliteral"> ? $self->{'dba'}->get_AnalysisAdaptor->fetch_by_dbID( $self->{'dba'}->get_AnalysisJobAdaptor->fetch_by_dbID( $run_job_id )->analysis_id )</span></div>
+<div class="line"><span class="stringliteral"> : $self->{'dba'}->get_AnalysisAdaptor->fetch_by_logic_name($self->{'logic_name'});</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($all_dead) { $queen->register_all_workers_dead(); }</span></div>
+<div class="line"><span class="stringliteral"> if($check_for_dead) { $queen->check_for_dead_workers($valley, 1); }</span></div>
+<div class="line"><span class="stringliteral"> if($balance_semaphores) { $self->{'dba'}->get_AnalysisJobAdaptor->balance_semaphores( $analysis && $analysis->dbID ); }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if ($max_loops) { # positive $max_loop means limited, negative means unlimited</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> run_autonomously($self, $max_loops, $keep_alive, $queen, $valley, $analysis, $run_job_id, $force);</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> # the output of several methods will look differently depending on $analysis being [un]defined</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($sync) {</span></div>
+<div class="line"><span class="stringliteral"> $queen->synchronize_hive($analysis);</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> $queen->print_analysis_status($analysis) unless($self->{'no_analysis_stats'});</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($show_worker_stats) {</span></div>
+<div class="line"><span class="stringliteral"> print "</span>\n===== List of live Workers according to the Queen: ======\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> foreach my $worker (@{ $queen->fetch_overdue_workers(0) }) {</span></div>
+<div class="line"><span class="stringliteral"> print $worker->toString()."</span>\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> $queen->print_running_worker_counts;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> Bio::EnsEMBL::Hive::Scheduler::schedule_workers_resync_if_necessary($queen, $valley, $analysis); # show what would be submitted, but do not actually submit</span></div>
+<div class="line"><span class="stringliteral"> $queen->get_remaining_jobs_show_hive_progress();</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($show_failed_jobs) {</span></div>
+<div class="line"><span class="stringliteral"> print("</span>===== failed jobs\n<span class="stringliteral">");</span></div>
+<div class="line"><span class="stringliteral"> my $failed_job_list = $self->{'dba'}->get_AnalysisJobAdaptor->fetch_all_by_analysis_id_status($analysis && $analysis->dbID, 'FAILED');</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> foreach my $job (@{$failed_job_list}) {</span></div>
+<div class="line"><span class="stringliteral"> $job->print_job();</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if ($self->{'monitor'}) {</span></div>
+<div class="line"><span class="stringliteral"> $queen->monitor();</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> exit(0);</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div><p>Undocumented method</p>
+<div id="codesection-main" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-main-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-main-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-main-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">main</a> {</div>
+<div class="line"> my ($reg_conf, $reg_type, $reg_alias, $url, $sqlcmd, $extra, $to_params, $verbose, $help, $report_versions);</div>
+<div class="line"></div>
+<div class="line"> GetOptions(</div>
+<div class="line"> # connect to the database:</div>
+<div class="line"> <span class="stringliteral">'reg_conf=s'</span> => \$reg_conf,</div>
+<div class="line"> <span class="stringliteral">'reg_type=s'</span> => \$reg_type,</div>
+<div class="line"> <span class="stringliteral">'reg_alias=s'</span> => \$reg_alias,</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'url=s'</span> => \$url,</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'sqlcmd=s'</span> => \$sqlcmd,</div>
+<div class="line"> <span class="stringliteral">'extra=s'</span> => \$extra,</div>
+<div class="line"> <span class="stringliteral">'to_params!'</span> => \$to_params,</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'verbose!'</span> => \$verbose,</div>
+<div class="line"> <span class="stringliteral">'help!'</span> => \$help,</div>
+<div class="line"> <span class="stringliteral">'v|versions!'</span> => \$report_versions,</div>
+<div class="line"> );</div>
+<div class="line"></div>
+<div class="line"> my $dbc_hash;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($help) {</div>
+<div class="line"></div>
+<div class="line"> script_usage(0);</div>
+<div class="line"></div>
+<div class="line"> } elsif($report_versions) {</div>
+<div class="line"></div>
+<div class="line"> report_versions();</div>
+<div class="line"> exit(0);</div>
+<div class="line"></div>
+<div class="line"> } elsif($reg_alias) {</div>
+<div class="line"> script_usage(1) if $url;</div>
+<div class="line"> Bio::EnsEMBL::Registry->load_all($reg_conf);</div>
+<div class="line"></div>
+<div class="line"> my $species = Bio::EnsEMBL::Registry->get_alias($reg_alias)</div>
+<div class="line"> || die "Could not solve the alias '$reg_alias'".($reg_conf ? " via the registry file '$reg_conf'" : "");</div>
+<div class="line"></div>
+<div class="line"> my $dba;</div>
+<div class="line"> if ($reg_type) {</div>
+<div class="line"> $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $reg_type)</div>
+<div class="line"> || die <span class="stringliteral">"Could not find any database for '$species' (alias: '$reg_alias') with the type '$reg_type'"</span>.($reg_conf ? <span class="stringliteral">" via the registry file '$reg_conf'"</span> : <span class="stringliteral">""</span>);</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"></div>
+<div class="line"> my $dbas = Bio::EnsEMBL::Registry->get_all_DBAdaptors(-species => $species);</div>
+<div class="line"> <span class="keywordflow">if</span> (scalar(@$dbas) == 0) {</div>
+<div class="line"><span class="preprocessor"> # I think this case cannot happen: if there are no databases, the alias does not exist and get_alias() should have failed</span></div>
+<div class="line"><span class="preprocessor"></span> die <span class="stringliteral">"Could not find any database for '$species' (alias: '$reg_alias')"</span>.($reg_conf ? <span class="stringliteral">" via the registry file '$reg_conf'"</span> : <span class="stringliteral">""</span>);</div>
+<div class="line"></div>
+<div class="line"> } elsif (scalar(@$dbas) >= 2) {</div>
+<div class="line"> die <span class="stringliteral">"There are several databases for '$species' (alias: '$reg_alias'). Please set -reg_type to one of: "</span>.join(<span class="stringliteral">", "</span>, map {$_->group} @$dbas);</div>
+<div class="line"> };</div>
+<div class="line"> $dba = $dbas->[0];</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $dbc = $dba->dbc();</div>
+<div class="line"></div>
+<div class="line"> $dbc_hash = {</div>
+<div class="line"> <span class="stringliteral">'driver'</span> => $dbc->driver,</div>
+<div class="line"> <span class="stringliteral">'host'</span> => $dbc->host,</div>
+<div class="line"> <span class="stringliteral">'port'</span> => $dbc->port,</div>
+<div class="line"> <span class="stringliteral">'user'</span> => $dbc->username,</div>
+<div class="line"> <span class="stringliteral">'pass'</span> => $dbc->password,</div>
+<div class="line"> <span class="stringliteral">'dbname'</span> => $dbc->dbname,</div>
+<div class="line"> };</div>
+<div class="line"> } elsif($url) {</div>
+<div class="line"> $dbc_hash = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l.html#ac80cc911eba215fb0ed17104861fe5f7">Bio::EnsEMBL::Hive::Utils::URL::parse</a>( $url )</div>
+<div class="line"> || die <span class="stringliteral">"Could not parse URL '$url'"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> script_usage(1);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $cmd = <a class="code" href="db__cmd_8pl.html#aa9d6dbdd85d225abef029815f3ca0336">dbc_hash_to_cmd</a>( $dbc_hash, $sqlcmd, $extra, $to_params );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($to_params) {</div>
+<div class="line"> print <span class="stringliteral">"$cmd\n"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"\nRunning command:\t$cmd\n\n"</span> <span class="keywordflow">if</span>($verbose);</div>
+<div class="line"></div>
+<div class="line"> exec($cmd);</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div><p>Undocumented method</p>
+<div id="codesection-main" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-main-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-main-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-main-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">main</a> {</div>
+<div class="line"></div>
+<div class="line"> my ($url, $reg_conf, $reg_type, $reg_alias, $nosqlvc, $help, $verbose, $mode, $start_date, $end_date, $output, $top, $default_memory, $default_cores);</div>
+<div class="line"></div>
+<div class="line"> GetOptions(</div>
+<div class="line"> # connect to the database:</div>
+<div class="line"> <span class="stringliteral">'url=s'</span> => \$url,</div>
+<div class="line"> <span class="stringliteral">'reg_conf|regfile=s'</span> => \$reg_conf,</div>
+<div class="line"> <span class="stringliteral">'reg_type=s'</span> => \$reg_type,</div>
+<div class="line"> <span class="stringliteral">'reg_alias|regname=s'</span> => \$reg_alias,</div>
+<div class="line"> <span class="stringliteral">'nosqlvc=i'</span> => \$nosqlvc, # <span class="keyword">using</span> <span class="stringliteral">"=i"</span> instead of <span class="stringliteral">"!"</span> <span class="keywordflow">for</span> consistency with scripts where it is a propagated option</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'verbose!'</span> => \$verbose,</div>
+<div class="line"> <span class="stringliteral">'h|help'</span> => \$help,</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'start_date=s'</span> => \$start_date,</div>
+<div class="line"> <span class="stringliteral">'end_date=s'</span> => \$end_date,</div>
+<div class="line"> <span class="stringliteral">'mode=s'</span> => \$mode,</div>
+<div class="line"> <span class="stringliteral">'top=f'</span> => \$top,</div>
+<div class="line"> <span class="stringliteral">'mem=i'</span> => \$default_memory,</div>
+<div class="line"> <span class="stringliteral">'n_core=i'</span> => \$default_cores,</div>
+<div class="line"> <span class="stringliteral">'output=s'</span> => \$output,</div>
+<div class="line"> );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span> ($help) { script_usage(0); }</div>
+<div class="line"></div>
+<div class="line"> my $hive_dba;</div>
+<div class="line"> <span class="keywordflow">if</span>($url or $reg_alias) {</div>
+<div class="line"> $hive_dba = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#abf2b541c5d7e3b124323a34356e3ace6">new</a>(</div>
+<div class="line"> -url => $url,</div>
+<div class="line"> -reg_conf => $reg_conf,</div>
+<div class="line"> -reg_type => $reg_type,</div>
+<div class="line"> -reg_alias => $reg_alias,</div>
+<div class="line"> -no_sql_schema_version_check => $nosqlvc,</div>
+<div class="line"> );</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"\nERROR: Connection parameters (url or reg_conf+reg_alias) need to be specified\n"</span>;</div>
+<div class="line"> script_usage(1);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Check whether $mode is valid</span></div>
+<div class="line"><span class="preprocessor"></span> my %allowed_modes = (</div>
+<div class="line"> workers => <span class="stringliteral">'Number of workers'</span>,</div>
+<div class="line"> memory => <span class="stringliteral">'Memory asked (Gb)'</span>,</div>
+<div class="line"> cores => <span class="stringliteral">'Number of CPU cores'</span>,</div>
+<div class="line"> unused_memory => <span class="stringliteral">'Unused memory (Gb)'</span>,</div>
+<div class="line"> unused_cores => <span class="stringliteral">'Number of unused CPU cores'</span>,</div>
+<div class="line"> pending_workers => <span class="stringliteral">'Number of pending workers'</span>,</div>
+<div class="line"> );</div>
+<div class="line"> <span class="keywordflow">if</span> ($mode) {</div>
+<div class="line"> die <span class="stringliteral">"Unknown mode '$mode'. Allowed modes are: "</span>.join(<span class="stringliteral">", "</span>, keys %allowed_modes) unless exists $allowed_modes{$mode};</div>
+<div class="line"> $default_memory = 100 unless $default_memory;</div>
+<div class="line"> $default_cores = 1 unless $default_cores;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $mode = <span class="stringliteral">'workers'</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Palette generated with R: c(brewer.pal(9, "Set1"), brewer.pal(12, "Set3")). #FFFFB3 is removed because it is too close to white</span></div>
+<div class="line"><span class="preprocessor"></span> my @palette = qw(#E41A1C #377EB8 #4DAF4A #984EA3 #FF7F00 #FFFF33 #A65628 #F781BF #999999 #8DD3C7 #BEBADA #FB8072 #80B1D3 #FDB462 #B3DE69 #FCCDE5 #D9D9D9 #BC80BD #CCEBC5 #FFED6F #2F4F4F);</div>
+<div class="line"></div>
+<div class="line"> my %terminal_mapping = (</div>
+<div class="line"> <span class="stringliteral">'emf'</span> => <span class="stringliteral">'emf'</span>,</div>
+<div class="line"> <span class="stringliteral">'png'</span> => <span class="stringliteral">'png'</span>,</div>
+<div class="line"> <span class="stringliteral">'svg'</span> => <span class="stringliteral">'svg'</span>,</div>
+<div class="line"> <span class="stringliteral">'jpg'</span> => <span class="stringliteral">'jpeg'</span>,</div>
+<div class="line"> <span class="stringliteral">'gif'</span> => <span class="stringliteral">'gif'</span>,</div>
+<div class="line"> <span class="stringliteral">'ps'</span> => <span class="stringliteral">'postscript eps enhanced color'</span>,</div>
+<div class="line"> <span class="stringliteral">'pdf'</span> => <span class="stringliteral">'pdf color enhanced'</span>,</div>
+<div class="line"> );</div>
+<div class="line"> my $gnuplot_terminal = undef;</div>
+<div class="line"> <span class="keywordflow">if</span> ($output and $output =~ /\.(\w+)$/) {</div>
+<div class="line"> $gnuplot_terminal = $1;</div>
+<div class="line"> die <span class="stringliteral">"The format '$gnuplot_terminal' is not currently supported."</span> <span class="keywordflow">if</span> not exists $terminal_mapping{$gnuplot_terminal};</div>
+<div class="line"> require Chart::Gnuplot;</div>
+<div class="line"></div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"> my $dbh = $hive_dba->dbc->db_handle();</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Get the memory usage from each resource_class</span></div>
+<div class="line"><span class="preprocessor"></span> my %mem_resources = ();</div>
+<div class="line"> my %cpu_resources = ();</div>
+<div class="line"> {</div>
+<div class="line"> my $sql_resource_descriptions = <span class="stringliteral">'SELECT resource_class_id, meadow_type, submission_cmd_args FROM resource_description'</span>;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $db_entry (@{$dbh->selectall_arrayref($sql_resource_descriptions)}) {</div>
+<div class="line"> my ($resource_class_id, $meadow_type, $submission_cmd_args) = @$db_entry;</div>
+<div class="line"> <span class="keywordflow">if</span> ($meadow_type eq <span class="stringliteral">'LSF'</span>) {</div>
+<div class="line"> $mem_resources{$resource_class_id} = $1 <span class="keywordflow">if</span> $submission_cmd_args =~ m/mem=(\d+)/;</div>
+<div class="line"> $cpu_resources{$resource_class_id} = $1 <span class="keywordflow">if</span> $submission_cmd_args =~ m/-n\s*(\d+)/;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> warn <span class="stringliteral">"mem_resources: "</span>, Dumper \%mem_resources <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"> warn <span class="stringliteral">"cpu_resources: "</span>, Dumper \%cpu_resources <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Get the memory used by each worker</span></div>
+<div class="line"><span class="preprocessor"></span> my %used_res = ();</div>
+<div class="line"> <span class="keywordflow">if</span> (($mode eq <span class="stringliteral">'unused_memory'</span>) or ($mode eq <span class="stringliteral">'unused_cores'</span>)) {</div>
+<div class="line"> my $sql_used_res = <span class="stringliteral">'SELECT meadow_name, process_id, mem_megs, cpu_sec/lifespan_sec FROM lsf_report'</span>;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $db_entry (@{$dbh->selectall_arrayref($sql_used_res)}) {</div>
+<div class="line"> my ($meadow_name, $process_id, $mem_megs, $cpu_usage) = @$db_entry;</div>
+<div class="line"> $used_res{$meadow_name.<span class="stringliteral">"_____"</span>.$process_id} = [$mem_megs, $cpu_usage];</div>
+<div class="line"> }</div>
+<div class="line"> warn scalar(keys %used_res), <span class="stringliteral">" process info loaded from lsf_report\n"</span> <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Get the info about the analysis</span></div>
+<div class="line"><span class="preprocessor"></span> my %default_resource_class = ();</div>
+<div class="line"> my %analysis_name = ();</div>
+<div class="line"> {</div>
+<div class="line"> my $sql_analysis_info = <span class="stringliteral">'SELECT analysis_id, logic_name, resource_class_id FROM analysis_base'</span>;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $db_entry (@{$dbh->selectall_arrayref($sql_analysis_info)}) {</div>
+<div class="line"> my ($analysis_id, $logic_name, $resource_class_id) = @$db_entry;</div>
+<div class="line"> $analysis_name{$analysis_id} = $logic_name;</div>
+<div class="line"> $default_resource_class{$analysis_id} = $resource_class_id;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> warn <span class="stringliteral">"default_resource_class: "</span>, Dumper \%default_resource_class <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"> warn <span class="stringliteral">"analysis_name: "</span>, Dumper \%analysis_name <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"> warn scalar(keys %analysis_name), <span class="stringliteral">" analysis\n"</span> <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Get the events from the database</span></div>
+<div class="line"><span class="preprocessor"></span> my %events = ();</div>
+<div class="line"> <span class="keywordflow">if</span> ($mode ne <span class="stringliteral">'pending_workers'</span>) {</div>
+<div class="line"> my @tmp_dates = @{$dbh->selectall_arrayref(<span class="stringliteral">'SELECT DATE_FORMAT(born, "%Y-%m-%dT%T"), DATE_FORMAT(died, "%Y-%m-%dT%T"), analysis_id, meadow_name, process_id, resource_class_id FROM worker WHERE analysis_id IS NOT NULL'</span>)};</div>
+<div class="line"> warn scalar(@tmp_dates), <span class="stringliteral">" events\n"</span> <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $db_entry (@tmp_dates) {</div>
+<div class="line"> my ($birth_date, $death_date, $analysis_id, $meadow_name, $process_id, $resource_class_id) = @$db_entry;</div>
+<div class="line"> $resource_class_id = $default_resource_class{$analysis_id} unless $resource_class_id;</div>
+<div class="line"> my $offset = 0;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span> ($mode eq <span class="stringliteral">'workers'</span>) {</div>
+<div class="line"> $offset = 1;</div>
+<div class="line"> } elsif ($mode eq <span class="stringliteral">'memory'</span>) {</div>
+<div class="line"> $offset = ($mem_resources{$resource_class_id} || $default_memory) / 1024.;</div>
+<div class="line"> } elsif ($mode eq <span class="stringliteral">'cores'</span>) {</div>
+<div class="line"> $offset = ($cpu_resources{$resource_class_id} || $default_cores);</div>
+<div class="line"> } elsif ($mode eq <span class="stringliteral">'unused_memory'</span>) {</div>
+<div class="line"> my $process_signature = $meadow_name.<span class="stringliteral">"_____"</span>.$process_id;</div>
+<div class="line"> <span class="keywordflow">if</span> (exists $used_res{$process_signature}) {</div>
+<div class="line"> $offset = (($mem_resources{$resource_class_id} || $default_memory) - $used_res{$process_signature}->[0]) / 1024.;</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> my $process_signature = $meadow_name.<span class="stringliteral">"_____"</span>.$process_id;</div>
+<div class="line"> <span class="keywordflow">if</span> (exists $used_res{$process_signature}) {</div>
+<div class="line"> $offset = ($cpu_resources{$resource_class_id} || $default_cores) - $used_res{$process_signature}->[1];</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> $events{$birth_date}{$analysis_id} += $offset <span class="keywordflow">if</span> $offset > 0;</div>
+<div class="line"> $events{$death_date}{$analysis_id} -= $offset <span class="keywordflow">if</span> ($offset > 0) and $death_date;</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> my @tmp_dates = @{$dbh->selectall_arrayref(<span class="stringliteral">'SELECT DATE_FORMAT(DATE_SUB(born, INTERVAL pending_sec SECOND), "%Y-%m-%dT%T"), DATE_FORMAT(born, "%Y-%m-%dT%T"), analysis_id FROM worker JOIN lsf_report USING (meadow_name, process_id) WHERE analysis_id IS NOT NULL AND meadow_type = "LSF" AND pending_sec > 0'</span>)};</div>
+<div class="line"> warn scalar(@tmp_dates), <span class="stringliteral">" events\n"</span> <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $db_entry (@tmp_dates) {</div>
+<div class="line"> my ($start_pending, $start_running, $analysis_id) = @$db_entry;</div>
+<div class="line"> $events{$start_pending}{$analysis_id} += 1;</div>
+<div class="line"> $events{$start_running}{$analysis_id} -= 1;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> my @event_dates = sort {$a cmp $b} (keys %events);</div>
+<div class="line"> warn scalar(@event_dates), <span class="stringliteral">" dates\n"</span> <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"></div>
+<div class="line"> my $max_workers = 0;</div>
+<div class="line"> my @data_timings = ();</div>
+<div class="line"> my %tot_analysis = ();</div>
+<div class="line"></div>
+<div class="line"> my $num_curr_workers = 0;</div>
+<div class="line"> my %hash_curr_workers = (map {$_ => 0 } (keys %analysis_name));</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $event_date (@event_dates) {</div>
+<div class="line"></div>
+<div class="line"> last <span class="keywordflow">if</span> $end_date and ($event_date gt $end_date);</div>
+<div class="line"></div>
+<div class="line"> my $topup_hash = $events{$event_date};</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $analysis_id (keys %$topup_hash) {</div>
+<div class="line"> $hash_curr_workers{$analysis_id} += $topup_hash->{$analysis_id};</div>
+<div class="line"> $num_curr_workers += $topup_hash->{$analysis_id};</div>
+<div class="line"> }</div>
+<div class="line"><span class="preprocessor"> # Due to rounding errors, the sums may be slightly different</span></div>
+<div class="line"><span class="preprocessor"></span> die sum(values %hash_curr_workers).<span class="stringliteral">"!=$num_curr_workers"</span> <span class="keywordflow">if</span> abs(sum(values %hash_curr_workers) - $num_curr_workers) > 0.05;</div>
+<div class="line"></div>
+<div class="line"> next <span class="keywordflow">if</span> $start_date and ($event_date lt $start_date);</div>
+<div class="line"></div>
+<div class="line"> my %hash_interval = %hash_curr_workers;</div>
+<div class="line"><span class="preprocessor"> #FIXME It should be normalised by the length of the time interval</span></div>
+<div class="line"><span class="preprocessor"></span> map {$tot_analysis{$_} += $hash_interval{$_}} keys %hash_interval;</div>
+<div class="line"></div>
+<div class="line"> $max_workers = $num_curr_workers <span class="keywordflow">if</span> ($num_curr_workers > $max_workers);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # We need to repeat the previous value to have an histogram shape</span></div>
+<div class="line"><span class="preprocessor"></span> push @data_timings, [$event_date, $data_timings[-1]->[1]] <span class="keywordflow">if</span> @data_timings;</div>
+<div class="line"> push @data_timings, [$event_date, \%hash_interval];</div>
+<div class="line"> }</div>
+<div class="line"> warn $max_workers <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"> warn Dumper \%tot_analysis <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"></div>
+<div class="line"> my $total_total = sum(values %tot_analysis);</div>
+<div class="line"></div>
+<div class="line"> my @sorted_analysis_ids = sort {($tot_analysis{$b} <=> $tot_analysis{$a}) || (lc $analysis_name{$a} cmp lc $analysis_name{$b})} (grep {$tot_analysis{$_}} keys %tot_analysis);</div>
+<div class="line"> warn Dumper \@sorted_analysis_ids <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"> warn Dumper([map {$analysis_name{$_}} @sorted_analysis_ids]) <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span> (not $gnuplot_terminal) {</div>
+<div class="line"> print join(<span class="stringliteral">"\t"</span>, <span class="stringliteral">'date'</span>, <span class="stringliteral">"OVERALL_$mode"</span>, map {$analysis_name{$_}} @sorted_analysis_ids), <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print join(<span class="stringliteral">"\t"</span>, <span class="stringliteral">'total'</span>, $total_total, map {$tot_analysis{$_}} @sorted_analysis_ids), <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print join(<span class="stringliteral">"\t"</span>, <span class="stringliteral">'proportion'</span>, <span class="stringliteral">'NA'</span>, map {$tot_analysis{$_}/$total_total} @sorted_analysis_ids), <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> my $s = 0;</div>
+<div class="line"> print join(<span class="stringliteral">"\t"</span>, <span class="stringliteral">'cum_proportion'</span>, <span class="stringliteral">'NA'</span>, map {$s+=$tot_analysis{$_}/$total_total} @sorted_analysis_ids), <span class="stringliteral">"\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $row (@data_timings) {</div>
+<div class="line"> print join(<span class="stringliteral">"\t"</span>, $row->[0], sum(values %{$row->[1]}), map {$row->[1]->{$_}} @sorted_analysis_ids).<span class="stringliteral">"\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Get the number of analysis we want to display</span></div>
+<div class="line"><span class="preprocessor"></span> my $n_relevant_analysis = scalar(@sorted_analysis_ids);</div>
+<div class="line"> <span class="keywordflow">if</span> ($top and ($top > 0)) {</div>
+<div class="line"> <span class="keywordflow">if</span> ($top < 1) {</div>
+<div class="line"> my $s = 0;</div>
+<div class="line"> $n_relevant_analysis = 0;</div>
+<div class="line"> map {my $pre_s = $s; $s += $tot_analysis{$_}/$total_total; $pre_s < $top && $n_relevant_analysis++} @sorted_analysis_ids;</div>
+<div class="line"> } elsif ($top < scalar(@sorted_analysis_ids)) {</div>
+<div class="line"> $n_relevant_analysis = $top;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"><span class="preprocessor"> # cap based on the length of the palette</span></div>
+<div class="line"><span class="preprocessor"></span> my $need_other_analysis = $n_relevant_analysis < scalar(@sorted_analysis_ids) ? 1 : 0;</div>
+<div class="line"> <span class="keywordflow">if</span> (($n_relevant_analysis+$need_other_analysis) > scalar(@palette)) {</div>
+<div class="line"> $n_relevant_analysis = scalar(@palette) - 1;</div>
+<div class="line"> $need_other_analysis = 1;</div>
+<div class="line"> }</div>
+<div class="line"> $top = $n_relevant_analysis unless $top;</div>
+<div class="line"> warn <span class="stringliteral">"$n_relevant_analysis relevant analysis\n"</span> <span class="keywordflow">if</span> $verbose;</div>
+<div class="line"></div>
+<div class="line"> my @xdata = map {$_->[0]} @data_timings;</div>
+<div class="line"></div>
+<div class="line"> my @datasets = ();</div>
+<div class="line"></div>
+<div class="line"> my $pseudo_zero_value = -$max_workers / 50;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # The background plot: the sum of all the analysis</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span> ($need_other_analysis) {</div>
+<div class="line"> my @ydata = ();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $row (@data_timings) {</div>
+<div class="line"> push @ydata, sum(map {$row->[1]->{$_}} @sorted_analysis_ids ) || $pseudo_zero_value;</div>
+<div class="line"><span class="preprocessor"> # Due to rounding errors, values are not always decreased to 0</span></div>
+<div class="line"><span class="preprocessor"></span> $ydata[-1] = $pseudo_zero_value <span class="keywordflow">if</span> $ydata[-1] < 0.05;</div>
+<div class="line"> }</div>
+<div class="line"> push @datasets, Chart::Gnuplot::DataSet->new(</div>
+<div class="line"> xdata => \@xdata,</div>
+<div class="line"> ydata => \@ydata,</div>
+<div class="line"> timefmt => <span class="stringliteral">'%Y-%m-%dT%H:%M:%S'</span>,</div>
+<div class="line"> title => <span class="stringliteral">'OTHER'</span>,</div>
+<div class="line"> style => <span class="stringliteral">'filledcurves x1'</span>,</div>
+<div class="line"> linewidth => <span class="charliteral">'0'</span>,</div>
+<div class="line"> color => $palette[$n_relevant_analysis],</div>
+<div class="line"> );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Each analysis is plotted as the sum of itself and the top ones</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">foreach</span> my $i (reverse 1..$n_relevant_analysis) {</div>
+<div class="line"> my @ydata;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $row (@data_timings) {</div>
+<div class="line"> push @ydata, sum(map {$row->[1]->{$_} || 0} @sorted_analysis_ids[0..($i-1)] ) || $pseudo_zero_value;</div>
+<div class="line"><span class="preprocessor"> # Due to rounding errors, values are not always decreased to 0</span></div>
+<div class="line"><span class="preprocessor"></span> $ydata[-1] = $pseudo_zero_value <span class="keywordflow">if</span> $ydata[-1] < 0.05;</div>
+<div class="line"> }</div>
+<div class="line"> my $dataset = Chart::Gnuplot::DataSet->new(</div>
+<div class="line"> xdata => \@xdata,</div>
+<div class="line"> ydata => \@ydata,</div>
+<div class="line"> timefmt => <span class="stringliteral">'%Y-%m-%dT%H:%M:%S'</span>,</div>
+<div class="line"> title => $analysis_name{$sorted_analysis_ids[$i-1]},</div>
+<div class="line"> style => <span class="stringliteral">'filledcurves x1'</span>,</div>
+<div class="line"> linewidth => <span class="charliteral">'0'</span>,</div>
+<div class="line"> color => $palette[$i-1],</div>
+<div class="line"> );</div>
+<div class="line"> push @datasets, $dataset;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $chart = Chart::Gnuplot->new(</div>
+<div class="line"> title => sprintf(<span class="stringliteral">'Profile of %s'</span>, $n_relevant_analysis < scalar(@sorted_analysis_ids) ? ($top < 1 ? sprintf(<span class="stringliteral">'%.1f%% of %s'</span>, 100*$top, $url) : <span class="stringliteral">"the $top top-analysis of $url"</span>) : $url).($start_date ? <span class="stringliteral">" from $start_date"</span> : <span class="stringliteral">""</span>).($end_date ? <span class="stringliteral">" to $end_date"</span> : <span class="stringliteral">""</span>),</div>
+<div class="line"> timeaxis => <span class="charliteral">'x'</span>,</div>
+<div class="line"> legend => {</div>
+<div class="line"> position => <span class="stringliteral">'outside right'</span>,</div>
+<div class="line"> align => <span class="stringliteral">'left'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> xtics => {</div>
+<div class="line"> labelfmt => <span class="stringliteral">'%b %d\n %H:%M'</span>,</div>
+<div class="line"> along => <span class="stringliteral">'out nomirror'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> bg => {</div>
+<div class="line"> color => <span class="stringliteral">'white'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> grid => <span class="stringliteral">'on'</span>,</div>
+<div class="line"> imagesize => <span class="stringliteral">'1400, 800'</span>,</div>
+<div class="line"> output => $output,</div>
+<div class="line"> terminal => $terminal_mapping{$gnuplot_terminal},</div>
+<div class="line"> ylabel => $allowed_modes{$mode},</div>
+<div class="line"> yrange => [$pseudo_zero_value, undef],</div>
+<div class="line"> );</div>
+<div class="line"> $chart->plot2d(@datasets);</div>
+<div class="line"></div>
+<div class="line">}</div>
+</div><!-- fragment --> </div><p>Undocumented method</p>
+<div id="codesection-main" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-main-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-main-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-main-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">main</a> {</div>
+<div class="line"> my ($url, $reg_conf, $reg_type, $reg_alias, $nosqlvc, $before_datetime, $days_ago);</div>
+<div class="line"></div>
+<div class="line"> GetOptions(</div>
+<div class="line"> # connect to the database:</div>
+<div class="line"> <span class="stringliteral">'url=s'</span> => \$url,</div>
+<div class="line"> <span class="stringliteral">'reg_conf|regfile=s'</span> => \$reg_conf,</div>
+<div class="line"> <span class="stringliteral">'reg_type=s'</span> => \$reg_type,</div>
+<div class="line"> <span class="stringliteral">'reg_alias|regname=s'</span> => \$reg_alias,</div>
+<div class="line"> <span class="stringliteral">'nosqlvc=i'</span> => \$nosqlvc, # <span class="keyword">using</span> <span class="stringliteral">"=i"</span> instead of <span class="stringliteral">"!"</span> <span class="keywordflow">for</span> consistency with scripts where it is a propagated option</div>
+<div class="line"></div>
+<div class="line"> # specify the threshold datetime:</div>
+<div class="line"> <span class="stringliteral">'before_datetime=s'</span> => \$before_datetime,</div>
+<div class="line"> <span class="stringliteral">'days_ago=f'</span> => \$days_ago,</div>
+<div class="line"> );</div>
+<div class="line"></div>
+<div class="line"> my $hive_dba;</div>
+<div class="line"> <span class="keywordflow">if</span>($url or $reg_alias) {</div>
+<div class="line"> $hive_dba = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#abf2b541c5d7e3b124323a34356e3ace6">new</a>(</div>
+<div class="line"> -url => $url,</div>
+<div class="line"> -reg_conf => $reg_conf,</div>
+<div class="line"> -reg_type => $reg_type,</div>
+<div class="line"> -reg_alias => $reg_alias,</div>
+<div class="line"> -no_sql_schema_version_check => $nosqlvc,</div>
+<div class="line"> );</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"\nERROR: Connection parameters (url or reg_conf+reg_alias) need to be specified\n"</span>;</div>
+<div class="line"> script_usage(1);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $threshold_datetime_expression;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($before_datetime) {</div>
+<div class="line"> $threshold_datetime_expression = <span class="stringliteral">"'$before_datetime'"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> unless($before_datetime or $days_ago) {</div>
+<div class="line"> warn <span class="stringliteral">"Neither -before_datetime or -days_ago was defined, assuming '-days_ago 7'\n"</span>;</div>
+<div class="line"> $days_ago = 7;</div>
+<div class="line"> }</div>
+<div class="line"> $threshold_datetime_expression = <span class="stringliteral">"from_unixtime(unix_timestamp(now())-3600*24*$days_ago)"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $sql = qq{</div>
+<div class="line"> DELETE j FROM job j</div>
+<div class="line"> WHERE j.status=<span class="stringliteral">'DONE'</span></div>
+<div class="line"> AND j.completed < $threshold_datetime_expression</div>
+<div class="line"> };</div>
+<div class="line"></div>
+<div class="line"> my $dbc = $hive_dba->dbc();</div>
+<div class="line"> $dbc->do( $sql );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div><p>Undocumented method</p>
+<div id="codesection-main" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-main-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-main-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-main-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">main</a> {</div>
+<div class="line"> my $file_or_module = shift @ARGV or script_usage(0);</div>
+<div class="line"></div>
+<div class="line"> my $config_module = load_file_or_module( $file_or_module );</div>
+<div class="line"></div>
+<div class="line"> my $config_object = $config_module->new();</div>
+<div class="line"> $config_object->process_options();</div>
+<div class="line"> $config_object->run();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div><p>Undocumented method</p>
+<div id="codesection-main" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-main-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-main-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-main-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">main</a> {</div>
+<div class="line"></div>
+<div class="line"> my ($url, $reg_conf, $reg_type, $reg_alias, $nosqlvc, $bacct_source_line, $lsf_user, $help, $start_date, $end_date);</div>
+<div class="line"></div>
+<div class="line"> GetOptions(</div>
+<div class="line"> # connect to the database:</div>
+<div class="line"> <span class="stringliteral">'url=s'</span> => \$url,</div>
+<div class="line"> <span class="stringliteral">'reg_conf|regfile=s'</span> => \$reg_conf,</div>
+<div class="line"> <span class="stringliteral">'reg_type=s'</span> => \$reg_type,</div>
+<div class="line"> <span class="stringliteral">'reg_alias|regname=s'</span> => \$reg_alias,</div>
+<div class="line"> <span class="stringliteral">'nosqlvc=i'</span> => \$nosqlvc, # <span class="keyword">using</span> <span class="stringliteral">"=i"</span> instead of <span class="stringliteral">"!"</span> <span class="keywordflow">for</span> consistency with scripts where it is a propagated option</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'dump|file=s'</span> => \$bacct_source_line,</div>
+<div class="line"> <span class="stringliteral">'lu|lsf_user=s'</span> => \$lsf_user,</div>
+<div class="line"> <span class="stringliteral">'sd|start_date=s'</span> => \$start_date,</div>
+<div class="line"> <span class="stringliteral">'ed|end_date=s'</span> => \$end_date,</div>
+<div class="line"> <span class="stringliteral">'h|help'</span> => \$help,</div>
+<div class="line"> );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span> ($help) { script_usage(0); }</div>
+<div class="line"></div>
+<div class="line"> my $hive_dba;</div>
+<div class="line"> <span class="keywordflow">if</span>($url or $reg_alias) {</div>
+<div class="line"> $hive_dba = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#abf2b541c5d7e3b124323a34356e3ace6">new</a>(</div>
+<div class="line"> -url => $url,</div>
+<div class="line"> -reg_conf => $reg_conf,</div>
+<div class="line"> -reg_type => $reg_type,</div>
+<div class="line"> -reg_alias => $reg_alias,</div>
+<div class="line"> -no_sql_schema_version_check => $nosqlvc,</div>
+<div class="line"> );</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"\nERROR: Connection parameters (url or reg_conf+reg_alias) need to be specified\n"</span>;</div>
+<div class="line"> script_usage(1);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $dbc = $hive_dba->dbc();</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"Creating the 'lsf_report' table if it doesn't exist...\n"</span>;</div>
+<div class="line"> $dbc->do (qq{</div>
+<div class="line"> CREATE TABLE IF NOT EXISTS lsf_report (</div>
+<div class="line"> meadow_name varchar(255) NOT NULL,</div>
+<div class="line"> process_id varchar(255) NOT NULL,</div>
+<div class="line"> status varchar(20) NOT NULL,</div>
+<div class="line"> mem_megs <span class="keywordtype">float</span> NOT NULL,</div>
+<div class="line"> swap_megs <span class="keywordtype">float</span> NOT NULL,</div>
+<div class="line"> pending_sec integer NOT NULL,</div>
+<div class="line"> cpu_sec <span class="keywordtype">float</span> NOT NULL,</div>
+<div class="line"> lifespan_sec integer NOT NULL,</div>
+<div class="line"> exception_status varchar(40) NOT NULL,</div>
+<div class="line"></div>
+<div class="line"> PRIMARY KEY (meadow_name,process_id),</div>
+<div class="line"> KEY process_id_idx (process_id)</div>
+<div class="line"></div>
+<div class="line"> ) ENGINE=InnoDB;</div>
+<div class="line"> });</div>
+<div class="line"></div>
+<div class="line"> warn "Creating the 'lsf_usage' view if it doesn't exist...\n";</div>
+<div class="line"> $dbc->do (qq{</div>
+<div class="line"> CREATE OR REPLACE VIEW lsf_usage AS</div>
+<div class="line"> SELECT CONCAT(logic_name,<span class="charliteral">'('</span>,analysis_id,<span class="charliteral">')'</span>) analysis,</div>
+<div class="line"> CONCAT(rc.name,'(',rc.resource_class_id,')') resource_class,</div>
+<div class="line"> count(*) workers,</div>
+<div class="line"> min(mem_megs), avg(mem_megs), max(mem_megs),</div>
+<div class="line"> min(swap_megs), avg(swap_megs), max(swap_megs)</div>
+<div class="line"> FROM analysis_base</div>
+<div class="line"> JOIN resource_class rc USING(resource_class_id)</div>
+<div class="line"> LEFT JOIN worker w USING(analysis_id)</div>
+<div class="line"> LEFT JOIN lsf_report USING (meadow_name, process_id)</div>
+<div class="line"> WHERE w.meadow_type='LSF'</div>
+<div class="line"> GROUP BY analysis_id</div>
+<div class="line"> ORDER BY analysis_id;</div>
+<div class="line"> });</div>
+<div class="line"></div>
+<div class="line"> my $this_lsf_farm = Bio::EnsEMBL::Hive::Meadow::LSF::name();</div>
+<div class="line"> die "Cannot find the name of the current farm.\n" unless $this_lsf_farm;</div>
+<div class="line"></div>
+<div class="line"> if( $bacct_source_line && -r $bacct_source_line ) {</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"Parsing given bacct file '$bacct_source_line'...\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"No bacct information given, finding out the time interval when the pipeline was run on '$this_lsf_farm' ...\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $offset_died_expression = ($dbc->driver eq <span class="stringliteral">'sqlite'</span>)</div>
+<div class="line"> ? <span class="stringliteral">"datetime(max(died), '+1 minute')"</span></div>
+<div class="line"> : <span class="stringliteral">"FROM_UNIXTIME(UNIX_TIMESTAMP(max(died))+60)"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $sth_times = $dbc->prepare( <span class="stringliteral">"SELECT min(born), $offset_died_expression FROM worker WHERE meadow_type='LSF' AND meadow_name='$this_lsf_farm' AND status='DEAD'"</span> );</div>
+<div class="line"> $sth_times->execute();</div>
+<div class="line"> my ($from_time, $to_time) = $sth_times->fetchrow_array();</div>
+<div class="line"> $sth_times->finish();</div>
+<div class="line"></div>
+<div class="line"> unless(defined($from_time) and defined($to_time)) {</div>
+<div class="line"> die <span class="stringliteral">"There seems to be no information on workers, exiting...\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span> (defined $start_date) {</div>
+<div class="line"> die <span class="stringliteral">"start_date must be in a format like '2012/01/25/13:46'"</span> unless $start_date =~ /^\d{4}\/\d{2}\/\d{2}\/\d{2}:\d{2}$/;</div>
+<div class="line"> $from_time = $start_date;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $from_time=~s/[- ]/\<span class="comment">//g;</span></div>
+<div class="line"> $from_time=~s/:\d\d$<span class="comment">//;</span></div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span> (defined $end_date) {</div>
+<div class="line"> die <span class="stringliteral">"end_date must be in a format like '2012/01/25/13:46'"</span> unless $end_date =~ /^\d{4}\/\d{2}\/\d{2}\/\d{2}:\d{2}$/;</div>
+<div class="line"> $to_time = $end_date;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $to_time=~s/[- ]/\<span class="comment">//g;</span></div>
+<div class="line"> $to_time=~s/:\d\d$<span class="comment">//;</span></div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"\tfrom=$from_time, to=$to_time\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> $lsf_user = $lsf_user ? <span class="stringliteral">"-u $lsf_user"</span> : <span class="stringliteral">''</span>;</div>
+<div class="line"> my $tee = $bacct_source_line ? <span class="stringliteral">"| tee $bacct_source_line"</span> : <span class="stringliteral">''</span>;</div>
+<div class="line"> $bacct_source_line = <span class="stringliteral">"bacct -l -C $from_time,$to_time $lsf_user $tee |"</span>;</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">'Will run the following command to obtain '</span>.($tee ? <span class="stringliteral">'and dump '</span> : <span class="stringliteral">''</span>).<span class="stringliteral">"bacct information: '$bacct_source_line' (may take a few minutes)\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $sth_replace = $dbc->prepare( <span class="stringliteral">'REPLACE INTO lsf_report (meadow_name, process_id, status, mem_megs, swap_megs, pending_sec, cpu_sec, lifespan_sec, exception_status) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)'</span> );</div>
+<div class="line"> {</div>
+<div class="line"> local $/ = <span class="stringliteral">"------------------------------------------------------------------------------\n\n"</span>;</div>
+<div class="line"> my %units_converter = ( <span class="charliteral">'K'</span> => 1.0/1024, <span class="charliteral">'M'</span> => 1, <span class="charliteral">'G'</span> => 1024, <span class="charliteral">'T'</span> => 1024*1024 );</div>
+<div class="line"></div>
+<div class="line"> open(my $bacct_fh, $bacct_source_line);</div>
+<div class="line"> my $record = <$bacct_fh>; # skip the header</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">for</span> my $record (<$bacct_fh>) {</div>
+<div class="line"> chomp $record;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # warn "RECORD:\n$record";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my @lines = split(/\n/, $record);</div>
+<div class="line"> <span class="keywordflow">if</span>( my ($process_id) = $lines[0]=~/^Job <(\d+(?:\[\d+\])?)>/) {</div>
+<div class="line"></div>
+<div class="line"> my $exception_status = <span class="stringliteral">''</span>;</div>
+<div class="line"> <span class="keywordflow">foreach</span> (@lines) {</div>
+<div class="line"> <span class="keywordflow">if</span>(/^\s*EXCEPTION STATUS:\s*(.*?)\s*$/) {</div>
+<div class="line"> $exception_status = $1;</div>
+<div class="line"> $exception_status =~s/\s+/;/g;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my (@keys) = split(/\s+/, <span class="charliteral">' '</span>.$lines[@lines-2]);</div>
+<div class="line"> my (@values) = split(/\s+/, <span class="charliteral">' '</span>.$lines[@lines-1]);</div>
+<div class="line"> my %usage = map { ($keys[$_] => $values[$_]) } (0..@keys-1);</div>
+<div class="line"></div>
+<div class="line"> my ($mem_in_units, $mem_unit) = $usage{<span class="stringliteral">'MEM'</span>} =~ /^([\d\.]+)([KMGT])$/;</div>
+<div class="line"> my ($swap_in_units, $swap_unit) = $usage{<span class="stringliteral">'SWAP'</span>} =~ /^([\d\.]+)([KMGT])$/;</div>
+<div class="line"></div>
+<div class="line"> my $mem_megs = $mem_in_units * $units_converter{$mem_unit};</div>
+<div class="line"> my $swap_megs = $swap_in_units * $units_converter{$swap_unit};</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> #warn join(', ', map {sprintf('%s=%s', $_, $usage{$_})} (sort keys %usage)), "\n";</span></div>
+<div class="line"><span class="preprocessor"></span> $sth_replace->execute( $this_lsf_farm, $process_id, $usage{STATUS}, $mem_megs, $swap_megs, $usage{WAIT}, $usage{CPU_T}, $usage{TURNAROUND}, $exception_status );</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> close $bacct_fh;</div>
+<div class="line"> }</div>
+<div class="line"> $sth_replace->finish();</div>
+<div class="line"> warn <span class="stringliteral">"\nReport has been loaded into pipeline's lsf_report table. Enjoy.\n"</span>;</div>
+<div class="line"></div>
+<div class="line">}</div>
+</div><!-- fragment --> </div><p>Undocumented method</p>
+<div id="codesection-main" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-main-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-main-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-main-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">main</a> {</div>
+<div class="line"> my ($url, $reg_conf, $reg_type, $reg_alias, $nosqlvc, $analysis_id, $logic_name, $input_id);</div>
+<div class="line"></div>
+<div class="line"> GetOptions(</div>
+<div class="line"> # connect to the database:</div>
+<div class="line"> <span class="stringliteral">'url=s'</span> => \$url,</div>
+<div class="line"> <span class="stringliteral">'reg_conf|regfile=s'</span> => \$reg_conf,</div>
+<div class="line"> <span class="stringliteral">'reg_type=s'</span> => \$reg_type,</div>
+<div class="line"> <span class="stringliteral">'reg_alias|regname=s'</span> => \$reg_alias,</div>
+<div class="line"> <span class="stringliteral">'nosqlvc=i'</span> => \$nosqlvc, # <span class="keyword">using</span> <span class="stringliteral">"=i"</span> instead of <span class="stringliteral">"!"</span> <span class="keywordflow">for</span> consistency with scripts where it is a propagated option</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"> # identify the analysis:</div>
+<div class="line"> <span class="stringliteral">'analysis_id=i'</span> => \$analysis_id,</div>
+<div class="line"> <span class="stringliteral">'logic_name=s'</span> => \$logic_name,</div>
+<div class="line"></div>
+<div class="line"> # specify the input_id (as a <span class="keywordtype">string</span>):</div>
+<div class="line"> <span class="stringliteral">'input_id=s'</span> => \$input_id,</div>
+<div class="line"> );</div>
+<div class="line"></div>
+<div class="line"> my $hive_dba;</div>
+<div class="line"> <span class="keywordflow">if</span>($url or $reg_alias) {</div>
+<div class="line"> $hive_dba = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#abf2b541c5d7e3b124323a34356e3ace6">new</a>(</div>
+<div class="line"> -url => $url,</div>
+<div class="line"> -reg_conf => $reg_conf,</div>
+<div class="line"> -reg_type => $reg_type,</div>
+<div class="line"> -reg_alias => $reg_alias,</div>
+<div class="line"> -no_sql_schema_version_check => $nosqlvc,</div>
+<div class="line"> );</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"\nERROR: Connection parameters (url or reg_conf+reg_alias) need to be specified\n"</span>;</div>
+<div class="line"> script_usage(1);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $analysis_adaptor = $hive_dba->get_AnalysisAdaptor;</div>
+<div class="line"> my $analysis; </div>
+<div class="line"> <span class="keywordflow">if</span>($logic_name) {</div>
+<div class="line"> $analysis = $analysis_adaptor->fetch_by_logic_name( $logic_name )</div>
+<div class="line"> or die <span class="stringliteral">"Could not fetch analysis '$logic_name'"</span>;</div>
+<div class="line"> } elsif($analysis_id) {</div>
+<div class="line"> $analysis = $analysis_adaptor->fetch_by_dbID( $analysis_id )</div>
+<div class="line"> or die <span class="stringliteral">"Could not fetch analysis with dbID='$analysis_id'"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> <a class="code" href="seed__pipeline_8pl.html#ae56eff1c83733ae5dcc4d7f7d6d25ff8">show_seedable_analyses</a>($hive_dba);</div>
+<div class="line"> exit(0);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> unless($input_id) {</div>
+<div class="line"> $input_id = <span class="stringliteral">'{}'</span>;</div>
+<div class="line"> warn <span class="stringliteral">"Since -input_id has not been set, assuming input_id='$input_id'\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $job = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb83a9f0a1fa1cd38bc5ae626bfd6b51">new</a>(</div>
+<div class="line"> -prev_job_id => undef, # <span class="keyword">this</span> job has been created by the initialization script, not by another job</div>
+<div class="line"> -analysis_id => $analysis->dbID,</div>
+<div class="line"> -input_id => destringify( $input_id ), # Make sure all job creations undergo re-stringification to avoid alternative <span class="stringliteral">"spellings"</span> of the same input_id hash</div>
+<div class="line"> );</div>
+<div class="line"></div>
+<div class="line"> my ($job_id) = @{ $hive_dba->get_AnalysisJobAdaptor->store_jobs_and_adjust_counters( [ $job ] ) };</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($job_id) {</div>
+<div class="line"></div>
+<div class="line"> print <span class="stringliteral">"Job $job_id [ "</span>.$analysis->logic_name.<span class="charliteral">'('</span>.$analysis->dbID.<span class="stringliteral">")] : '$input_id'\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"Could not create job '$input_id' (it may have been created already)\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af314298b28a69538fb25aa7eb1327c98"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public run_autonomously </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-run_autonomously" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run_autonomously-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run_autonomously-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run_autonomously-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="beekeeper_8pl.html#af314298b28a69538fb25aa7eb1327c98">run_autonomously</a> {</div>
+<div class="line"> my ($self, $max_loops, $keep_alive, $queen, $valley, $run_analysis, $run_job_id, $force) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $resourceless_worker_cmd = <a class="code" href="beekeeper_8pl.html#ad7de8680eb8b39e160cee04957ccd668">generate_worker_cmd</a>($self, $run_analysis, $run_job_id, $force);</div>
+<div class="line"> my $special_task = $run_analysis || $run_job_id;</div>
+<div class="line"></div>
+<div class="line"> my $rc_id2name = $self->{<span class="stringliteral">'dba'</span>}->get_ResourceClassAdaptor->fetch_HASHED_FROM_resource_class_id_TO_name();</div>
+<div class="line"> my %meadow_type_rc_name2resource_param_list = ();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $rd (@{ $self->{<span class="stringliteral">'dba'</span>}->get_ResourceDescriptionAdaptor->fetch_all() }) {</div>
+<div class="line"> $meadow_type_rc_name2resource_param_list{ $rd->meadow_type() }{ $rc_id2name->{$rd->resource_class_id} } = [ $rd->submission_cmd_args, $rd->worker_cmd_args ];</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $beekeeper_pid = $$;</div>
+<div class="line"></div>
+<div class="line"> my $iteration=0;</div>
+<div class="line"> my $num_of_remaining_jobs=0;</div>
+<div class="line"> my $failed_analyses=0;</div>
+<div class="line"> <span class="keywordflow">do</span> {</div>
+<div class="line"> <span class="keywordflow">if</span>($iteration++) {</div>
+<div class="line"> $queen->monitor();</div>
+<div class="line"> $self->{<span class="stringliteral">'dba'</span>}->dbc->disconnect_if_idle;</div>
+<div class="line"> printf(<span class="stringliteral">"sleep %.2f minutes. Next loop at %s\n"</span>, $self->{<span class="stringliteral">'sleep_minutes'</span>}, scalar localtime(time+$self->{<span class="stringliteral">'sleep_minutes'</span>}*60));</div>
+<div class="line"> sleep($self->{<span class="stringliteral">'sleep_minutes'</span>}*60); </div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> print(<span class="stringliteral">"\n======= beekeeper loop ** $iteration **==========\n"</span>);</div>
+<div class="line"></div>
+<div class="line"> $queen->check_for_dead_workers($valley, 0);</div>
+<div class="line"></div>
+<div class="line"> $queen->print_analysis_status unless($self->{<span class="stringliteral">'no_analysis_stats'</span>});</div>
+<div class="line"> $queen->print_running_worker_counts;</div>
+<div class="line"></div>
+<div class="line"> my $workers_to_submit_by_meadow_type_rc_name</div>
+<div class="line"> = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#a65f7b429d0ffbda238faeda2451350a8">Bio::EnsEMBL::Hive::Scheduler::schedule_workers_resync_if_necessary</a>($queen, $valley, $run_analysis);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( keys %$workers_to_submit_by_meadow_type_rc_name ) {</div>
+<div class="line"></div>
+<div class="line"> my $submit_log_subdir;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $self->{<span class="stringliteral">'submit_log_dir'</span>} ) {</div>
+<div class="line"> $submit_log_subdir = $self->{<span class="stringliteral">'submit_log_dir'</span>}.<span class="stringliteral">"/submit_bk${beekeeper_pid}_iter${iteration}"</span>;</div>
+<div class="line"> make_path( $submit_log_subdir );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $meadow_type (keys %$workers_to_submit_by_meadow_type_rc_name) {</div>
+<div class="line"></div>
+<div class="line"> my $this_meadow = $valley->available_meadow_hash->{$meadow_type};</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $rc_name (keys %{ $workers_to_submit_by_meadow_type_rc_name->{$meadow_type} }) {</div>
+<div class="line"> my $this_meadow_rc_worker_count = $workers_to_submit_by_meadow_type_rc_name->{$meadow_type}{$rc_name};</div>
+<div class="line"></div>
+<div class="line"> print <span class="stringliteral">"Submitting $this_meadow_rc_worker_count workers (rc_name=$rc_name) to "</span>.$this_meadow->signature().<span class="stringliteral">"\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> my ($submission_cmd_args, $worker_cmd_args) = @{ $meadow_type_rc_name2resource_param_list{ $meadow_type }{ $rc_name } || [] };</div>
+<div class="line"></div>
+<div class="line"> my $specific_worker_cmd = $resourceless_worker_cmd</div>
+<div class="line"> . ($special_task ? <span class="stringliteral">''</span> : <span class="stringliteral">" -rc_name $rc_name"</span>)</div>
+<div class="line"> . (defined($worker_cmd_args) ? <span class="stringliteral">" $worker_cmd_args"</span> : <span class="stringliteral">''</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $self->{<span class="stringliteral">'submit_log_dir'</span>} ) {</div>
+<div class="line"> $self->{<span class="stringliteral">'submit_stdout_file'</span>} = $submit_log_subdir . <span class="stringliteral">"/log_${rc_name}_%J_%I.out"</span>;</div>
+<div class="line"> $self->{<span class="stringliteral">'submit_stderr_file'</span>} = $submit_log_subdir . <span class="stringliteral">"/log_${rc_name}_%J_%I.err"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $this_meadow->submit_workers($specific_worker_cmd, $this_meadow_rc_worker_count, $iteration,</div>
+<div class="line"> $rc_name, $submission_cmd_args || <span class="stringliteral">''</span>,</div>
+<div class="line"> $self->{<span class="stringliteral">'submit_stdout_file'</span>}, $self->{<span class="stringliteral">'submit_stderr_file'</span>});</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> print <span class="stringliteral">"Not submitting any workers this iteration\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $failed_analyses = $queen->get_num_failed_analyses($run_analysis);</div>
+<div class="line"> $num_of_remaining_jobs = $queen->get_remaining_jobs_show_hive_progress();</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">while</span>( $keep_alive</div>
+<div class="line"> or (!$failed_analyses and $num_of_remaining_jobs and $iteration!=$max_loops) );</div>
+<div class="line"></div>
+<div class="line"> print <span class="stringliteral">"The Beekeeper has stopped because "</span>.(</div>
+<div class="line"> $failed_analyses ? <span class="stringliteral">"there were $failed_analyses failed analyses"</span></div>
+<div class="line"> : !$num_of_remaining_jobs ? <span class="stringliteral">"there is nothing left to do"</span></div>
+<div class="line"> : <span class="stringliteral">"the number of loops was limited by $max_loops and this limit expired"</span></div>
+<div class="line"> ).<span class="stringliteral">"\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> printf(<span class="stringliteral">"dbc %d disconnect cycles\n"</span>, $self->{<span class="stringliteral">'dba'</span>}->dbc->disconnect_count);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="dir_5fc43faac24a7b81dcfb81b231064839.html">scripts</a></li><li class="navelem"><a class="el" href="beekeeper_8pl.html">beekeeper.pl</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/beekeeper_8pl.js b/docs/doxygen/beekeeper_8pl.js
new file mode 100644
index 0000000000000000000000000000000000000000..98627ccc278293b893423cbc364cec95b3bf01c1
--- /dev/null
+++ b/docs/doxygen/beekeeper_8pl.js
@@ -0,0 +1,6 @@
+var beekeeper_8pl =
+[
+ [ "generate_worker_cmd", "beekeeper_8pl.html#ad7de8680eb8b39e160cee04957ccd668", null ],
+ [ "main", "beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2", null ],
+ [ "run_autonomously", "beekeeper_8pl.html#af314298b28a69538fb25aa7eb1327c98", null ]
+];
\ No newline at end of file
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator-members.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator-members.html
new file mode 100644
index 0000000000000000000000000000000000000000..e3155fbe3ad084d7075674ab86d3ac9a0388af4f
--- /dev/null
+++ b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator-members.html
@@ -0,0 +1,132 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
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+ <div id="nav-sync" class="sync"></div>
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+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Accumulator Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html">Bio::EnsEMBL::Hive::Accumulator</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a7dd96c5cf6b8c8c4b4b1447923250373">adaptor</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html">Bio::EnsEMBL::Hive::Accumulator</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a16b156d26595a7d16e0e04b60d5f6f36">dataflow</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html">Bio::EnsEMBL::Hive::Accumulator</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#ac035312016653df35c35398474835764">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html">Bio::EnsEMBL::Hive::Accumulator</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a9348142e49053884868319ec512435cd">signature_template</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html">Bio::EnsEMBL::Hive::Accumulator</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a0a2118e2f81d95101bf4d0e69d90852a">struct_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html">Bio::EnsEMBL::Hive::Accumulator</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#af5ca59dde1b1f4f1dba1c9154490a23a">url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html">Bio::EnsEMBL::Hive::Accumulator</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html
new file mode 100644
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--- /dev/null
+++ b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html
@@ -0,0 +1,358 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Bio::EnsEMBL::Hive::Accumulator Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<script type="text/javascript">
+ $(document).ready(initResizable);
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+</script>
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+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+ </span>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
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+ <div id="nav-sync" class="sync"></div>
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+ class="ui-resizable-handle">
+ </div>
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+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html','');});
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+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Accumulator Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:ac035312016653df35c35398474835764"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#ac035312016653df35c35398474835764">new</a> ()</td></tr>
+<tr class="separator:ac035312016653df35c35398474835764"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7dd96c5cf6b8c8c4b4b1447923250373"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a7dd96c5cf6b8c8c4b4b1447923250373">adaptor</a> ()</td></tr>
+<tr class="separator:a7dd96c5cf6b8c8c4b4b1447923250373"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0a2118e2f81d95101bf4d0e69d90852a"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a0a2118e2f81d95101bf4d0e69d90852a">struct_name</a> ()</td></tr>
+<tr class="separator:a0a2118e2f81d95101bf4d0e69d90852a"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9348142e49053884868319ec512435cd"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a9348142e49053884868319ec512435cd">signature_template</a> ()</td></tr>
+<tr class="separator:a9348142e49053884868319ec512435cd"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:af5ca59dde1b1f4f1dba1c9154490a23a"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#af5ca59dde1b1f4f1dba1c9154490a23a">url</a> ()</td></tr>
+<tr class="separator:af5ca59dde1b1f4f1dba1c9154490a23a"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a16b156d26595a7d16e0e04b60d5f6f36"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a16b156d26595a7d16e0e04b60d5f6f36">dataflow</a> ()</td></tr>
+<tr class="separator:a16b156d26595a7d16e0e04b60d5f6f36"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A data container object that defines parameters for accumulated dataflow.
+ This object is generated from specially designed datalow URLs.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a7dd96c5cf6b8c8c4b4b1447923250373"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Accumulator::adaptor </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-adaptor" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-adaptor-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-adaptor-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-adaptor-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a7dd96c5cf6b8c8c4b4b1447923250373">adaptor</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_adaptor'</span>} = shift @_;</div>
+<div class="line"> weaken $self->{<span class="stringliteral">'_adaptor'</span>};</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_adaptor'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a16b156d26595a7d16e0e04b60d5f6f36"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Accumulator::dataflow </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-dataflow" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dataflow-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dataflow-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dataflow-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a16b156d26595a7d16e0e04b60d5f6f36">dataflow</a> {</div>
+<div class="line"> my ( $self, $output_ids, $emitting_job ) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $sending_job_id = $emitting_job->dbID();</div>
+<div class="line"> my $receiving_job_id = $emitting_job->semaphored_job_id() || die <span class="stringliteral">"No semaphored job, cannot perform accumulated dataflow"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $struct_name = $self->struct_name();</div>
+<div class="line"> my $signature_template = $self->signature_template();</div>
+<div class="line"></div>
+<div class="line"> my @rows = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $output_id (@$output_ids) {</div>
+<div class="line"></div>
+<div class="line"> my $key_signature = $signature_template;</div>
+<div class="line"> $key_signature=~s/(\w+)/$emitting_job->_param_possibly_overridden($1,$output_id)/eg;</div>
+<div class="line"></div>
+<div class="line"> push @rows, {</div>
+<div class="line"> <span class="stringliteral">'sending_job_id'</span> => $sending_job_id,</div>
+<div class="line"> <span class="stringliteral">'receiving_job_id'</span> => $receiving_job_id,</div>
+<div class="line"> <span class="stringliteral">'struct_name'</span> => $struct_name,</div>
+<div class="line"> <span class="stringliteral">'key_signature'</span> => $key_signature,</div>
+<div class="line"> <span class="stringliteral">'value'</span> => stringify( $emitting_job->_param_possibly_overridden($struct_name, $output_id) ),</div>
+<div class="line"> };</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->adaptor->store( \@rows );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac035312016653df35c35398474835764"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Accumulator::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = bless {}, $class;</div>
+<div class="line"></div>
+<div class="line"> my ($adaptor, $struct_name, $signature_template) = </div>
+<div class="line"> rearrange([qw(<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a7dd96c5cf6b8c8c4b4b1447923250373">adaptor</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a0a2118e2f81d95101bf4d0e69d90852a">struct_name</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a9348142e49053884868319ec512435cd">signature_template</a>) ], @_);</div>
+<div class="line"></div>
+<div class="line"> $self->adaptor($adaptor) <span class="keywordflow">if</span>(defined($adaptor));</div>
+<div class="line"> $self->struct_name($struct_name) <span class="keywordflow">if</span>(defined($struct_name));</div>
+<div class="line"> $self->signature_template($signature_template) <span class="keywordflow">if</span>(defined($signature_template));</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9348142e49053884868319ec512435cd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Accumulator::signature_template </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-signature_template" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-signature_template-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-signature_template-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-signature_template-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a9348142e49053884868319ec512435cd">signature_template</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_signature_template'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_signature_template'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0a2118e2f81d95101bf4d0e69d90852a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Accumulator::struct_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-struct_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-struct_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-struct_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-struct_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a0a2118e2f81d95101bf4d0e69d90852a">struct_name</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_struct_name'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_struct_name'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af5ca59dde1b1f4f1dba1c9154490a23a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Accumulator::url </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-url" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-url-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-url-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-url-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#af5ca59dde1b1f4f1dba1c9154490a23a">url</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $ref_dba = shift @_; # <span class="keywordflow">if</span> reference dba is the same as <span class="stringliteral">'our'</span> dba, a shorter <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#af5ca59dde1b1f4f1dba1c9154490a23a">url</a> can be generated</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $adaptor = $self->adaptor) {</div>
+<div class="line"> my $dbc_prefix = ($adaptor->db == $ref_dba) ? <span class="stringliteral">':///'</span> : $adaptor->db->dbc->url();</div>
+<div class="line"> <span class="keywordflow">return</span> $dbc_prefix .<span class="stringliteral">'/accu?'</span>.$self->struct_name(). <span class="charliteral">'='</span> . $self->signature_template();</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> <span class="keywordflow">return</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_accumulator_8pm.html">Accumulator.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html">Accumulator</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+ [ "signature_template", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a9348142e49053884868319ec512435cd", null ],
+ [ "struct_name", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a0a2118e2f81d95101bf4d0e69d90852a", null ],
+ [ "url", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#af5ca59dde1b1f4f1dba1c9154490a23a", null ]
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
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+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="search/search.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
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+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
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+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
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+ name="MSearchResults" id="MSearchResults">
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+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Analysis Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a>, including all inherited members.</p>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9371f668649753210a7a301b02f6f855">can_be_empty</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a7ed5f556571a2e8e8b9eec34d19935e1">failed_job_tolerance</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#aa3cfa679262a347a86a83079bde1037d">get_compiled_module_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9fbc0420b87a63af05d8e741b14ef14a">max_retry_count</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac41c5978a943fb1bf45a7c42507460ef">meadow_type</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac491521c673320cec2ce7cecf1d841cd">module</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ad61a51a522d45f6a30e2a596b5165524">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
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+ <div class="headertitle">
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+<tr class="memitem:a9126fe194c13785419034751cf611c44"><td class="memItemLeft" align="right" valign="top">public String </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9126fe194c13785419034751cf611c44">url</a> ()</td></tr>
+<tr class="separator:a9126fe194c13785419034751cf611c44"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6ff6efb50bd9f7dbb2d2b221920e73a1"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6ff6efb50bd9f7dbb2d2b221920e73a1">stats</a> ()</td></tr>
+<tr class="separator:a6ff6efb50bd9f7dbb2d2b221920e73a1"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a19564942a29c32c01248d9b84bc15c83"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a19564942a29c32c01248d9b84bc15c83">toString</a> ()</td></tr>
+<tr class="separator:a19564942a29c32c01248d9b84bc15c83"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ An Analysis object represents a "stage" of the Hive pipeline that groups together
+ all jobs that share the same module and the same common parameters.
+
+ Individual Jobs are said to "belong" to an Analysis.
+
+ Control rules unblock when their condition Analyses are done.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a0ecb60e98a4410c8bbf7bdb0784c9785"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::analysis_capacity </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-analysis_capacity" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-analysis_capacity-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-analysis_capacity-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-analysis_capacity-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a0ecb60e98a4410c8bbf7bdb0784c9785">analysis_capacity</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_analysis_capacity'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_analysis_capacity'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9371f668649753210a7a301b02f6f855"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::can_be_empty </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-can_be_empty" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-can_be_empty-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-can_be_empty-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-can_be_empty-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9371f668649753210a7a301b02f6f855">can_be_empty</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_can_be_empty'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_can_be_empty'</span>} = 0 unless(defined($self->{<span class="stringliteral">'_can_be_empty'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_can_be_empty'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7ed5f556571a2e8e8b9eec34d19935e1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::failed_job_tolerance </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-failed_job_tolerance" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-failed_job_tolerance-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-failed_job_tolerance-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-failed_job_tolerance-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a7ed5f556571a2e8e8b9eec34d19935e1">failed_job_tolerance</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_failed_job_tolerance'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_failed_job_tolerance'</span>} = 0 unless(defined($self->{<span class="stringliteral">'_failed_job_tolerance'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_failed_job_tolerance'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa3cfa679262a347a86a83079bde1037d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::get_compiled_module_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_compiled_module_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_compiled_module_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_compiled_module_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_compiled_module_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#aa3cfa679262a347a86a83079bde1037d">get_compiled_module_name</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> my $runnable_module_name = $self->module</div>
+<div class="line"> or die <span class="stringliteral">"Analysis '"</span>.$self->logic_name.<span class="stringliteral">"' does not have its 'module' defined"</span>;</div>
+<div class="line"></div>
+<div class="line"> eval <span class="stringliteral">"require $runnable_module_name"</span>;</div>
+<div class="line"> die <span class="stringliteral">"The runnable module '$runnable_module_name' cannot be loaded or compiled:\n$@"</span> <span class="keywordflow">if</span>($@);</div>
+<div class="line"> die <span class="stringliteral">"Problem accessing methods in '$runnable_module_name'. Please check that it inherits from Bio::EnsEMBL::Hive::Process and is named correctly.\n"</span></div>
+<div class="line"> unless($runnable_module_name->isa(<span class="stringliteral">'Bio::EnsEMBL::Hive::Process'</span>));</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $runnable_module_name;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a6528be48120416c630abe32227e70bdb"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::logic_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-logic_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-logic_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-logic_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-logic_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6528be48120416c630abe32227e70bdb">logic_name</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_logic_name'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_logic_name'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9fbc0420b87a63af05d8e741b14ef14a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::max_retry_count </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-max_retry_count" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-max_retry_count-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-max_retry_count-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-max_retry_count-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9fbc0420b87a63af05d8e741b14ef14a">max_retry_count</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_max_retry_count'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_max_retry_count'</span>} = 3 unless(defined($self->{<span class="stringliteral">'_max_retry_count'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_max_retry_count'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac41c5978a943fb1bf45a7c42507460ef"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::meadow_type </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-meadow_type" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-meadow_type-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-meadow_type-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-meadow_type-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac41c5978a943fb1bf45a7c42507460ef">meadow_type</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_meadow_type'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_meadow_type'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac491521c673320cec2ce7cecf1d841cd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::module </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-module" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-module-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-module-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-module-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac491521c673320cec2ce7cecf1d841cd">module</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_module'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_module'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad61a51a522d45f6a30e2a596b5165524"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = $class->SUPER::new( @_ ); # deal with Storable stuff</div>
+<div class="line"></div>
+<div class="line"> my ($logic_name, $module, $parameters, $resource_class_id, $failed_job_tolerance, $max_retry_count, $can_be_empty, $priority, $meadow_type, $analysis_capacity) =</div>
+<div class="line"> rearrange([qw(<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6528be48120416c630abe32227e70bdb">logic_name</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac491521c673320cec2ce7cecf1d841cd">module</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#aa4d07a94412dd36e4dbb0d3db533c419">parameters</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a30049fd09f42f0b709d6785191168587">resource_class_id</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a7ed5f556571a2e8e8b9eec34d19935e1">failed_job_tolerance</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9fbc0420b87a63af05d8e741b14ef14a">max_retry_count</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9371f668649753210a7a301b02f6f855">can_be_empty</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ab1e00ad283310e3e6870b133cb029183">priority</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac41c5978a943fb1bf45a7c42507460ef">meadow_type</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a0ecb60e98a4410c8bbf7bdb0784c9785">analysis_capacity</a>) ], @_);</div>
+<div class="line"></div>
+<div class="line"> $self->logic_name($logic_name) <span class="keywordflow">if</span>($logic_name);</div>
+<div class="line"> $self->module($module) <span class="keywordflow">if</span>($module);</div>
+<div class="line"> $self->parameters($parameters) <span class="keywordflow">if</span>($parameters);</div>
+<div class="line"> $self->resource_class_id($resource_class_id) <span class="keywordflow">if</span>($resource_class_id);</div>
+<div class="line"> $self->failed_job_tolerance($failed_job_tolerance) <span class="keywordflow">if</span>($failed_job_tolerance);</div>
+<div class="line"> $self->max_retry_count($max_retry_count) <span class="keywordflow">if</span>($max_retry_count);</div>
+<div class="line"> $self->can_be_empty($can_be_empty) <span class="keywordflow">if</span>($can_be_empty);</div>
+<div class="line"> $self->priority($priority) <span class="keywordflow">if</span>($priority);</div>
+<div class="line"> $self->meadow_type($meadow_type) <span class="keywordflow">if</span>($meadow_type);</div>
+<div class="line"> $self->analysis_capacity($analysis_capacity) <span class="keywordflow">if</span>( defined($analysis_capacity) );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa4d07a94412dd36e4dbb0d3db533c419"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::parameters </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-parameters" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-parameters-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-parameters-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-parameters-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#aa4d07a94412dd36e4dbb0d3db533c419">parameters</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> my $parameters = shift @_;</div>
+<div class="line"> $self->{<span class="stringliteral">'_parameters'</span>} = ref($parameters) ? stringify($parameters) : $parameters;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_parameters'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab1e00ad283310e3e6870b133cb029183"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::priority </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-priority" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-priority-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-priority-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-priority-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ab1e00ad283310e3e6870b133cb029183">priority</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_priority'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_priority'</span>} = 0 unless(defined($self->{<span class="stringliteral">'_priority'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_priority'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a45dd4f95b7b508ddf2ba2d620734d96c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> Bio::EnsEMBL::Hive::Analysis::process </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : none
+ Example :</pre><div class="fragment"><div class="line">$process = $analysis->process;</div>
+</div><!-- fragment --> <pre> Description: construct a <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Process</a> object from the $analysis->module name
+ Returntype : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> subclass
+ Exceptions : none
+ Caller : general</pre><pre> </pre><div id="codesection-process" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-process-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-process-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-process-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a45dd4f95b7b508ddf2ba2d620734d96c">process</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> my $runnable_object = $self->get_compiled_module_name-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>( -analysis => $self );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $runnable_object;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a30049fd09f42f0b709d6785191168587"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::resource_class_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-resource_class_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-resource_class_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-resource_class_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-resource_class_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a30049fd09f42f0b709d6785191168587">resource_class_id</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_resource_class_id'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_resource_class_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a6ff6efb50bd9f7dbb2d2b221920e73a1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a> Bio::EnsEMBL::Hive::Analysis::stats </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : none
+ Example :</pre><div class="fragment"><div class="line">$stats = $analysis->stats;</div>
+</div><!-- fragment --> <pre> Description: returns the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">AnalysisStats</a> object associated with this <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Analysis</a>
+ object. Does not cache, but pull from database by using the
+ <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Analysis</a> objects adaptor->db.
+ Returntype : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a> object
+ Exceptions : none
+ Caller : general</pre><pre> </pre><div id="codesection-stats" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-stats-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-stats-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-stats-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6ff6efb50bd9f7dbb2d2b221920e73a1">stats</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Not cached internally since we want it to always be in sync with the database.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # Otherwise the user application would need to be aware of the sync state and send explicit 'sync' calls.</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my $stats = $self->adaptor->db->get_AnalysisStatsAdaptor->fetch_by_analysis_id($self->dbID);</div>
+<div class="line"> <span class="keywordflow">return</span> $stats;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a19564942a29c32c01248d9b84bc15c83"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Analysis::toString </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-toString" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-toString-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-toString-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-toString-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a19564942a29c32c01248d9b84bc15c83">toString</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> (ref($self).<span class="stringliteral">': '</span>.join(<span class="stringliteral">', '</span>, map { $_.<span class="stringliteral">'="'</span>.$self->$_().<span class="charliteral">'"'</span> } qw(dbID <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6528be48120416c630abe32227e70bdb">logic_name</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac491521c673320cec2ce7cecf1d841cd">module</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#aa4d07a94412dd36e4dbb0d3db533c419">parameters</a>) ));</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9126fe194c13785419034751cf611c44"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public String Bio::EnsEMBL::Hive::Analysis::url </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : none
+ Example :</pre><div class="fragment"><div class="line">$url = $analysis->url;</div>
+</div><!-- fragment --> <pre> Description: Constructs a URL string for this database connection
+ Follows the general URL rules.
+ Returntype : string of format
+ mysql://<user>:<pass><host>:<port>/<dbname>/analysis?logic_name=<name>
+ Exceptions : none
+ Caller : general</pre><pre> </pre><div id="codesection-url" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-url-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-url-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-url-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9126fe194c13785419034751cf611c44">url</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> undef unless($self->adaptor);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->adaptor->db->dbc->url . <span class="stringliteral">'/analysis?logic_name='</span> . $self->logic_name;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_analysis_8pm.html">Analysis.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Analysis</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+ [ "new", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ad61a51a522d45f6a30e2a596b5165524", null ],
+ [ "parameters", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#aa4d07a94412dd36e4dbb0d3db533c419", null ],
+ [ "priority", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ab1e00ad283310e3e6870b133cb029183", null ],
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+ [ "url", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9126fe194c13785419034751cf611c44", null ]
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+</div><!--header-->
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+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ab689e0f33659659ebdc4396b237df113">adaptor</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#a7cec568f2499ba88040334c408efeb6b">condition_analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa1408c2380cfa9fc9d4b22458bdfd1cb">condition_analysis_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa7553c12b9b1af1c15d147dd5f5d4fac">ctrled_analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4c95d1a0114e3d438f8b3b71d40cd70">ctrled_analysis_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#a22338588d57d7bf475159a73b4fb10da">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4532406dd4e302fa5a2f2531ff3df73">toString</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a></td><td class="entry"></td></tr>
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diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::AnalysisCtrlRule Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a22338588d57d7bf475159a73b4fb10da"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#a22338588d57d7bf475159a73b4fb10da">new</a> ()</td></tr>
+<tr class="separator:a22338588d57d7bf475159a73b4fb10da"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab689e0f33659659ebdc4396b237df113"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ab689e0f33659659ebdc4396b237df113">adaptor</a> ()</td></tr>
+<tr class="separator:ab689e0f33659659ebdc4396b237df113"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4c95d1a0114e3d438f8b3b71d40cd70"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4c95d1a0114e3d438f8b3b71d40cd70">ctrled_analysis_id</a> ()</td></tr>
+<tr class="separator:ac4c95d1a0114e3d438f8b3b71d40cd70"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aa1408c2380cfa9fc9d4b22458bdfd1cb"><td class="memItemLeft" align="right" valign="top">public String </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa1408c2380cfa9fc9d4b22458bdfd1cb">condition_analysis_url</a> ()</td></tr>
+<tr class="separator:aa1408c2380cfa9fc9d4b22458bdfd1cb"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aa7553c12b9b1af1c15d147dd5f5d4fac"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa7553c12b9b1af1c15d147dd5f5d4fac">ctrled_analysis</a> ()</td></tr>
+<tr class="separator:aa7553c12b9b1af1c15d147dd5f5d4fac"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7cec568f2499ba88040334c408efeb6b"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#a7cec568f2499ba88040334c408efeb6b">condition_analysis</a> ()</td></tr>
+<tr class="separator:a7cec568f2499ba88040334c408efeb6b"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4532406dd4e302fa5a2f2531ff3df73"><td class="memItemLeft" align="right" valign="top">public String </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4532406dd4e302fa5a2f2531ff3df73">toString</a> ()</td></tr>
+<tr class="separator:ac4532406dd4e302fa5a2f2531ff3df73"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ An 'analysis control rule' is a high level blocking control structure where there is
+ a 'ctrled_analysis' which is 'BLOCKED' from running until all of its 'condition_analysis' are 'DONE'.
+ If a ctrled_analysis requires multiple analysis to be DONE before it can run, a separate
+ AnalysisCtrlRule must be created/stored for each condtion analysis.
+
+ Allows the 'condition' analysis to be specified with a network savy URL like
+ mysql://ensadmin:<pass>\@ecs2:3361/compara_hive_test?analysis.logic_name='blast_NCBI34'
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ab689e0f33659659ebdc4396b237df113"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisCtrlRule::adaptor </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-adaptor" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-adaptor-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-adaptor-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-adaptor-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ab689e0f33659659ebdc4396b237df113">adaptor</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_adaptor'</span>} = shift @_;</div>
+<div class="line"> weaken $self->{<span class="stringliteral">'_adaptor'</span>};</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_adaptor'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7cec568f2499ba88040334c408efeb6b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> Bio::EnsEMBL::Hive::AnalysisCtrlRule::condition_analysis </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg[1] : (optional) <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> object
+ Usage : $self->condition_analysis($anal);
+ Function: Get/set method for the analysis which must be 'DONE' in order for
+ the controlled analysis to be un-BLOCKED
+ Returns : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a></pre><pre> </pre><div id="codesection-condition_analysis" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-condition_analysis-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-condition_analysis-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-condition_analysis-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#a7cec568f2499ba88040334c408efeb6b">condition_analysis</a> {</div>
+<div class="line"> my ($self,$analysis) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( defined $analysis ) {</div>
+<div class="line"> unless ($analysis->isa(<span class="stringliteral">'Bio::EnsEMBL::Hive::Analysis'</span>)) {</div>
+<div class="line"> <span class="keywordflow">throw</span>(</div>
+<div class="line"> <span class="stringliteral">"condition_analysis arg must be a [Bio::EnsEMBL::Hive::Analysis]"</span>.</div>
+<div class="line"> <span class="stringliteral">"not a [$analysis]"</span>);</div>
+<div class="line"> }</div>
+<div class="line"> $self->{<span class="stringliteral">'_condition_analysis'</span>} = $analysis;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> #if the 'condition' and 'ctrled' share the same adaptor, then use a simple logic_name</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #for the URL rather than a full network distributed URL</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>($self->ctrled_analysis and ($self->ctrled_analysis->adaptor == $analysis->adaptor)) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_condition_analysis_url'</span>} = $analysis-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6528be48120416c630abe32227e70bdb">logic_name</a>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $self->{<span class="stringliteral">'_condition_analysis_url'</span>} = $analysis->url;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"><span class="preprocessor"> # lazy load the analysis object if I can</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>(!defined($self->{<span class="stringliteral">'_condition_analysis'</span>}) and defined($self->condition_analysis_url)) {</div>
+<div class="line"> $analysis = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">fetch</a>($self->condition_analysis_url);</div>
+<div class="line"> unless($analysis) {</div>
+<div class="line"> $analysis =</div>
+<div class="line"> $self->adaptor->db->get_AnalysisAdaptor->fetch_by_logic_name($self->condition_analysis_url);</div>
+<div class="line"> }</div>
+<div class="line"> $self->{<span class="stringliteral">'_condition_analysis'</span>} = $analysis;</div>
+<div class="line"> </div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_condition_analysis'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa1408c2380cfa9fc9d4b22458bdfd1cb"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public String Bio::EnsEMBL::Hive::AnalysisCtrlRule::condition_analysis_url </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg[1] : (optional) string $url
+ Usage : $self->condition_analysis_url($url);
+ Function: Get/set method for the analysis which must be 'DONE' in order for
+ the controlled analysis to be un-BLOCKED. Specified as a URL.
+ Returns : string</pre><pre> </pre><div id="codesection-condition_analysis_url" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-condition_analysis_url-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-condition_analysis_url-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-condition_analysis_url-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa1408c2380cfa9fc9d4b22458bdfd1cb">condition_analysis_url</a> {</div>
+<div class="line"> my ($self,$url) = @_;</div>
+<div class="line"> <span class="keywordflow">if</span>($url) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_condition_analysis_url'</span>} = $url;</div>
+<div class="line"> $self->{<span class="stringliteral">'_condition_analysis'</span>} = undef;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_condition_analysis_url'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa7553c12b9b1af1c15d147dd5f5d4fac"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> Bio::EnsEMBL::Hive::AnalysisCtrlRule::ctrled_analysis </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg[1] : (optional) <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> object
+ Usage : $self->ctrled_analysis($anal);
+ Function: Get/set method for the analysis which will be BLOCKED until all
+ of its condition analyses are 'DONE'
+ Returns : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a></pre><pre> </pre><div id="codesection-ctrled_analysis" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-ctrled_analysis-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-ctrled_analysis-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-ctrled_analysis-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa7553c12b9b1af1c15d147dd5f5d4fac">ctrled_analysis</a> {</div>
+<div class="line"> my ($self,$analysis) = @_;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # setter mode</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>( defined $analysis ) {</div>
+<div class="line"> unless ($analysis->isa(<span class="stringliteral">'Bio::EnsEMBL::Hive::Analysis'</span>)) {</div>
+<div class="line"> <span class="keywordflow">throw</span>(</div>
+<div class="line"> <span class="stringliteral">"ctrled_analysis arg must be a [Bio::EnsEMBL::Hive::Analysis]"</span>.</div>
+<div class="line"> <span class="stringliteral">"not a [$analysis]"</span>);</div>
+<div class="line"> }</div>
+<div class="line"> $self->{<span class="stringliteral">'_ctrled_analysis'</span>} = $analysis;</div>
+<div class="line"> $self->{<span class="stringliteral">'_ctrled_analysis_id'</span>} = $analysis->dbID;</div>
+<div class="line"> }</div>
+<div class="line"> </div>
+<div class="line"><span class="preprocessor"> # lazy load the analysis object if I can</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>(!defined($self->{<span class="stringliteral">'_ctrled_analysis'</span>})</div>
+<div class="line"> and defined($self->ctrled_analysis_id)</div>
+<div class="line"> and defined($self->adaptor))</div>
+<div class="line"> {</div>
+<div class="line"> $self->{<span class="stringliteral">'_ctrled_analysis'</span>} = $self->adaptor->db->get_AnalysisAdaptor->fetch_by_dbID($self->ctrled_analysis_id);</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_ctrled_analysis'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac4c95d1a0114e3d438f8b3b71d40cd70"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Int Bio::EnsEMBL::Hive::AnalysisCtrlRule::ctrled_analysis_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg[1] : (optional) int $dbID
+ Usage : $self->ctrled_analysis_id($dbID);
+ Function: Get/set method for the analysis which will be BLOCKED until all
+ of its condition analyses are 'DONE'. Specified as a dbID.
+ Returns : integer</pre><pre> </pre><div id="codesection-ctrled_analysis_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-ctrled_analysis_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-ctrled_analysis_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-ctrled_analysis_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4c95d1a0114e3d438f8b3b71d40cd70">ctrled_analysis_id</a> {</div>
+<div class="line"> my ($self,$analysis_id) = @_;</div>
+<div class="line"> <span class="keywordflow">if</span>($analysis_id) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_ctrled_analysis_id'</span>} = $analysis_id;</div>
+<div class="line"> $self->{<span class="stringliteral">'_ctrled_analysis'</span>} = undef;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_ctrled_analysis_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a22338588d57d7bf475159a73b4fb10da"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a> Bio::EnsEMBL::Hive::AnalysisCtrlRule::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : new
+ Usage : ...AnalysisCtrlRule->new;
+ Function: Constructor for empty <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">AnalysisCtrlRule</a> object
+ Returns : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+ Args : none</pre><pre> </pre><div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"> my $self = bless {}, $class;</div>
+<div class="line"> </div>
+<div class="line"> my ( $dbID, $adaptor, $condition_analysis_url, $ctrled_analysis_id ) =</div>
+<div class="line"> rearrange( [ qw (DBID ADAPTOR CONDITION_ANALYSIS_URL CTRLED_ANALYSIS_ID) ], @_ );</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # database persistence:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->dbID( $dbID ) <span class="keywordflow">if</span>(defined($dbID));</div>
+<div class="line"> $self->adaptor( $adaptor ) <span class="keywordflow">if</span>(defined($adaptor));</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # simple scalars:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->condition_analysis_url( $condition_analysis_url ) <span class="keywordflow">if</span>(defined($condition_analysis_url));</div>
+<div class="line"> $self->ctrled_analysis_id( $ctrled_analysis_id ) <span class="keywordflow">if</span>(defined($ctrled_analysis_id));</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac4532406dd4e302fa5a2f2531ff3df73"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public String Bio::EnsEMBL::Hive::AnalysisCtrlRule::toString </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Args : (none)
+ Example :</pre><div class="fragment"><div class="line">print $c_rule->toString().<span class="stringliteral">"\n"</span>;</div>
+</div><!-- fragment --> <pre> Description: returns a stringified representation of the rule
+ Returntype : string</pre><pre> </pre><div id="codesection-toString" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-toString-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-toString-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-toString-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4532406dd4e302fa5a2f2531ff3df73">toString</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> join(<span class="stringliteral">''</span>,</div>
+<div class="line"> <span class="stringliteral">'AnalysisCtrlRule'</span>,</div>
+<div class="line"># <span class="stringliteral">'(dbID='</span>, ($self->dbID || <span class="charliteral">'?'</span>), <span class="charliteral">')'</span>, # <span class="keyword">this</span> <span class="keywordtype">object</span> doesn<span class="stringliteral">'t have a dbID</span></div>
+<div class="line"><span class="stringliteral"> '</span>: <span class="stringliteral">',</span></div>
+<div class="line"><span class="stringliteral"> $self->condition_analysis_url,</span></div>
+<div class="line"><span class="stringliteral"> '</span> -| <span class="stringliteral">',</span></div>
+<div class="line"><span class="stringliteral"> $self->ctrled_analysis->logic_name,</span></div>
+<div class="line"><span class="stringliteral"> );</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_analysis_ctrl_rule_8pm.html">AnalysisCtrlRule.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">AnalysisCtrlRule</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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@@ -0,0 +1,10 @@
+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule =
+[
+ [ "adaptor", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ab689e0f33659659ebdc4396b237df113", null ],
+ [ "condition_analysis", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#a7cec568f2499ba88040334c408efeb6b", null ],
+ [ "condition_analysis_url", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa1408c2380cfa9fc9d4b22458bdfd1cb", null ],
+ [ "ctrled_analysis", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa7553c12b9b1af1c15d147dd5f5d4fac", null ],
+ [ "ctrled_analysis_id", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4c95d1a0114e3d438f8b3b71d40cd70", null ],
+ [ "new", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#a22338588d57d7bf475159a73b4fb10da", null ],
+ [ "toString", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4532406dd4e302fa5a2f2531ff3df73", null ]
+];
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+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
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+  <span id="projectnumber">1.9</span>
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+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
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+<!-- window showing the filter options -->
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+ name="MSearchResults" id="MSearchResults">
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+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::AnalysisJob Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a0536cad5480d931d7982fe0f049ebfaf">_param_possibly_overridden</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a416e12ae4a4511ba13ba427cfc2361d5">_param_silent</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a960052271c6be58027f13c1cadbe5ad8">_subst_one_hashpair</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1a33fd570abad2c0f79c22bc5d77d652">accu_hash</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52165b28650c26a24b621da4ff2e777a">accu_id_stack</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ad43a29a7f535cc507f91702fad70b310">analysis_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ac5bab7c3ffa521e44370d1bdc34cf11a">autoflow</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#adf437552d1a1b96a0fb1868b7ee58e0b">completed</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a77d324a4242b0c01f6f1288846db43d6">csvq</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a02aa287f1ac4ae8ff473bb550dcf5355">dataflow_output_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae830f1e7b046d1787e65ece0cebc30cd">dataflow_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a48bcb9722516ca9456c53dd1732c394d">fan_cache</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a7ba3562d4484fea866441d7d501d4900">incomplete</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a9dd7289999985b60a8299ac66327f3ce">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1fb261840767255efd596b84312532d1">lethal_for_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7c9b7527f3745f962277b5022d1d09ca">mysql_conn</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7660586a322000f6f797927a3a216676">mysql_dbname</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb83a9f0a1fa1cd38bc5ae626bfd6b51">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#aacc3d8e3ec1b0f940cc274c95c93e834">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a46b02fdd5e620c96f4f8abe8e1bc017b">param_exists</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb5e9b464027c776b1bd01eaf7b9cfe7">param_id_stack</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a03f67c01a12beaa839338be4da9bf9cb">param_init</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#ad6dba01319677081085a59310e235c51">param_is_defined</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a82a8b3a737120fdf27b3152bc1c63bab">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a261b12abc17c65fac5fd4ccffbb73d6d">param_substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a097e33f4921749e52972e051032809c4">prev_job_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a6080b20b6f65b3a31e72de743db62dac">print_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ab69fe83605e95a9dafb3025e655082b5">query_count</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae3bad87fd4aff80e2b4ee41185494c64">retry_count</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#af050b0e809253aef004926eeaf6cdf75">runtime_msec</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a75263a4a15c449f509bf35cbead2c54c">semaphore_count</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1e2d7fa5ae29570bfc2e389dc3abd824">semaphored_job_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ab65c1a11b3be9af06c4e47a71294b757">status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a817a316519b8f04e340458abf0a0cf1e">stderr_file</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#aa110de6559e3966aa60049145b77be0c">stdout_file</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a65bafee37ae9da96499433c2dd73f9bd">toString</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52d6385c42523ebbd5c42c75e892fa31">transient_error</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae14890c144f67fd2ff32b99bbba8f121">update_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a00e809b1c03cf9e47212905b4284c140">warning</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#af38047d73f933f30cde285c5dab5dffb">worker_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="entry"></td></tr>
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+<div class="title">Bio::EnsEMBL::Hive::AnalysisJob Class Reference</div> </div>
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+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::AnalysisJob:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
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+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::AnalysisJob:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
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+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:abb83a9f0a1fa1cd38bc5ae626bfd6b51"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb83a9f0a1fa1cd38bc5ae626bfd6b51">new</a> ()</td></tr>
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+<tr class="memitem:a82a8b3a737120fdf27b3152bc1c63bab inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memItemLeft" align="right" valign="top">public Any </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a82a8b3a737120fdf27b3152bc1c63bab">param_required</a> ()</td></tr>
+<tr class="separator:a82a8b3a737120fdf27b3152bc1c63bab inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a46b02fdd5e620c96f4f8abe8e1bc017b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a46b02fdd5e620c96f4f8abe8e1bc017b">param_exists</a> ()</td></tr>
+<tr class="separator:a46b02fdd5e620c96f4f8abe8e1bc017b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad6dba01319677081085a59310e235c51 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#ad6dba01319677081085a59310e235c51">param_is_defined</a> ()</td></tr>
+<tr class="separator:ad6dba01319677081085a59310e235c51 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aacc3d8e3ec1b0f940cc274c95c93e834 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memItemLeft" align="right" valign="top">public Any </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#aacc3d8e3ec1b0f940cc274c95c93e834">param</a> ()</td></tr>
+<tr class="separator:aacc3d8e3ec1b0f940cc274c95c93e834 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a261b12abc17c65fac5fd4ccffbb73d6d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a261b12abc17c65fac5fd4ccffbb73d6d">param_substitute</a> ()</td></tr>
+<tr class="separator:a261b12abc17c65fac5fd4ccffbb73d6d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7c9b7527f3745f962277b5022d1d09ca inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7c9b7527f3745f962277b5022d1d09ca">mysql_conn</a> ()</td></tr>
+<tr class="separator:a7c9b7527f3745f962277b5022d1d09ca inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7660586a322000f6f797927a3a216676 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7660586a322000f6f797927a3a216676">mysql_dbname</a> ()</td></tr>
+<tr class="separator:a7660586a322000f6f797927a3a216676 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a77d324a4242b0c01f6f1288846db43d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a77d324a4242b0c01f6f1288846db43d6">csvq</a> ()</td></tr>
+<tr class="separator:a77d324a4242b0c01f6f1288846db43d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a960052271c6be58027f13c1cadbe5ad8 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a960052271c6be58027f13c1cadbe5ad8">_subst_one_hashpair</a> ()</td></tr>
+<tr class="separator:a960052271c6be58027f13c1cadbe5ad8 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ An AnalysisJob is the link between the input_id control data, the analysis and
+ the rule system. It also tracks the state of the job as it is processed
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a1a33fd570abad2c0f79c22bc5d77d652"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::accu_hash </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-accu_hash" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-accu_hash-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-accu_hash-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-accu_hash-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1a33fd570abad2c0f79c22bc5d77d652">accu_hash</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_accu_hash'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_accu_hash'</span>} = {} unless(defined($self->{<span class="stringliteral">'_accu_hash'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_accu_hash'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a52165b28650c26a24b621da4ff2e777a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::accu_id_stack </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-accu_id_stack" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-accu_id_stack-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-accu_id_stack-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-accu_id_stack-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52165b28650c26a24b621da4ff2e777a">accu_id_stack</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_accu_id_stack'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_accu_id_stack'</span>} = <span class="stringliteral">''</span> unless(defined($self->{<span class="stringliteral">'_accu_id_stack'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_accu_id_stack'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad43a29a7f535cc507f91702fad70b310"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::analysis_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-analysis_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-analysis_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-analysis_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-analysis_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ad43a29a7f535cc507f91702fad70b310">analysis_id</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_analysis_id'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_analysis_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac5bab7c3ffa521e44370d1bdc34cf11a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Boolean Bio::EnsEMBL::Hive::AnalysisJob::autoflow </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : autoflow
+ Function: Gets/sets flag for whether the job should
+ be automatically dataflowed on branch 1 when the job completes.
+ If the subclass manually sends a job along branch 1 with dataflow_output_id,
+ the autoflow will turn itself off.
+ Returns : boolean (1=default|0)</pre><pre> </pre><div id="codesection-autoflow" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-autoflow-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-autoflow-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-autoflow-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ac5bab7c3ffa521e44370d1bdc34cf11a">autoflow</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_autoflow'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_autoflow'</span>} = 1 unless(defined($self->{<span class="stringliteral">'_autoflow'</span>})); </div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_autoflow'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="adf437552d1a1b96a0fb1868b7ee58e0b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::completed </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-completed" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-completed-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-completed-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-completed-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#adf437552d1a1b96a0fb1868b7ee58e0b">completed</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_completed'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_completed'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a02aa287f1ac4ae8ff473bb550dcf5355"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::dataflow_output_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : dataflow_output_id
+ Arg[1](req) : <string> $output_id
+ Arg[2](opt) : <int> $branch_name_or_code (optional, defaults to 1)
+ Usage : $self->dataflow_output_id($output_id, $branch_name_or_code);
+ Function:
+ If a RunnableDB(Process) needs to create jobs, this allows it to have jobs
+ created and flowed through the dataflow rules of the workflow graph.
+ This 'output_id' becomes the 'input_id' of the newly created job at
+ the ends of the dataflow pipes. The optional 'branch_name_or_code' determines
+ which dataflow pipe(s) to flow the job through.</pre><pre> </pre><div id="codesection-dataflow_output_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dataflow_output_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dataflow_output_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dataflow_output_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a02aa287f1ac4ae8ff473bb550dcf5355">dataflow_output_id</a> {</div>
+<div class="line"> my ($self, $output_ids, $branch_name_or_code, $create_job_options) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $input_id = $self->input_id();</div>
+<div class="line"> my $param_id_stack = $self->param_id_stack();</div>
+<div class="line"> my $accu_id_stack = $self->accu_id_stack();</div>
+<div class="line"></div>
+<div class="line"> my $job_adaptor = $self->adaptor();</div>
+<div class="line"> my $hive_use_param_stack = $job_adaptor && $job_adaptor->db->hive_use_param_stack();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($hive_use_param_stack) {</div>
+<div class="line"> <span class="keywordflow">if</span>($input_id and ($input_id ne <span class="stringliteral">'{}'</span>)) { # add the parent to the <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb5e9b464027c776b1bd01eaf7b9cfe7">param_id_stack</a> <span class="keywordflow">if</span> it had non-trivial extra parameters</div>
+<div class="line"> $param_id_stack = ($param_id_stack ? $param_id_stack.<span class="charliteral">','</span> : <span class="stringliteral">''</span>).$self->dbID();</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">if</span>(scalar(keys %{$self->accu_hash()})) { # add the parent to the <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52165b28650c26a24b621da4ff2e777a">accu_id_stack</a> <span class="keywordflow">if</span> it had <span class="stringliteral">"own"</span> accumulator</div>
+<div class="line"> $accu_id_stack = ($accu_id_stack ? $accu_id_stack.<span class="charliteral">','</span> : <span class="stringliteral">''</span>).$self->dbID();</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $output_ids ||= [ $hive_use_param_stack ? {} : $input_id ]; # by <span class="keywordflow">default</span> replicate the parameters of the parent in the child</div>
+<div class="line"> $output_ids = [ $output_ids ] unless(ref($output_ids) eq <span class="stringliteral">'ARRAY'</span>); # force previously used single values into an arrayref</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($create_job_options) {</div>
+<div class="line"> die <span class="stringliteral">"Please consider configuring semaphored dataflow from PipeConfig rather than setting it up manually"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # map branch names to numbers:</span></div>
+<div class="line"><span class="preprocessor"></span> my $branch_code = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a529c8c386c3e60cb1a737231775bf77c">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor::branch_name_2_code</a>($branch_name_or_code);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # if branch_code is set to 1 (explicitly or impliticly), turn off automatic dataflow:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->autoflow(0) <span class="keywordflow">if</span>($branch_code == 1);</div>
+<div class="line"></div>
+<div class="line"> my @output_job_ids = ();</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # sort rules to make sure the fan rules come before funnel rules for the same branch_code:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">foreach</span> my $rule (sort {($b->funnel_dataflow_rule_id||0) <=> ($a->funnel_dataflow_rule_id||0)} @{ $self->dataflow_rules( $branch_code ) }) {</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # parameter substitution into input_id_template is rule-specific</span></div>
+<div class="line"><span class="preprocessor"></span> my $output_ids_for_this_rule;</div>
+<div class="line"> <span class="keywordflow">if</span>(my $template_string = $rule->input_id_template()) {</div>
+<div class="line"> my $template_hash = destringify($template_string);</div>
+<div class="line"> $output_ids_for_this_rule = [ map { $self->param_substitute($template_hash, $_) } @$output_ids ];</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $output_ids_for_this_rule = $output_ids;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $target_analysis_or_table = $rule->to_analysis();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($target_analysis_or_table->can(<span class="stringliteral">'dataflow'</span>)) {</div>
+<div class="line"></div>
+<div class="line"> $target_analysis_or_table->dataflow( $output_ids_for_this_rule, $self );</div>
+<div class="line"></div>
+<div class="line"> } elsif(my $funnel_dataflow_rule_id = $rule->funnel_dataflow_rule_id()) { # members of a semaphored fan will have to wait in cache until the funnel is created:</div>
+<div class="line"></div>
+<div class="line"> my $fan_cache_this_branch = $self->fan_cache()->{$funnel_dataflow_rule_id} ||= [];</div>
+<div class="line"> push @$fan_cache_this_branch, map { <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb83a9f0a1fa1cd38bc5ae626bfd6b51">new</a>(</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a097e33f4921749e52972e051032809c4">prev_job_id</a> => $self->dbID,</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ad43a29a7f535cc507f91702fad70b310">analysis_id</a> => $target_analysis_or_table->dbID, # expecting an Analysis</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a9dd7289999985b60a8299ac66327f3ce">input_id</a> => $_,</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb5e9b464027c776b1bd01eaf7b9cfe7">param_id_stack</a> => $param_id_stack,</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52165b28650c26a24b621da4ff2e777a">accu_id_stack</a> => $accu_id_stack,</div>
+<div class="line"> # -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1e2d7fa5ae29570bfc2e389dc3abd824">semaphored_job_id</a> => to be set when the $funnel_job has been stored</div>
+<div class="line"> ) } @$output_ids_for_this_rule;</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> { # either a semaphored funnel or a non-semaphored dataflow:</div>
+<div class="line"></div>
+<div class="line"> my $fan_jobs = <span class="keyword">delete</span> $self->fan_cache()->{$rule->dbID}; # clear the cache at the same time</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($fan_jobs && @$fan_jobs) { # a semaphored funnel</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( (my $funnel_job_count = scalar(@$output_ids_for_this_rule)) !=1 ) {</div>
+<div class="line"></div>
+<div class="line"> $self->transient_error(0);</div>
+<div class="line"> die <span class="stringliteral">"Asked to dataflow into $funnel_job_count funnel jobs instead of 1"</span>;</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> my $funnel_job = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb83a9f0a1fa1cd38bc5ae626bfd6b51">new</a>(</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a097e33f4921749e52972e051032809c4">prev_job_id</a> => $self->dbID,</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ad43a29a7f535cc507f91702fad70b310">analysis_id</a> => $target_analysis_or_table->dbID, # expecting an Analysis</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a9dd7289999985b60a8299ac66327f3ce">input_id</a> => $output_ids_for_this_rule->[0],</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb5e9b464027c776b1bd01eaf7b9cfe7">param_id_stack</a> => $param_id_stack,</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52165b28650c26a24b621da4ff2e777a">accu_id_stack</a> => $accu_id_stack,</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a75263a4a15c449f509bf35cbead2c54c">semaphore_count</a> => scalar(@$fan_jobs), # <span class="stringliteral">"pre-increase"</span> the semaphore count before creating the dependent jobs</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1e2d7fa5ae29570bfc2e389dc3abd824">semaphored_job_id</a> => $self->semaphored_job_id(), # propagate parent<span class="stringliteral">'s semaphore if any</span></div>
+<div class="line"><span class="stringliteral"> );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my ($funnel_job_id) = @{ $job_adaptor->store_jobs_and_adjust_counters( [ $funnel_job ], 0) };</span></div>
+<div class="line"><span class="stringliteral"> if($funnel_job_id) { # if a semaphored funnel job creation succeeded, then store the fan out of the cache:</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> foreach my $fan_job (@$fan_jobs) { # set the funnel in every fan'</span>s job:</div>
+<div class="line"> $fan_job->semaphored_job_id( $funnel_job_id );</div>
+<div class="line"> }</div>
+<div class="line"> push @output_job_ids, $funnel_job_id, @{ $job_adaptor->store_jobs_and_adjust_counters( $fan_jobs, 1) };</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> { # non-semaphored dataflow (but potentially propagating any existing semaphores)</div>
+<div class="line"> my @non_semaphored_jobs = map { <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb83a9f0a1fa1cd38bc5ae626bfd6b51">new</a>(</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a097e33f4921749e52972e051032809c4">prev_job_id</a> => $self->dbID,</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ad43a29a7f535cc507f91702fad70b310">analysis_id</a> => $target_analysis_or_table->dbID, # expecting an Analysis</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a9dd7289999985b60a8299ac66327f3ce">input_id</a> => $_,</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb5e9b464027c776b1bd01eaf7b9cfe7">param_id_stack</a> => $param_id_stack,</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52165b28650c26a24b621da4ff2e777a">accu_id_stack</a> => $accu_id_stack,</div>
+<div class="line"> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1e2d7fa5ae29570bfc2e389dc3abd824">semaphored_job_id</a> => $self->semaphored_job_id(), # propagate parent<span class="stringliteral">'s semaphore if any</span></div>
+<div class="line"><span class="stringliteral"> ) } @$output_ids_for_this_rule;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> push @output_job_ids, @{ $job_adaptor->store_jobs_and_adjust_counters( \@non_semaphored_jobs, 0) };</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> } # /if</span></div>
+<div class="line"><span class="stringliteral"> } # /foreach my $rule</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> return \@output_job_ids;</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae830f1e7b046d1787e65ece0cebc30cd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::dataflow_rules </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-dataflow_rules" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dataflow_rules-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dataflow_rules-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dataflow_rules-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae830f1e7b046d1787e65ece0cebc30cd">dataflow_rules</a> { # <span class="keywordflow">if</span> ever set will prevent the Job from fetching rules from the DB</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $branch_name_or_code = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $branch_code = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a529c8c386c3e60cb1a737231775bf77c">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor::branch_name_2_code</a>($branch_name_or_code);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_dataflow_rules'</span>}{$branch_code} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_dataflow_rules'</span>} ||= $self->adaptor->db->get_DataflowRuleAdaptor->fetch_all_by_from_analysis_id_HASHED_FROM_branch_code( $self->analysis_id );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_dataflow_rules'</span>}{$branch_code} || [];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a48bcb9722516ca9456c53dd1732c394d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::fan_cache </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fan_cache" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fan_cache-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fan_cache-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fan_cache-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a48bcb9722516ca9456c53dd1732c394d">fan_cache</a> { # a <span class="keyword">self</span>-initializing getter (no setting)</div>
+<div class="line"> <span class="preprocessor"># Returns a hash-of-lists { 2 => [list of jobs waiting to be funneled into 2], 3 => [list of jobs waiting to be funneled into 3], etc}</span></div>
+<div class="line"><span class="preprocessor"></span> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_fan_cache'</span>} ||= {};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7ba3562d4484fea866441d7d501d4900"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::incomplete </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-incomplete" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-incomplete-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-incomplete-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-incomplete-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a7ba3562d4484fea866441d7d501d4900">incomplete</a> { # Job should set <span class="keyword">this</span> to 0 prior to throwing <span class="keywordflow">if</span> the job is done,</div>
+<div class="line"><span class="preprocessor"> # but it wants the thrown message to be recorded with is_error=0.</span></div>
+<div class="line"><span class="preprocessor"></span> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_incomplete'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_incomplete'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9dd7289999985b60a8299ac66327f3ce"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::input_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-input_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-input_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-input_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-input_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a9dd7289999985b60a8299ac66327f3ce">input_id</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> my $input_id = shift @_;</div>
+<div class="line"> $self->{<span class="stringliteral">'_input_id'</span>} = ref($input_id) ? stringify($input_id) : $input_id;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_input_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1fb261840767255efd596b84312532d1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::lethal_for_worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-lethal_for_worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-lethal_for_worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-lethal_for_worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-lethal_for_worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1fb261840767255efd596b84312532d1">lethal_for_worker</a> { # Job should set <span class="keyword">this</span> to 1 prior to dying (or before running code that might cause death - such as RunnableDB<span class="stringliteral">'s compilation)</span></div>
+<div class="line"><span class="stringliteral"> # if it believes that the state of things will not allow the Worker to continue normally.</span></div>
+<div class="line"><span class="stringliteral"> # The Worker will check the flag and commit suicide if it is set to true.</span></div>
+<div class="line"><span class="stringliteral"> my $self = shift;</span></div>
+<div class="line"><span class="stringliteral"> $self->{'</span>_lethal_for_worker<span class="stringliteral">'} = shift if(@_);</span></div>
+<div class="line"><span class="stringliteral"> return $self->{'</span>_lethal_for_worker<span class="stringliteral">'};</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="abb83a9f0a1fa1cd38bc5ae626bfd6b51"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = $class->SUPER::new( @_ ); # deal with Storable stuff</div>
+<div class="line"></div>
+<div class="line"> my($prev_job_id, $analysis_id, $input_id, $param_id_stack, $accu_id_stack, $worker_id, $status, $retry_count, $completed, $runtime_msec, $query_count, $semaphore_count, $semaphored_job_id) =</div>
+<div class="line"> rearrange([qw(<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a097e33f4921749e52972e051032809c4">prev_job_id</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ad43a29a7f535cc507f91702fad70b310">analysis_id</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a9dd7289999985b60a8299ac66327f3ce">input_id</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb5e9b464027c776b1bd01eaf7b9cfe7">param_id_stack</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52165b28650c26a24b621da4ff2e777a">accu_id_stack</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#af38047d73f933f30cde285c5dab5dffb">worker_id</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ab65c1a11b3be9af06c4e47a71294b757">status</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae3bad87fd4aff80e2b4ee41185494c64">retry_count</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#adf437552d1a1b96a0fb1868b7ee58e0b">completed</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#af050b0e809253aef004926eeaf6cdf75">runtime_msec</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ab69fe83605e95a9dafb3025e655082b5">query_count</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a75263a4a15c449f509bf35cbead2c54c">semaphore_count</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1e2d7fa5ae29570bfc2e389dc3abd824">semaphored_job_id</a>) ], @_);</div>
+<div class="line"></div>
+<div class="line"> $self->prev_job_id($prev_job_id) <span class="keywordflow">if</span>(defined($prev_job_id));</div>
+<div class="line"> $self->analysis_id($analysis_id) <span class="keywordflow">if</span>(defined($analysis_id));</div>
+<div class="line"> $self->input_id($input_id) <span class="keywordflow">if</span>(defined($input_id));</div>
+<div class="line"> $self->param_id_stack($param_id_stack) <span class="keywordflow">if</span>(defined($param_id_stack));</div>
+<div class="line"> $self->accu_id_stack($accu_id_stack) <span class="keywordflow">if</span>(defined($accu_id_stack));</div>
+<div class="line"> $self->worker_id($worker_id) <span class="keywordflow">if</span>(defined($worker_id));</div>
+<div class="line"> $self->status($status) <span class="keywordflow">if</span>(defined($status));</div>
+<div class="line"> $self->retry_count($retry_count) <span class="keywordflow">if</span>(defined($retry_count));</div>
+<div class="line"> $self->completed($completed) <span class="keywordflow">if</span>(defined($completed));</div>
+<div class="line"> $self->runtime_msec($runtime_msec) <span class="keywordflow">if</span>(defined($runtime_msec));</div>
+<div class="line"> $self->query_count($query_count) <span class="keywordflow">if</span>(defined($query_count));</div>
+<div class="line"> $self->semaphore_count($semaphore_count) <span class="keywordflow">if</span>(defined($semaphore_count));</div>
+<div class="line"> $self->semaphored_job_id($semaphored_job_id) <span class="keywordflow">if</span>(defined($semaphored_job_id));</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="abb5e9b464027c776b1bd01eaf7b9cfe7"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::param_id_stack </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-param_id_stack" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_id_stack-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_id_stack-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_id_stack-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb5e9b464027c776b1bd01eaf7b9cfe7">param_id_stack</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_param_id_stack'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_param_id_stack'</span>} = <span class="stringliteral">''</span> unless(defined($self->{<span class="stringliteral">'_param_id_stack'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_param_id_stack'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a097e33f4921749e52972e051032809c4"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::prev_job_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-prev_job_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-prev_job_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-prev_job_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-prev_job_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a097e33f4921749e52972e051032809c4">prev_job_id</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_prev_job_id'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_prev_job_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a6080b20b6f65b3a31e72de743db62dac"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::print_job </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-print_job" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-print_job-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-print_job-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-print_job-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a6080b20b6f65b3a31e72de743db62dac">print_job</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> my $logic_name = $self->adaptor()</div>
+<div class="line"> ? $self->adaptor->db->get_AnalysisAdaptor->fetch_by_dbID($self->analysis_id)->logic_name()</div>
+<div class="line"> : <span class="stringliteral">''</span>;</div>
+<div class="line"></div>
+<div class="line"> printf(<span class="stringliteral">"job_id=%d %35s(%5d) retry=%d input_id='%s'\n"</span>, </div>
+<div class="line"> $self->dbID,</div>
+<div class="line"> $logic_name,</div>
+<div class="line"> $self->analysis_id,</div>
+<div class="line"> $self->retry_count,</div>
+<div class="line"> $self->input_id);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab69fe83605e95a9dafb3025e655082b5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::query_count </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-query_count" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-query_count-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-query_count-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-query_count-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ab69fe83605e95a9dafb3025e655082b5">query_count</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_query_count'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_query_count'</span>} = 0 unless(defined($self->{<span class="stringliteral">'_query_count'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_query_count'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae3bad87fd4aff80e2b4ee41185494c64"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::retry_count </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-retry_count" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-retry_count-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-retry_count-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-retry_count-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae3bad87fd4aff80e2b4ee41185494c64">retry_count</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_retry_count'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_retry_count'</span>} = 0 unless(defined($self->{<span class="stringliteral">'_retry_count'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_retry_count'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af050b0e809253aef004926eeaf6cdf75"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::runtime_msec </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-runtime_msec" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-runtime_msec-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-runtime_msec-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-runtime_msec-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#af050b0e809253aef004926eeaf6cdf75">runtime_msec</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_runtime_msec'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_runtime_msec'</span>} = 0 unless(defined($self->{<span class="stringliteral">'_runtime_msec'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_runtime_msec'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a75263a4a15c449f509bf35cbead2c54c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::semaphore_count </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-semaphore_count" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-semaphore_count-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-semaphore_count-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-semaphore_count-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a75263a4a15c449f509bf35cbead2c54c">semaphore_count</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_semaphore_count'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_semaphore_count'</span>} = 0 unless(defined($self->{<span class="stringliteral">'_semaphore_count'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_semaphore_count'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1e2d7fa5ae29570bfc2e389dc3abd824"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::semaphored_job_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-semaphored_job_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-semaphored_job_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-semaphored_job_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-semaphored_job_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1e2d7fa5ae29570bfc2e389dc3abd824">semaphored_job_id</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_semaphored_job_id'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_semaphored_job_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab65c1a11b3be9af06c4e47a71294b757"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ab65c1a11b3be9af06c4e47a71294b757">status</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_status'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_status'</span>} = ( ($self->semaphore_count>0) ? <span class="stringliteral">'SEMAPHORED'</span> : <span class="stringliteral">'READY'</span> ) unless(defined($self->{<span class="stringliteral">'_status'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_status'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a817a316519b8f04e340458abf0a0cf1e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::stderr_file </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-stderr_file" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-stderr_file-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-stderr_file-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-stderr_file-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a817a316519b8f04e340458abf0a0cf1e">stderr_file</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_stderr_file'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_stderr_file'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa110de6559e3966aa60049145b77be0c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::stdout_file </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-stdout_file" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-stdout_file-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-stdout_file-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-stdout_file-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#aa110de6559e3966aa60049145b77be0c">stdout_file</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_stdout_file'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_stdout_file'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a65bafee37ae9da96499433c2dd73f9bd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::toString </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-toString" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-toString-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-toString-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-toString-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a65bafee37ae9da96499433c2dd73f9bd">toString</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'Job '</span>.$self->dbID.<span class="stringliteral">" input_id='"</span>.$self->input_id.<span class="stringliteral">"', retry="</span>.$self->retry_count;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a52d6385c42523ebbd5c42c75e892fa31"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::transient_error </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-transient_error" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-transient_error-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-transient_error-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-transient_error-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52d6385c42523ebbd5c42c75e892fa31">transient_error</a> { # Job should set <span class="keyword">this</span> to 1 prior to dying (or before running code that might cause death)</div>
+<div class="line"> <span class="preprocessor"># if it believes that it makes sense to retry the same job without any changes.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # It may also set it to 0 prior to dying (or before running code that might cause death)</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # if it believes that there is no point in re-trying (say, if the parameters are wrong).</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # The Worker will check the flag and make necessary adjustments to the database state.</span></div>
+<div class="line"><span class="preprocessor"></span> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_transient_error'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_transient_error'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae14890c144f67fd2ff32b99bbba8f121"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::update_status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-update_status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-update_status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-update_status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-update_status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae14890c144f67fd2ff32b99bbba8f121">update_status</a> {</div>
+<div class="line"> my ($self, $status ) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> unless($self->adaptor);</div>
+<div class="line"> $self->status($status);</div>
+<div class="line"> $self->adaptor->update_status($self);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a00e809b1c03cf9e47212905b4284c140"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::warning </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: records a non-error message in 'log_message' table linked to the current job</pre><pre> </pre><div id="codesection-warning" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-warning-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-warning-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-warning-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a00e809b1c03cf9e47212905b4284c140">warning</a> {</div>
+<div class="line"> my ($self, $msg) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( my $job_adaptor = $self->adaptor ) {</div>
+<div class="line"> $job_adaptor->db->get_LogMessageAdaptor()->store_job_message($self->dbID, $msg, 0);</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> print STDERR <span class="stringliteral">"Warning: $msg\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af38047d73f933f30cde285c5dab5dffb"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisJob::worker_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-worker_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-worker_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-worker_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-worker_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#af38047d73f933f30cde285c5dab5dffb">worker_id</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_worker_id'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_worker_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_analysis_job_8pm.html">AnalysisJob.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">AnalysisJob</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+<div class="title">Bio::EnsEMBL::Hive::AnalysisStats Member List</div> </div>
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+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a9dea5f797f92fa7dd1e06a67f0bcd401">analysis_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4015806ce9a0a952ec992386f323ecd4">avg_input_msec_per_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0aee41e0ab6ecb6e1726a2254a1c5256">avg_msec_per_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a763d7539d36a921ba14409ffdd805a04">avg_output_msec_per_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adc046b69d9e806527342f79319818631">avg_run_msec_per_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4889ae9b5d00bcb53add084060676301">batch_size</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac5a95b82fd9ad6752c5eeb4527714d8e">behaviour</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a5d40dc556b755e7aed76e02fe6550b65">check_blocking_control_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a2f551acaf61aa9bf888e5d2246002170">determine_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a8cbcb7b573a6c3277ac69456dca161fa">done_job_count</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a49f5385adef0220da9708e24eeba68e2">failed_job_count</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ab3a0f109fab512fdae003e708d4c28df">get_analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac31170452fe2a74986b93ed13eb697c3">get_or_estimate_batch_size</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adf47bc7ce9c36899897d76f526e26e72">hive_capacity</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a859730fee45d764bdc4fbaa50be04ca3">inprogress_job_count</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aa2d5e93ea9239788909138d5eecf044e">input_capacity</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a9ef9078ce15a6892e795bf93643ff3cd">job_count_breakout</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a089b03c15eeb063a7cbae758f72f6637">last_update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ab1aa9f23e9feaec53f6e404dfe19f000">min_batch_time</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a63bec749348099898cac9401d6af959b">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0f14ca66c121617e2e6a4f2f7327caa1">num_required_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae2ece1ac33d251baa674803832bdae70">num_running_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac64ad37ccf27356c480b1d058315d4dd">output_capacity</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#af55400b3e85544df26608ac63d98f7bc">ready_job_count</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac704b4deb0a318afca57dddff2d891df">refresh</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae96201f918c87593f69279e032fea2a5">seconds_since_last_update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0a75c8843ba392c7df7a213a0767739f">semaphored_job_count</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a08a4fb1e1066710e635b0b078f9e3adb">status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac66bdac33e42b171ca6917480de34063">sync_lock</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a8f23e63cd393a1d4b4fa7489e070a1e0">toString</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a97f57d2303a39d59fb6828c681d1302d">total_job_count</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aea393680de6bbeeb5cea86e986887fdf">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aae68800782db346b681387c0412dd05f">update_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="entry"></td></tr>
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+  <span id="projectnumber">1.9</span>
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+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::AnalysisStats:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::AnalysisStats:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats_coll__map">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:ab1aa9f23e9feaec53f6e404dfe19f000"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ab1aa9f23e9feaec53f6e404dfe19f000">min_batch_time</a> ()</td></tr>
+<tr class="separator:ab1aa9f23e9feaec53f6e404dfe19f000"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a63bec749348099898cac9401d6af959b"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a63bec749348099898cac9401d6af959b">new</a> ()</td></tr>
+<tr class="separator:a63bec749348099898cac9401d6af959b"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9dea5f797f92fa7dd1e06a67f0bcd401"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a9dea5f797f92fa7dd1e06a67f0bcd401">analysis_id</a> ()</td></tr>
+<tr class="separator:a9dea5f797f92fa7dd1e06a67f0bcd401"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4889ae9b5d00bcb53add084060676301"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4889ae9b5d00bcb53add084060676301">batch_size</a> ()</td></tr>
+<tr class="separator:a4889ae9b5d00bcb53add084060676301"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adf47bc7ce9c36899897d76f526e26e72"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adf47bc7ce9c36899897d76f526e26e72">hive_capacity</a> ()</td></tr>
+<tr class="separator:adf47bc7ce9c36899897d76f526e26e72"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a08a4fb1e1066710e635b0b078f9e3adb"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a08a4fb1e1066710e635b0b078f9e3adb">status</a> ()</td></tr>
+<tr class="separator:a08a4fb1e1066710e635b0b078f9e3adb"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a97f57d2303a39d59fb6828c681d1302d"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a97f57d2303a39d59fb6828c681d1302d">total_job_count</a> ()</td></tr>
+<tr class="separator:a97f57d2303a39d59fb6828c681d1302d"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0a75c8843ba392c7df7a213a0767739f"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0a75c8843ba392c7df7a213a0767739f">semaphored_job_count</a> ()</td></tr>
+<tr class="separator:a0a75c8843ba392c7df7a213a0767739f"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:af55400b3e85544df26608ac63d98f7bc"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a8cbcb7b573a6c3277ac69456dca161fa"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a49f5385adef0220da9708e24eeba68e2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a49f5385adef0220da9708e24eeba68e2">failed_job_count</a> ()</td></tr>
+<tr class="separator:a49f5385adef0220da9708e24eeba68e2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae2ece1ac33d251baa674803832bdae70"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae2ece1ac33d251baa674803832bdae70">num_running_workers</a> ()</td></tr>
+<tr class="separator:ae2ece1ac33d251baa674803832bdae70"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0f14ca66c121617e2e6a4f2f7327caa1"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0f14ca66c121617e2e6a4f2f7327caa1">num_required_workers</a> ()</td></tr>
+<tr class="separator:a0f14ca66c121617e2e6a4f2f7327caa1"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac5a95b82fd9ad6752c5eeb4527714d8e"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac5a95b82fd9ad6752c5eeb4527714d8e">behaviour</a> ()</td></tr>
+<tr class="separator:ac5a95b82fd9ad6752c5eeb4527714d8e"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aa2d5e93ea9239788909138d5eecf044e"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aa2d5e93ea9239788909138d5eecf044e">input_capacity</a> ()</td></tr>
+<tr class="separator:aa2d5e93ea9239788909138d5eecf044e"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac64ad37ccf27356c480b1d058315d4dd"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac64ad37ccf27356c480b1d058315d4dd">output_capacity</a> ()</td></tr>
+<tr class="separator:ac64ad37ccf27356c480b1d058315d4dd"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0aee41e0ab6ecb6e1726a2254a1c5256"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0aee41e0ab6ecb6e1726a2254a1c5256">avg_msec_per_job</a> ()</td></tr>
+<tr class="separator:a0aee41e0ab6ecb6e1726a2254a1c5256"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4015806ce9a0a952ec992386f323ecd4"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4015806ce9a0a952ec992386f323ecd4">avg_input_msec_per_job</a> ()</td></tr>
+<tr class="separator:a4015806ce9a0a952ec992386f323ecd4"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adc046b69d9e806527342f79319818631"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adc046b69d9e806527342f79319818631">avg_run_msec_per_job</a> ()</td></tr>
+<tr class="separator:adc046b69d9e806527342f79319818631"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a763d7539d36a921ba14409ffdd805a04"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a763d7539d36a921ba14409ffdd805a04">avg_output_msec_per_job</a> ()</td></tr>
+<tr class="separator:a763d7539d36a921ba14409ffdd805a04"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a089b03c15eeb063a7cbae758f72f6637"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a089b03c15eeb063a7cbae758f72f6637">last_update</a> ()</td></tr>
+<tr class="separator:a089b03c15eeb063a7cbae758f72f6637"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae96201f918c87593f69279e032fea2a5"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae96201f918c87593f69279e032fea2a5">seconds_since_last_update</a> ()</td></tr>
+<tr class="separator:ae96201f918c87593f69279e032fea2a5"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac66bdac33e42b171ca6917480de34063"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac66bdac33e42b171ca6917480de34063">sync_lock</a> ()</td></tr>
+<tr class="separator:ac66bdac33e42b171ca6917480de34063"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac704b4deb0a318afca57dddff2d891df"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac704b4deb0a318afca57dddff2d891df">refresh</a> ()</td></tr>
+<tr class="separator:ac704b4deb0a318afca57dddff2d891df"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aea393680de6bbeeb5cea86e986887fdf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aea393680de6bbeeb5cea86e986887fdf">update</a> ()</td></tr>
+<tr class="separator:aea393680de6bbeeb5cea86e986887fdf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aae68800782db346b681387c0412dd05f"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aae68800782db346b681387c0412dd05f">update_status</a> ()</td></tr>
+<tr class="separator:aae68800782db346b681387c0412dd05f"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab3a0f109fab512fdae003e708d4c28df"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ab3a0f109fab512fdae003e708d4c28df">get_analysis</a> ()</td></tr>
+<tr class="separator:ab3a0f109fab512fdae003e708d4c28df"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac31170452fe2a74986b93ed13eb697c3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac31170452fe2a74986b93ed13eb697c3">get_or_estimate_batch_size</a> ()</td></tr>
+<tr class="separator:ac31170452fe2a74986b93ed13eb697c3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a859730fee45d764bdc4fbaa50be04ca3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a859730fee45d764bdc4fbaa50be04ca3">inprogress_job_count</a> ()</td></tr>
+<tr class="separator:a859730fee45d764bdc4fbaa50be04ca3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9ef9078ce15a6892e795bf93643ff3cd"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a9ef9078ce15a6892e795bf93643ff3cd">job_count_breakout</a> ()</td></tr>
+<tr class="separator:a9ef9078ce15a6892e795bf93643ff3cd"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8f23e63cd393a1d4b4fa7489e070a1e0"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a8f23e63cd393a1d4b4fa7489e070a1e0">toString</a> ()</td></tr>
+<tr class="separator:a8f23e63cd393a1d4b4fa7489e070a1e0"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5d40dc556b755e7aed76e02fe6550b65"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a5d40dc556b755e7aed76e02fe6550b65">check_blocking_control_rules</a> ()</td></tr>
+<tr class="separator:a5d40dc556b755e7aed76e02fe6550b65"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2f551acaf61aa9bf888e5d2246002170"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a2f551acaf61aa9bf888e5d2246002170">determine_status</a> ()</td></tr>
+<tr class="separator:a2f551acaf61aa9bf888e5d2246002170"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ An object that maintains counters for jobs in different states. This data is used by the Scheduler.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a9dea5f797f92fa7dd1e06a67f0bcd401"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::analysis_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-analysis_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-analysis_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-analysis_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-analysis_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a9dea5f797f92fa7dd1e06a67f0bcd401">analysis_id</a> { # an alias</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> <span class="keywordflow">return</span> $self->dbID(@_);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4015806ce9a0a952ec992386f323ecd4"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::avg_input_msec_per_job </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-avg_input_msec_per_job" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-avg_input_msec_per_job-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-avg_input_msec_per_job-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-avg_input_msec_per_job-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4015806ce9a0a952ec992386f323ecd4">avg_input_msec_per_job</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_avg_input_msec_per_job'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_avg_input_msec_per_job'</span>}=0 unless($self->{<span class="stringliteral">'_avg_input_msec_per_job'</span>});</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_avg_input_msec_per_job'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0aee41e0ab6ecb6e1726a2254a1c5256"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::avg_msec_per_job </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-avg_msec_per_job" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-avg_msec_per_job-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-avg_msec_per_job-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-avg_msec_per_job-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0aee41e0ab6ecb6e1726a2254a1c5256">avg_msec_per_job</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_avg_msec_per_job'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_avg_msec_per_job'</span>}=0 unless($self->{<span class="stringliteral">'_avg_msec_per_job'</span>});</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_avg_msec_per_job'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a763d7539d36a921ba14409ffdd805a04"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::avg_output_msec_per_job </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-avg_output_msec_per_job" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-avg_output_msec_per_job-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-avg_output_msec_per_job-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-avg_output_msec_per_job-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a763d7539d36a921ba14409ffdd805a04">avg_output_msec_per_job</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_avg_output_msec_per_job'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_avg_output_msec_per_job'</span>}=0 unless($self->{<span class="stringliteral">'_avg_output_msec_per_job'</span>});</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_avg_output_msec_per_job'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="adc046b69d9e806527342f79319818631"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::avg_run_msec_per_job </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-avg_run_msec_per_job" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-avg_run_msec_per_job-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-avg_run_msec_per_job-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-avg_run_msec_per_job-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adc046b69d9e806527342f79319818631">avg_run_msec_per_job</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_avg_run_msec_per_job'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_avg_run_msec_per_job'</span>}=0 unless($self->{<span class="stringliteral">'_avg_run_msec_per_job'</span>});</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_avg_run_msec_per_job'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4889ae9b5d00bcb53add084060676301"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::batch_size </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-batch_size" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-batch_size-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-batch_size-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-batch_size-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4889ae9b5d00bcb53add084060676301">batch_size</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_batch_size'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_batch_size'</span>} = 1 unless(defined($self->{<span class="stringliteral">'_batch_size'</span>})); # only initialize when undefined, so <span class="keywordflow">if</span> defined as 0 will stay 0</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_batch_size'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac5a95b82fd9ad6752c5eeb4527714d8e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::behaviour </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-behaviour" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-behaviour-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-behaviour-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-behaviour-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac5a95b82fd9ad6752c5eeb4527714d8e">behaviour</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_behaviour'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_behaviour'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a5d40dc556b755e7aed76e02fe6550b65"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::check_blocking_control_rules </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-check_blocking_control_rules" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-check_blocking_control_rules-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-check_blocking_control_rules-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-check_blocking_control_rules-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a5d40dc556b755e7aed76e02fe6550b65">check_blocking_control_rules</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> </div>
+<div class="line"> my $ctrl_rules = $self->adaptor->db->get_AnalysisCtrlRuleAdaptor->fetch_all_by_ctrled_analysis_id($self->analysis_id);</div>
+<div class="line"></div>
+<div class="line"> my $all_conditions_satisfied = 1;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(scalar @$ctrl_rules) { # there are blocking ctrl_rules to check</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $ctrl_rule (@$ctrl_rules) {</div>
+<div class="line"><span class="preprocessor"> #use this method because the condition_analysis objects can be</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #network distributed to a different database so use it's adaptor to get</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #the AnalysisStats object</span></div>
+<div class="line"><span class="preprocessor"></span> my $condition_analysis = $ctrl_rule->condition_analysis;</div>
+<div class="line"> my $condition_stats = $condition_analysis && $condition_analysis->stats;</div>
+<div class="line"> my $condition_status = $condition_stats && $condition_stats->status;</div>
+<div class="line"> my $condition_cbe = $condition_analysis && $condition_analysis->can_be_empty;</div>
+<div class="line"> my $condition_tjc = $condition_stats && $condition_stats->total_job_count;</div>
+<div class="line"></div>
+<div class="line"> my $this_condition_satisfied = ($condition_status eq <span class="stringliteral">'DONE'</span>)</div>
+<div class="line"> || ($condition_cbe && !$condition_tjc); # probably safer than saying ($condition_status eq <span class="stringliteral">'EMPTY'</span>) because of the sync order</div>
+<div class="line"></div>
+<div class="line"> unless( $this_condition_satisfied ) {</div>
+<div class="line"> $all_conditions_satisfied = 0;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($all_conditions_satisfied) {</div>
+<div class="line"> <span class="keywordflow">if</span>($self->status eq <span class="stringliteral">'BLOCKED'</span>) { # unblock, since all conditions are met</div>
+<div class="line"> $self->update_status(<span class="stringliteral">'LOADING'</span>); # trigger sync</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> { # (re)block</div>
+<div class="line"> $self->update_status(<span class="stringliteral">'BLOCKED'</span>);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $all_conditions_satisfied;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2f551acaf61aa9bf888e5d2246002170"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::determine_status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-determine_status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-determine_status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-determine_status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-determine_status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a2f551acaf61aa9bf888e5d2246002170">determine_status</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->status ne <span class="stringliteral">'BLOCKED'</span>) {</div>
+<div class="line"> <span class="keywordflow">if</span>( !$self->total_job_count ) {</div>
+<div class="line"></div>
+<div class="line"> $self->status(<span class="stringliteral">'EMPTY'</span>);</div>
+<div class="line"></div>
+<div class="line"> } elsif( $self->total_job_count == $self->done_job_count + $self->failed_job_count ) { # all jobs of the analysis have been finished</div>
+<div class="line"> my $analysis = $self->get_analysis;</div>
+<div class="line"> my $absolute_tolerance = $analysis->failed_job_tolerance * $self->total_job_count / 100.0;</div>
+<div class="line"> <span class="keywordflow">if</span> ($self->failed_job_count > $absolute_tolerance) {</div>
+<div class="line"> $self->status(<span class="stringliteral">'FAILED'</span>);</div>
+<div class="line"> warn <span class="stringliteral">"\n##################################################\n"</span>;</div>
+<div class="line"> warn sprintf(<span class="stringliteral">"## ERROR: %-35s ##\n"</span>, $analysis->logic_name.<span class="stringliteral">" failed!"</span>);</div>
+<div class="line"> warn sprintf(<span class="stringliteral">"## %d jobs failed (tolerance: %d (%3d%%)) ##\n"</span>, $self->failed_job_count, $absolute_tolerance, $analysis->failed_job_tolerance);</div>
+<div class="line"> warn <span class="stringliteral">"##################################################\n\n"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $self->status(<span class="stringliteral">'DONE'</span>);</div>
+<div class="line"> }</div>
+<div class="line"> } elsif( $self->ready_job_count && !$self->inprogress_job_count ) { # there are claimable jobs, but nothing actually running</div>
+<div class="line"></div>
+<div class="line"> $self->status(<span class="stringliteral">'READY'</span>);</div>
+<div class="line"></div>
+<div class="line"> } elsif( !$self->ready_job_count ) { # there are no claimable jobs, possibly because some are semaphored</div>
+<div class="line"></div>
+<div class="line"> $self->status(<span class="stringliteral">'ALL_CLAIMED'</span>);</div>
+<div class="line"></div>
+<div class="line"> } elsif( $self->inprogress_job_count ) {</div>
+<div class="line"></div>
+<div class="line"> $self->status(<span class="stringliteral">'WORKING'</span>);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8cbcb7b573a6c3277ac69456dca161fa"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::done_job_count </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-done_job_count" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-done_job_count-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-done_job_count-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-done_job_count-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a8cbcb7b573a6c3277ac69456dca161fa">done_job_count</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_done_job_count'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_done_job_count'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a49f5385adef0220da9708e24eeba68e2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::failed_job_count </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-failed_job_count" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-failed_job_count-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-failed_job_count-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-failed_job_count-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a49f5385adef0220da9708e24eeba68e2">failed_job_count</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_failed_job_count'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_failed_job_count'</span>} = 0 unless(defined($self->{<span class="stringliteral">'_failed_job_count'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_failed_job_count'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab3a0f109fab512fdae003e708d4c28df"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::get_analysis </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_analysis" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_analysis-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_analysis-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_analysis-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ab3a0f109fab512fdae003e708d4c28df">get_analysis</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> unless($self->{<span class="stringliteral">'_analysis'</span>}) {</div>
+<div class="line"> unless($self->analysis_id) {</div>
+<div class="line"> <span class="keywordflow">throw</span>(<span class="stringliteral">"self->analysis_id undefined, please investigate"</span>);</div>
+<div class="line"> }</div>
+<div class="line"> $self->{<span class="stringliteral">'_analysis'</span>} = $self->adaptor->db->get_AnalysisAdaptor->fetch_by_dbID($self->analysis_id);</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_analysis'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac31170452fe2a74986b93ed13eb697c3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::get_or_estimate_batch_size </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_or_estimate_batch_size" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_or_estimate_batch_size-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_or_estimate_batch_size-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_or_estimate_batch_size-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac31170452fe2a74986b93ed13eb697c3">get_or_estimate_batch_size</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( (my $batch_size = $self->batch_size())>0 ) { # set to positive or not set (and <span class="keyword">auto</span>-initialized within $self->batch_size)</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $batch_size;</div>
+<div class="line"><span class="preprocessor"> # otherwise it is a request for dynamic estimation:</span></div>
+<div class="line"><span class="preprocessor"></span> } elsif( my $avg_msec_per_job = $self->avg_msec_per_job() ) { # further estimations from collected stats</div>
+<div class="line"></div>
+<div class="line"> $avg_msec_per_job = 100 <span class="keywordflow">if</span>($avg_msec_per_job<100);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> POSIX::ceil( $self->min_batch_time() / $avg_msec_per_job );</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> { # first estimation when no stats are available (take -$batch_size as first guess, <span class="keywordflow">if</span> not zero)</div>
+<div class="line"> <span class="keywordflow">return</span> -$batch_size || 1;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="adf47bc7ce9c36899897d76f526e26e72"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::hive_capacity </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-hive_capacity" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-hive_capacity-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-hive_capacity-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-hive_capacity-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adf47bc7ce9c36899897d76f526e26e72">hive_capacity</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_hive_capacity'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_hive_capacity'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a859730fee45d764bdc4fbaa50be04ca3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::inprogress_job_count </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-inprogress_job_count" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-inprogress_job_count-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-inprogress_job_count-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-inprogress_job_count-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a859730fee45d764bdc4fbaa50be04ca3">inprogress_job_count</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> <span class="keywordflow">return</span> $self->total_job_count</div>
+<div class="line"> - $self->semaphored_job_count</div>
+<div class="line"> - $self->ready_job_count</div>
+<div class="line"> - $self->done_job_count</div>
+<div class="line"> - $self->failed_job_count;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa2d5e93ea9239788909138d5eecf044e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::input_capacity </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-input_capacity" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-input_capacity-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-input_capacity-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-input_capacity-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aa2d5e93ea9239788909138d5eecf044e">input_capacity</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_input_capacity'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_input_capacity'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9ef9078ce15a6892e795bf93643ff3cd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::job_count_breakout </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-job_count_breakout" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-job_count_breakout-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-job_count_breakout-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-job_count_breakout-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a9ef9078ce15a6892e795bf93643ff3cd">job_count_breakout</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> my @count_list = ();</div>
+<div class="line"> my %count_hash = ();</div>
+<div class="line"> my $total_job_count = $self->total_job_count();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $count_method (qw(<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0a75c8843ba392c7df7a213a0767739f">semaphored_job_count</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#af55400b3e85544df26608ac63d98f7bc">ready_job_count</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a859730fee45d764bdc4fbaa50be04ca3">inprogress_job_count</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a8cbcb7b573a6c3277ac69456dca161fa">done_job_count</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a49f5385adef0220da9708e24eeba68e2">failed_job_count</a>)) {</div>
+<div class="line"> <span class="keywordflow">if</span>( my $count = $count_hash{$count_method} = $self->$count_method() ) {</div>
+<div class="line"> push @count_list, $count.substr($count_method,0,1);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> my $breakout_label = join(<span class="charliteral">'+'</span>, @count_list);</div>
+<div class="line"> $breakout_label .= <span class="charliteral">'='</span>.$total_job_count <span class="keywordflow">if</span>(scalar(@count_list)!=1); # only provide a total <span class="keywordflow">if</span> multiple or no categories available</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ($breakout_label, $total_job_count, \%count_hash);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a089b03c15eeb063a7cbae758f72f6637"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::last_update </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-last_update" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-last_update-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-last_update-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-last_update-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a089b03c15eeb063a7cbae758f72f6637">last_update</a> { # <span class="keyword">this</span> method is called by the initial store() [at which point it returns undef]</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_last_update'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_last_update'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab1aa9f23e9feaec53f6e404dfe19f000"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::min_batch_time </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-min_batch_time" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-min_batch_time-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-min_batch_time-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-min_batch_time-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ab1aa9f23e9feaec53f6e404dfe19f000">min_batch_time</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> 2*60*1000;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a63bec749348099898cac9401d6af959b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift;</div>
+<div class="line"></div>
+<div class="line"> my $self = $class->SUPER::new( @_ ); # deal with Storable stuff</div>
+<div class="line"></div>
+<div class="line"> my ( $analysis_id, $batch_size, $hive_capacity, $status,</div>
+<div class="line"> $total_job_count, $semaphored_job_count, $ready_job_count, $done_job_count, $failed_job_count, $num_running_workers, $num_required_workers,</div>
+<div class="line"> $behaviour, $input_capacity, $output_capacity, $avg_msec_per_job, $avg_input_msec_per_job, $avg_run_msec_per_job, $avg_output_msec_per_job,</div>
+<div class="line"> $seconds_since_last_update, $sync_lock) =</div>
+<div class="line"> rearrange([qw(<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a9dea5f797f92fa7dd1e06a67f0bcd401">analysis_id</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4889ae9b5d00bcb53add084060676301">batch_size</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adf47bc7ce9c36899897d76f526e26e72">hive_capacity</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a08a4fb1e1066710e635b0b078f9e3adb">status</a></div>
+<div class="line"> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a97f57d2303a39d59fb6828c681d1302d">total_job_count</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0a75c8843ba392c7df7a213a0767739f">semaphored_job_count</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#af55400b3e85544df26608ac63d98f7bc">ready_job_count</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a8cbcb7b573a6c3277ac69456dca161fa">done_job_count</a> failed_job_count <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae2ece1ac33d251baa674803832bdae70">num_running_workers</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0f14ca66c121617e2e6a4f2f7327caa1">num_required_workers</a></div>
+<div class="line"> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac5a95b82fd9ad6752c5eeb4527714d8e">behaviour</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aa2d5e93ea9239788909138d5eecf044e">input_capacity</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac64ad37ccf27356c480b1d058315d4dd">output_capacity</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0aee41e0ab6ecb6e1726a2254a1c5256">avg_msec_per_job</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4015806ce9a0a952ec992386f323ecd4">avg_input_msec_per_job</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adc046b69d9e806527342f79319818631">avg_run_msec_per_job</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a763d7539d36a921ba14409ffdd805a04">avg_output_msec_per_job</a></div>
+<div class="line"> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae96201f918c87593f69279e032fea2a5">seconds_since_last_update</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac66bdac33e42b171ca6917480de34063">sync_lock</a> ) ], @_);</div>
+<div class="line"> $self->analysis_id($analysis_id) <span class="keywordflow">if</span>(defined($analysis_id));</div>
+<div class="line"> $self->batch_size($batch_size) <span class="keywordflow">if</span>(defined($batch_size));</div>
+<div class="line"> $self->hive_capacity($hive_capacity) <span class="keywordflow">if</span>(defined($hive_capacity));</div>
+<div class="line"> $self->status($status) <span class="keywordflow">if</span>(defined($status));</div>
+<div class="line"> $self->total_job_count($total_job_count) <span class="keywordflow">if</span>(defined($total_job_count));</div>
+<div class="line"> $self->semaphored_job_count($semaphored_job_count) <span class="keywordflow">if</span>(defined($semaphored_job_count));</div>
+<div class="line"> $self->ready_job_count($ready_job_count) <span class="keywordflow">if</span>(defined($ready_job_count));</div>
+<div class="line"> $self->done_job_count($done_job_count) <span class="keywordflow">if</span>(defined($done_job_count));</div>
+<div class="line"> $self->failed_job_count($failed_job_count) <span class="keywordflow">if</span>(defined($failed_job_count));</div>
+<div class="line"> $self->num_running_workers($num_running_workers) <span class="keywordflow">if</span>(defined($num_running_workers));</div>
+<div class="line"> $self->num_required_workers($num_required_workers) <span class="keywordflow">if</span>(defined($num_required_workers));</div>
+<div class="line"> $self->behaviour($behaviour) <span class="keywordflow">if</span>(defined($behaviour));</div>
+<div class="line"> $self->input_capacity($input_capacity) <span class="keywordflow">if</span>(defined($input_capacity));</div>
+<div class="line"> $self->output_capacity($output_capacity) <span class="keywordflow">if</span>(defined($output_capacity));</div>
+<div class="line"> $self->avg_msec_per_job($avg_msec_per_job) <span class="keywordflow">if</span>(defined($avg_msec_per_job));</div>
+<div class="line"> $self->avg_input_msec_per_job($avg_input_msec_per_job) <span class="keywordflow">if</span>(defined($avg_input_msec_per_job));</div>
+<div class="line"> $self->avg_run_msec_per_job($avg_run_msec_per_job) <span class="keywordflow">if</span>(defined($avg_run_msec_per_job));</div>
+<div class="line"> $self->avg_output_msec_per_job($avg_output_msec_per_job) <span class="keywordflow">if</span>(defined($avg_output_msec_per_job));</div>
+<div class="line"> $self->seconds_since_last_update($seconds_since_last_update)<span class="keywordflow">if</span>(defined($seconds_since_last_update)); # NB: <span class="keyword">this</span> is an input_column_mapped field</div>
+<div class="line"> $self->sync_lock($sync_lock) <span class="keywordflow">if</span>(defined($sync_lock));</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0f14ca66c121617e2e6a4f2f7327caa1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::num_required_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-num_required_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-num_required_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-num_required_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-num_required_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0f14ca66c121617e2e6a4f2f7327caa1">num_required_workers</a> { # NB: the meaning of <span class="keyword">this</span> field is, again, <span class="stringliteral">"how many extra workers we need to add"</span></div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_num_required_workers'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_num_required_workers'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae2ece1ac33d251baa674803832bdae70"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::num_running_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-num_running_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-num_running_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-num_running_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-num_running_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae2ece1ac33d251baa674803832bdae70">num_running_workers</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_num_running_workers'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_num_running_workers'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac64ad37ccf27356c480b1d058315d4dd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::output_capacity </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-output_capacity" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-output_capacity-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-output_capacity-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-output_capacity-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac64ad37ccf27356c480b1d058315d4dd">output_capacity</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_output_capacity'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_output_capacity'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af55400b3e85544df26608ac63d98f7bc"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::ready_job_count </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-ready_job_count" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-ready_job_count-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-ready_job_count-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-ready_job_count-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#af55400b3e85544df26608ac63d98f7bc">ready_job_count</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_ready_job_count'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_ready_job_count'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac704b4deb0a318afca57dddff2d891df"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::refresh </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-refresh" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-refresh-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-refresh-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-refresh-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac704b4deb0a318afca57dddff2d891df">refresh</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->adaptor && $self->adaptor->refresh($self);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae96201f918c87593f69279e032fea2a5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::seconds_since_last_update </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-seconds_since_last_update" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-seconds_since_last_update-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-seconds_since_last_update-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-seconds_since_last_update-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae96201f918c87593f69279e032fea2a5">seconds_since_last_update</a> { # <span class="keyword">this</span> method is mostly used to convert between server time and local time</div>
+<div class="line"> my( $self, $value ) = @_;</div>
+<div class="line"> $self->{<span class="stringliteral">'_last_update'</span>} = time() - $value <span class="keywordflow">if</span>(defined($value));</div>
+<div class="line"> <span class="keywordflow">return</span> time() - $self->{<span class="stringliteral">'_last_update'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0a75c8843ba392c7df7a213a0767739f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::semaphored_job_count </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-semaphored_job_count" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-semaphored_job_count-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-semaphored_job_count-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-semaphored_job_count-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0a75c8843ba392c7df7a213a0767739f">semaphored_job_count</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_semaphored_job_count'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_semaphored_job_count'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a08a4fb1e1066710e635b0b078f9e3adb"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a08a4fb1e1066710e635b0b078f9e3adb">status</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_status'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_status'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac66bdac33e42b171ca6917480de34063"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::sync_lock </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-sync_lock" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-sync_lock-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-sync_lock-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-sync_lock-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac66bdac33e42b171ca6917480de34063">sync_lock</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_sync_lock'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_sync_lock'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8f23e63cd393a1d4b4fa7489e070a1e0"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::toString </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-toString" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-toString-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-toString-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-toString-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a8f23e63cd393a1d4b4fa7489e070a1e0">toString</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $analysis = $self->get_analysis;</div>
+<div class="line"></div>
+<div class="line"> my $output .= sprintf(<span class="stringliteral">"%-27s(%2d) %11s jobs(Sem:%d, Rdy:%d, InProg:%d, Done+Pass:%d, Fail:%d)=%d Ave_msec:%d, workers(Running:%d, Reqired:%d) "</span>,</div>
+<div class="line"> $analysis->logic_name,</div>
+<div class="line"> $self->analysis_id,</div>
+<div class="line"></div>
+<div class="line"> $self->status,</div>
+<div class="line"></div>
+<div class="line"> $self->semaphored_job_count,</div>
+<div class="line"> $self->ready_job_count,</div>
+<div class="line"> $self->inprogress_job_count,</div>
+<div class="line"> $self->done_job_count,</div>
+<div class="line"> $self->failed_job_count,</div>
+<div class="line"> $self->total_job_count,</div>
+<div class="line"></div>
+<div class="line"> $self->avg_msec_per_job,</div>
+<div class="line"></div>
+<div class="line"> $self->num_running_workers,</div>
+<div class="line"> $self->num_required_workers,</div>
+<div class="line"> );</div>
+<div class="line"> $output .= <span class="stringliteral">' h.cap:'</span> .( defined($self->hive_capacity) ? $self->hive_capacity : <span class="charliteral">'-'</span> )</div>
+<div class="line"> .<span class="stringliteral">' a.cap:'</span> .( defined($analysis->analysis_capacity) ? $analysis->analysis_capacity : <span class="charliteral">'-'</span>)</div>
+<div class="line"> .<span class="stringliteral">" (sync'd "</span> .$self->seconds_since_last_update.<span class="stringliteral">" sec ago)"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $output;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a97f57d2303a39d59fb6828c681d1302d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::total_job_count </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-total_job_count" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-total_job_count-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-total_job_count-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-total_job_count-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a97f57d2303a39d59fb6828c681d1302d">total_job_count</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_total_job_count'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_total_job_count'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aea393680de6bbeeb5cea86e986887fdf"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::update </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-update" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-update-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-update-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-update-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aea393680de6bbeeb5cea86e986887fdf">update</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> <span class="keywordflow">return</span> unless($self->adaptor);</div>
+<div class="line"> $self->adaptor->update($self);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aae68800782db346b681387c0412dd05f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::AnalysisStats::update_status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-update_status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-update_status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-update_status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-update_status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aae68800782db346b681387c0412dd05f">update_status</a> {</div>
+<div class="line"> my ($self, $status ) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> unless($self->adaptor);</div>
+<div class="line"> $self->adaptor->update_status($self->analysis_id, $status);</div>
+<div class="line"> $self->status($status);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_analysis_stats_8pm.html">AnalysisStats.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
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+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
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+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Configurable Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::Configurable:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable_inherit__map" alt="Inheritance graph"/></div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a38c57142acfd31f32e87a94717620baf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">config</a> ()</td></tr>
+<tr class="separator:a38c57142acfd31f32e87a94717620baf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a419025891535ecd7b2f05183cf2ce8e4"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">context</a> ()</td></tr>
+<tr class="separator:a419025891535ecd7b2f05183cf2ce8e4"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeed405377caddb6a1aa3cb605ed6304f"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">config_get</a> ()</td></tr>
+<tr class="separator:aeed405377caddb6a1aa3cb605ed6304f"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3e556c76396430193c3f613c6f3e4079"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">config_set</a> ()</td></tr>
+<tr class="separator:a3e556c76396430193c3f613c6f3e4079"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A base class for objects that we want to be configurable in the following sense:
+ 1) have a pointer to the $config
+ 2) know their context
+ 3) automatically apply that context when getting and setting
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a38c57142acfd31f32e87a94717620baf"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Configurable::config </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-config" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-config-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-config-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-config-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">config</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_config'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_config'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aeed405377caddb6a1aa3cb605ed6304f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Configurable::config_get </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-config_get" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-config_get-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-config_get-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-config_get-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">config_get</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->config->get( @{$self->context}, @_ );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3e556c76396430193c3f613c6f3e4079"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Configurable::config_set </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-config_set" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-config_set-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-config_set-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-config_set-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">config_set</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->config->set( @{$self->context}, @_ );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a419025891535ecd7b2f05183cf2ce8e4"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Configurable::context </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-context" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-context-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-context-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-context-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">context</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_context'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_context'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_configurable_8pm.html">Configurable.pm</a></li>
+</ul>
+</div><!-- contents -->
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+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
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+<div class="title">Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor Member List</div> </div>
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+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html#a300d9c9d8f8ade46655850dd61771472">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html#a5ecf1d84e9aabb00cffc7c4df537b98c">fetch_structures_for_job_ids</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b">keys_to_columns</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2a39cbb60a5021d1cd5a4e385da4000f">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#ad90a452430769ce22f854fb0d195e905">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor_inherit__map" alt="Inheritance graph"/></div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor_coll__map">
+<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html" title="Bio::EnsEMBL::Hive\l::DBSQL::NakedTableAdaptor" alt="" coords="6,187,204,229"/><area shape="rect" id="node3" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html" title="Bio::EnsEMBL::Hive\l::DBSQL::BaseAdaptor" alt="" coords="26,97,184,138"/></map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a300d9c9d8f8ade46655850dd61771472"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html#a300d9c9d8f8ade46655850dd61771472">default_table_name</a> ()</td></tr>
+<tr class="separator:a300d9c9d8f8ade46655850dd61771472"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5ecf1d84e9aabb00cffc7c4df537b98c"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html#a5ecf1d84e9aabb00cffc7c4df537b98c">fetch_structures_for_job_ids</a> ()</td></tr>
+<tr class="separator:a5ecf1d84e9aabb00cffc7c4df537b98c"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td></tr>
+<tr class="memitem:a2fd8279544ff4bd78e9b3fd09495542c inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">slicer</a> ()</td></tr>
+<tr class="separator:a2fd8279544ff4bd78e9b3fd09495542c inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad90a452430769ce22f854fb0d195e905 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#ad90a452430769ce22f854fb0d195e905">objectify</a> ()</td></tr>
+<tr class="separator:ad90a452430769ce22f854fb0d195e905 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2a39cbb60a5021d1cd5a4e385da4000f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2a39cbb60a5021d1cd5a4e385da4000f">mark_stored</a> ()</td></tr>
+<tr class="separator:a2a39cbb60a5021d1cd5a4e385da4000f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a74f3ead3ecf4d1183b667c5da544362b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b">keys_to_columns</a> ()</td></tr>
+<tr class="separator:a74f3ead3ecf4d1183b667c5da544362b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td></tr>
+<tr class="memitem:ae3e95ef6cee275aa2ace188e45da854a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae3e95ef6cee275aa2ace188e45da854a">default_table_name</a> ()</td></tr>
+<tr class="separator:ae3e95ef6cee275aa2ace188e45da854a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a129b813103eead72607723d43d3a6567 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a> ()</td></tr>
+<tr class="separator:a129b813103eead72607723d43d3a6567 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac73267d0e33aad126c188108f7e7c468 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a> ()</td></tr>
+<tr class="separator:ac73267d0e33aad126c188108f7e7c468 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2f77cbefb20d4b4e3a40cf75ce420036 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a> ()</td></tr>
+<tr class="separator:a2f77cbefb20d4b4e3a40cf75ce420036 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1f8bbd7bad6d23b679d4c07ab4121085 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a> ()</td></tr>
+<tr class="separator:a1f8bbd7bad6d23b679d4c07ab4121085 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac7e056384281180e1b314889fc7c317f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a> ()</td></tr>
+<tr class="separator:ac7e056384281180e1b314889fc7c317f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9ee7f9cfe42ad4993d0b544acfb4e1f5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a> ()</td></tr>
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+<tr class="memitem:acd1bde351fcbdfddf8fa9896c8716514 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a> ()</td></tr>
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+<tr class="memitem:ada55ab8c29c95535953efb0ca8c1d805 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a> ()</td></tr>
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+<tr class="memitem:ae98ea2fa8c6a85c6df918b9816bd6cbf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a> ()</td></tr>
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+<tr class="memitem:ae47ff32866fc8b69d8463680b5ead1d2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a> ()</td></tr>
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+<tr class="separator:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a1e7b244d27dcc1244453f725d81d3e54 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a> ()</td></tr>
+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$dba->get_AccumulatorAdaptor->store( \@rows );</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is currently an "objectless" adaptor for building accumulated structures.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a300d9c9d8f8ade46655850dd61771472"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html#a300d9c9d8f8ade46655850dd61771472">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'accu'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a5ecf1d84e9aabb00cffc7c4df537b98c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor::fetch_structures_for_job_ids </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_structures_for_job_ids" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_structures_for_job_ids-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_structures_for_job_ids-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_structures_for_job_ids-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html#a5ecf1d84e9aabb00cffc7c4df537b98c">fetch_structures_for_job_ids</a> {</div>
+<div class="line"> my ($self, $job_ids_csv, $id_scale, $id_offset) = @_;</div>
+<div class="line"> $id_scale ||= 1;</div>
+<div class="line"> $id_offset ||= 0;</div>
+<div class="line"></div>
+<div class="line"> my %structures = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $job_ids_csv ) {</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"SELECT receiving_job_id, struct_name, key_signature, value FROM accu WHERE receiving_job_id in ($job_ids_csv)"</span>;</div>
+<div class="line"> my $sth = $self->prepare( $sql );</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"></div>
+<div class="line"> ROW: <span class="keywordflow">while</span>(my ($receiving_job_id, $struct_name, $key_signature, $stringified_value) = $sth->fetchrow_array() ) {</div>
+<div class="line"></div>
+<div class="line"> my $value = destringify($stringified_value);</div>
+<div class="line"></div>
+<div class="line"> my $sptr = \$structures{$receiving_job_id * $id_scale + $id_offset}{$struct_name};</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>( $key_signature=~/(?:(?:\[(\d*)\])|(?:\{(.*?)\}))/g) {</div>
+<div class="line"> my ($array_index, $hash_key) = ($1, $2);</div>
+<div class="line"> <span class="keywordflow">if</span>(defined($array_index)) {</div>
+<div class="line"> unless(length($array_index)) {</div>
+<div class="line"> $array_index = scalar(@{$$sptr||[]});</div>
+<div class="line"> }</div>
+<div class="line"> $sptr = \$$sptr->[$array_index];</div>
+<div class="line"> } elsif(defined($hash_key)) {</div>
+<div class="line"> <span class="keywordflow">if</span>(length($hash_key)) {</div>
+<div class="line"> $sptr = \$$sptr->{$hash_key};</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $sptr = \$$sptr->{$value};</div>
+<div class="line"> $$sptr++;</div>
+<div class="line"> next ROW;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> $$sptr = $value;</div>
+<div class="line"> }</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> \%structures;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_accumulator_adaptor_8pm.html">AccumulatorAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html">AccumulatorAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<div class="title">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a462f42ba52299b0402dea71c1f265dba">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a50439fb73efbfd5e2ec3cfd8839c483c">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#ae87626fc8dec5f006d35ee4d780c090a">fetch_all_failed_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#afb5c2b354ab0889fff2d55ef7c87443e">fetch_by_logic_name_or_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a59abab89460a304db992a7a19669fcbc">fetch_by_url_query</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#abba4ea6afa8067b7e9eefd3278923d6f">object_class</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
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+ <div class="headertitle">
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor:</div>
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+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$analysis_adaptor = $db_adaptor->get_AnalysisAdaptor;</div>
+<div class="line"></div>
+<div class="line">$analysis_adaptor = $analysis_object->adaptor;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Module to encapsulate all db access for persistent class Analysis.
+ There should be just one such adaptor per application and database connection.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a462f42ba52299b0402dea71c1f265dba"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor::default_insertion_method </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_insertion_method" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_insertion_method-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_insertion_method-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_insertion_method-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a462f42ba52299b0402dea71c1f265dba">default_insertion_method</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'INSERT'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a50439fb73efbfd5e2ec3cfd8839c483c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a50439fb73efbfd5e2ec3cfd8839c483c">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'analysis_base'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae87626fc8dec5f006d35ee4d780c090a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor::fetch_all_failed_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_all_failed_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_all_failed_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_all_failed_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_all_failed_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#ae87626fc8dec5f006d35ee4d780c090a">fetch_all_failed_analyses</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_all( <span class="stringliteral">"JOIN analysis_stats s USING(analysis_id) WHERE s.status='FAILED'"</span> );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="afb5c2b354ab0889fff2d55ef7c87443e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor::fetch_by_logic_name_or_url </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: given a URL gets the analysis from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">URLFactory</a>, otherwise fetches it from the db</pre><pre> </pre><div id="codesection-fetch_by_logic_name_or_url" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_by_logic_name_or_url-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_by_logic_name_or_url-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_by_logic_name_or_url-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#afb5c2b354ab0889fff2d55ef7c87443e">fetch_by_logic_name_or_url</a> {</div>
+<div class="line"> my $self = shift @_; # can either be $self or <span class="keyword">class </span>name</div>
+<div class="line"> my $logic_name_or_url = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($logic_name_or_url =~ m{^\w*:<span class="comment">//}) {</span></div>
+<div class="line"> <span class="keywordflow">return</span> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">fetch</a>($logic_name_or_url, ref($self) && $self->db);</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_by_logic_name($logic_name_or_url);</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a59abab89460a304db992a7a19669fcbc"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor::fetch_by_url_query </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: fetches the analysis either by logic_name or by dbID (either coming from the tail of the URL)</pre><pre> </pre><div id="codesection-fetch_by_url_query" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_by_url_query-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_by_url_query-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_by_url_query-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a59abab89460a304db992a7a19669fcbc">fetch_by_url_query</a> {</div>
+<div class="line"> my ($self, $field_name, $field_value) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(!$field_name or !$field_value) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span>;</div>
+<div class="line"></div>
+<div class="line"> } elsif($field_name eq <span class="stringliteral">'logic_name'</span>) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_by_logic_name($field_value);</div>
+<div class="line"></div>
+<div class="line"> } elsif($field_name eq <span class="stringliteral">'dbID'</span>) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_by_dbID($field_value);</div>
+<div class="line"></div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="abba4ea6afa8067b7e9eefd3278923d6f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor::object_class </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-object_class" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-object_class-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-object_class-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-object_class-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#abba4ea6afa8067b7e9eefd3278923d6f">object_class</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'Bio::EnsEMBL::Hive::Analysis'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_analysis_adaptor_8pm.html">AnalysisAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html">AnalysisAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor =
+[
+ [ "default_insertion_method", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a462f42ba52299b0402dea71c1f265dba", null ],
+ [ "default_table_name", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a50439fb73efbfd5e2ec3cfd8839c483c", null ],
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+ [ "fetch_by_logic_name_or_url", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#afb5c2b354ab0889fff2d55ef7c87443e", null ],
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+];
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+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#a7a0b17cb2cc51e54df8397325bcc9b88">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#aa39019f2695173ed4d98c1e46277c1f7">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#a944fe8aee65ea55ba1bd54ee77f97849">object_class</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+  <span id="projectnumber">1.9</span>
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor Class Reference</div> </div>
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+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor_inherit__map" alt="Inheritance graph"/></div>
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:aa39019f2695173ed4d98c1e46277c1f7"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#aa39019f2695173ed4d98c1e46277c1f7">default_table_name</a> ()</td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td></tr>
+<tr class="memitem:a834186b707376a4ead29771860ab440f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a834186b707376a4ead29771860ab440f">object_class</a> ()</td></tr>
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+<tr class="memitem:a90b0359523ef5040fd0e839edd83cca4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a> ()</td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td></tr>
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+<tr class="separator:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a1e7b244d27dcc1244453f725d81d3e54 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> ()</td></tr>
+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> ()</td></tr>
+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$analysis_ctrl_rule_adaptor = $db_adaptor->get_AnalysisCtrlRuleAdaptor;</div>
+<div class="line">$analysis_ctrl_rule_adaptor = $analysisCtrlRuleObj->adaptor;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Module to encapsulate all db access for persistent class AnalysisCtrlRule.
+ There should be just one per application and database connection.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a7a0b17cb2cc51e54df8397325bcc9b88"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor::default_insertion_method </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_insertion_method" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_insertion_method-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_insertion_method-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_insertion_method-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#a7a0b17cb2cc51e54df8397325bcc9b88">default_insertion_method</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'INSERT_IGNORE'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa39019f2695173ed4d98c1e46277c1f7"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#aa39019f2695173ed4d98c1e46277c1f7">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'analysis_ctrl_rule'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a944fe8aee65ea55ba1bd54ee77f97849"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor::object_class </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-object_class" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-object_class-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-object_class-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-object_class-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#a944fe8aee65ea55ba1bd54ee77f97849">object_class</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'Bio::EnsEMBL::Hive::AnalysisCtrlRule'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_analysis_ctrl_rule_adaptor_8pm.html">AnalysisCtrlRuleAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html">AnalysisCtrlRuleAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.js b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.js
new file mode 100644
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--- /dev/null
+++ b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.js
@@ -0,0 +1,6 @@
+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor =
+[
+ [ "default_insertion_method", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#a7a0b17cb2cc51e54df8397325bcc9b88", null ],
+ [ "default_table_name", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#aa39019f2695173ed4d98c1e46277c1f7", null ],
+ [ "object_class", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#a944fe8aee65ea55ba1bd54ee77f97849", null ]
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
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+<div class="title">Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html#a32effe05fbc822b45f5505997faab25c">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b">keys_to_columns</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2a39cbb60a5021d1cd5a4e385da4000f">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#ad90a452430769ce22f854fb0d195e905">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html#ac8c0dae5bdef78d715b0f4b94853e8d1">store_if_needed</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor Class Reference</div> </div>
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor:</div>
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+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
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+<tr class="memitem:a32effe05fbc822b45f5505997faab25c"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html#a32effe05fbc822b45f5505997faab25c">default_table_name</a> ()</td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td></tr>
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+<tr class="separator:ac73267d0e33aad126c188108f7e7c468 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2f77cbefb20d4b4e3a40cf75ce420036 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a> ()</td></tr>
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+<tr class="memitem:ada55ab8c29c95535953efb0ca8c1d805 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a> ()</td></tr>
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+<tr class="memitem:ae98ea2fa8c6a85c6df918b9816bd6cbf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a> ()</td></tr>
+<tr class="separator:ae98ea2fa8c6a85c6df918b9816bd6cbf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae47ff32866fc8b69d8463680b5ead1d2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a> ()</td></tr>
+<tr class="separator:ae47ff32866fc8b69d8463680b5ead1d2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a> ()</td></tr>
+<tr class="separator:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a> ()</td></tr>
+<tr class="separator:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a> ()</td></tr>
+<tr class="separator:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a> ()</td></tr>
+<tr class="separator:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a> ()</td></tr>
+<tr class="separator:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a> ()</td></tr>
+<tr class="separator:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a1e7b244d27dcc1244453f725d81d3e54 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a> ()</td></tr>
+<tr class="separator:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> ()</td></tr>
+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a> ()</td></tr>
+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> ()</td></tr>
+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$dataDBA = $db_adaptor->get_AnalysisDataAdaptor;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ analysis_data table holds LONGTEXT data that is currently used as an extension of some fixed-width fields of 'job' table.
+ It is no longer general-purpose. Please avoid accessing this table directly or via the adaptor.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a32effe05fbc822b45f5505997faab25c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html#a32effe05fbc822b45f5505997faab25c">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'analysis_data'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac8c0dae5bdef78d715b0f4b94853e8d1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor::store_if_needed </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-store_if_needed" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-store_if_needed-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-store_if_needed-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-store_if_needed-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html#ac8c0dae5bdef78d715b0f4b94853e8d1">store_if_needed</a> {</div>
+<div class="line"> my ($self, $data) = @_;</div>
+<div class="line"></div>
+<div class="line"> my ($stored_hash) = $self->store({<span class="stringliteral">'data'</span>=> $data}, 1);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'_extended_data_id '</span> . $stored_hash->{<span class="stringliteral">'analysis_data_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_analysis_data_adaptor_8pm.html">AnalysisDataAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html">AnalysisDataAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor =
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+];
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
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+<script type="text/javascript" src="dynsections.js"></script>
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+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
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+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
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+ <div id="navrow1" class="tabs">
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
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+ </span>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
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+ class="ui-resizable-handle">
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+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
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+ name="MSearchResults" id="MSearchResults">
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+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ac9e28226315228b396483078e3823515">balance_semaphores</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a77f78d2fe7e5ac25737ff9322d40e4f9">CreateNewJob</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a1518bf5c281727593960180483f8554b">decrease_semaphore_count_for_jobid</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ad5638f98e14c623db7787ae6da2f38cf">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a0c5b6bbd627a70f5d1eb35b24b6e2d91">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#aad1bc73bd8052820705590bf853e34f0">fetch_all_by_analysis_id_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ae84a1895b984f71659306509aac7b3d3">fetch_all_incomplete_jobs_by_worker_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ab3ffe9d373143c197120510bbd7f85d7">fetch_by_url_query</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a33703ebaa739dc4c4924cad07e2abd25">fetch_input_ids_for_job_ids</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a171ed08ff5a07ce88413d1257093f7e5">fetch_some_by_analysis_id_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a64c5703becb2a1989bc85e449d961aba">gc_dataflow</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#aa023b41587da0be31418d3d871df7cdc">grab_jobs_for_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ac693f76b13041b3709e5d6a11ac03820">increase_semaphore_count_for_jobid</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#acaa839ac5ee54ada4e4e555205925592">object_class</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a375c57130791087ff6781f4cc6cc9b9e">release_and_age_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a25ddbb1f2f0fada5fc7c9078c887f7d8">release_undone_jobs_from_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a122b718f7e51f923fb50a1c01cb69805">reset_jobs_for_analysis_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a4dd834ac1243d05989bcb352021ede70">reset_or_grab_job_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a601af453349bdbe526fed38bcbbbe6af">store_jobs_and_adjust_counters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a67149e75208ca45c0df928213877ac53">store_out_files</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ad6424e27663135dc9d7dcd17d3b1d569">update_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="entry"></td></tr>
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+<tr class="memitem:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> ()</td></tr>
+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a> ()</td></tr>
+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> ()</td></tr>
+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$analysisJobAdaptor = $db_adaptor->get_AnalysisJobAdaptor;</div>
+<div class="line">$analysisJobAdaptor = $analysisJob->adaptor;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Module to encapsulate all db access for persistent class AnalysisJob.
+ There should be just one per application and database connection.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ac9e28226315228b396483078e3823515"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::balance_semaphores </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: Reset all semaphore_counts to the numbers of unDONE semaphoring jobs.</pre><pre> </pre><div id="codesection-balance_semaphores" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-balance_semaphores-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-balance_semaphores-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-balance_semaphores-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ac9e28226315228b396483078e3823515">balance_semaphores</a> {</div>
+<div class="line"> my ($self, $filter_analysis_id) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $find_sql = qq{</div>
+<div class="line"> SELECT * FROM (</div>
+<div class="line"> SELECT funnel.job_id, funnel.semaphore_count AS was, COALESCE(COUNT(CASE WHEN fan.status!=<span class="stringliteral">'DONE'</span> AND fan.status!=<span class="stringliteral">'PASSED_ON'</span> THEN 1 ELSE NULL END),0) AS should</div>
+<div class="line"> FROM job funnel</div>
+<div class="line"> LEFT JOIN job fan ON (funnel.job_id=fan.semaphored_job_id)</div>
+<div class="line"> WHERE }</div>
+<div class="line"> .($filter_analysis_id ? <span class="stringliteral">"funnel.analysis_id=$filter_analysis_id AND "</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> .qq{</div>
+<div class="line"> funnel.status=<span class="stringliteral">'SEMAPHORED'</span></div>
+<div class="line"> GROUP BY funnel.job_id</div>
+<div class="line"> ) AS <span class="keyword">internal</span> WHERE was<>should OR should=0</div>
+<div class="line"> };</div>
+<div class="line"></div>
+<div class="line"> my $update_sql = <span class="stringliteral">"UPDATE job SET "</span></div>
+<div class="line"> .<span class="stringliteral">" semaphore_count=semaphore_count+? , "</span></div>
+<div class="line"> .( ($self->dbc->driver eq <span class="stringliteral">'pgsql'</span>)</div>
+<div class="line"> ? <span class="stringliteral">"status = CAST(CASE WHEN semaphore_count>0 THEN 'SEMAPHORED' ELSE 'READY' END AS jw_status) "</span></div>
+<div class="line"> : <span class="stringliteral">"status = CASE WHEN semaphore_count>0 THEN 'SEMAPHORED' ELSE 'READY' END "</span></div>
+<div class="line"> ).<span class="stringliteral">" WHERE job_id=? AND status='SEMAPHORED'"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $find_sth = $self->prepare($find_sql);</div>
+<div class="line"> my $update_sth = $self->prepare($update_sql);</div>
+<div class="line"></div>
+<div class="line"> $find_sth->execute();</div>
+<div class="line"> <span class="keywordflow">while</span>(my ($job_id, $was, $should) = $find_sth->fetchrow_array()) {</div>
+<div class="line"> my $msg;</div>
+<div class="line"> <span class="keywordflow">if</span>(0<$should and $should<$was) { # we choose not to lower the counter <span class="keywordflow">if</span> it<span class="stringliteral">'s not time to unblock yet</span></div>
+<div class="line"><span class="stringliteral"> $msg = "Semaphore count may need rebalancing, but it is not critical now, so leaving it on automatic: $was -> $should";</span></div>
+<div class="line"><span class="stringliteral"> $self->db->get_LogMessageAdaptor->store_job_message( $job_id, $msg, 0 );</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> $update_sth->execute($should-$was, $job_id);</span></div>
+<div class="line"><span class="stringliteral"> $msg = "Semaphore count needed rebalancing now, so performing: $was -> $should";</span></div>
+<div class="line"><span class="stringliteral"> $self->db->get_LogMessageAdaptor->store_job_message( $job_id, $msg, 1 );</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> warn "[Job $job_id] $msg\n"; # TODO: integrate the STDERR diagnostic output with LogMessageAdaptor calls in general</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> $find_sth->finish;</span></div>
+<div class="line"><span class="stringliteral"> $update_sth->finish;</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a77f78d2fe7e5ac25737ff9322d40e4f9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Int Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::CreateNewJob </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Args : -input_id => string of input_id which will be passed to run the job (or a Perl hash that will be automagically stringified)
+ -analysis => <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> object stored in the database
+ -prev_job_id => (optional) job_id of job that is creating this job.
+ Used purely for book keeping.
+ Example :</pre><div class="fragment"><div class="line">$job_id = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a77f78d2fe7e5ac25737ff9322d40e4f9">CreateNewJob</a>(</div>
+<div class="line"> -input_id => <span class="stringliteral">'my input data'</span>,</div>
+<div class="line"> -analysis => $myAnalysis);</div>
+</div><!-- fragment --> <pre> Description: uses the analysis object to get the db connection from the adaptor to store a new
+ job in a hive. This is a class level method since it does not have any state.
+ Also updates corresponding analysis_stats by incrementing total_job_count,
+ ready_job_count and flagging the incremental update by changing the status
+ to 'LOADING' (but only if the analysis is not blocked).
+ NOTE: no <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">AnalysisJob</a> object is created in memory as the result of this call; it is simply a "fast store".
+ Returntype : int job_id on database analysis is from.
+ Exceptions : thrown if either -input_id or -analysis are not properly defined
+ Caller : general
+ Status :</p>
+<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000001">Deprecated:</a></b></dt><dd>. Please use $job_adaptor->store_jobs_and_adjust_counters( @jobs_to_store ) instead</dd></dl>
+</pre><pre> </pre><div id="codesection-CreateNewJob" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-CreateNewJob-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-CreateNewJob-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-CreateNewJob-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a77f78d2fe7e5ac25737ff9322d40e4f9">CreateNewJob</a> {</div>
+<div class="line"> my ($class, @args) = @_;</div>
+<div class="line"></div>
+<div class="line"> my ($prev_job, $prev_job_id, $analysis, $input_id, $param_id_stack, $accu_id_stack, $semaphore_count, $semaphored_job_id, $push_new_semaphore) =</div>
+<div class="line"> rearrange([qw(prev_job prev_job_id analysis input_id param_id_stack accu_id_stack semaphore_count semaphored_job_id push_new_semaphore)], @args);</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"CreateNewJob() method is deprecated. Please use \$job_adaptor->store_jobs_and_adjust_counters() instead.\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">throw</span>(<span class="stringliteral">"must define input_id"</span>) unless($input_id);</div>
+<div class="line"> <span class="keywordflow">throw</span>(<span class="stringliteral">"must define analysis"</span>) unless($analysis);</div>
+<div class="line"> <span class="keywordflow">throw</span>(<span class="stringliteral">"analysis must be [Bio::EnsEMBL::Hive::Analysis] not a [$analysis]"</span>) unless($analysis->isa(<span class="stringliteral">'Bio::EnsEMBL::Hive::Analysis'</span>));</div>
+<div class="line"> <span class="keywordflow">throw</span>(<span class="stringliteral">"analysis must have adaptor connected to database"</span>) unless($analysis->adaptor and $analysis->adaptor->db);</div>
+<div class="line"> <span class="keywordflow">throw</span>(<span class="stringliteral">"Please specify prev_job object instead of prev_job_id if available"</span>) <span class="keywordflow">if</span> ($prev_job_id); # <span class="stringliteral">'obsolete'</span> message</div>
+<div class="line"></div>
+<div class="line"> my $job = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb83a9f0a1fa1cd38bc5ae626bfd6b51">new</a>(</div>
+<div class="line"> -prev_job_id => $prev_job && $prev_job->dbID,</div>
+<div class="line"> -analysis_id => $analysis->dbID,</div>
+<div class="line"> -input_id => $input_id,</div>
+<div class="line"> -param_id_stack => $param_id_stack,</div>
+<div class="line"> -accu_id_stack => $accu_id_stack,</div>
+<div class="line"> -semaphore_count => $semaphore_count,</div>
+<div class="line"> -semaphored_job_id => $semaphored_job_id,</div>
+<div class="line"> );</div>
+<div class="line"> </div>
+<div class="line"> my ($job_id) = @{ $analysis->adaptor->db->get_AnalysisJobAdaptor->store_jobs_and_adjust_counters( [ $job ], $push_new_semaphore ) };</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $job_id;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1518bf5c281727593960180483f8554b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::decrease_semaphore_count_for_jobid </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-decrease_semaphore_count_for_jobid" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-decrease_semaphore_count_for_jobid-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-decrease_semaphore_count_for_jobid-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-decrease_semaphore_count_for_jobid-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a1518bf5c281727593960180483f8554b">decrease_semaphore_count_for_jobid</a> { # used in semaphore annihilation or unsuccessful creation</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $jobid = shift @_ or <span class="keywordflow">return</span>;</div>
+<div class="line"> my $dec = shift @_ || 1;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # NB: BOTH THE ORDER OF UPDATES AND EXACT WORDING IS ESSENTIAL FOR SYNCHRONOUS ATOMIC OPERATION,</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # otherwise the same command tends to behave differently on MySQL and SQLite (at least)</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span> my $sql = <span class="stringliteral">"UPDATE job "</span></div>
+<div class="line"> .( ($self->dbc->driver eq <span class="stringliteral">'pgsql'</span>)</div>
+<div class="line"> ? <span class="stringliteral">"SET status = CAST(CASE WHEN semaphore_count>$dec THEN 'SEMAPHORED' ELSE 'READY' END AS jw_status), "</span></div>
+<div class="line"> : <span class="stringliteral">"SET status = CASE WHEN semaphore_count>$dec THEN 'SEMAPHORED' ELSE 'READY' END, "</span></div>
+<div class="line"> ).qq{</div>
+<div class="line"> semaphore_count=semaphore_count-?</div>
+<div class="line"> WHERE job_id=? AND status=<span class="stringliteral">'SEMAPHORED'</span></div>
+<div class="line"> };</div>
+<div class="line"> </div>
+<div class="line"> $self->dbc->protected_prepare_execute( $sql, $dec, $jobid );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad5638f98e14c623db7787ae6da2f38cf"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::default_overflow_limit </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_overflow_limit" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_overflow_limit-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_overflow_limit-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_overflow_limit-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ad5638f98e14c623db7787ae6da2f38cf">default_overflow_limit</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'input_id'</span> => 255,</div>
+<div class="line"> <span class="stringliteral">'param_id_stack'</span> => 64,</div>
+<div class="line"> <span class="stringliteral">'accu_id_stack'</span> => 64,</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0c5b6bbd627a70f5d1eb35b24b6e2d91"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a0c5b6bbd627a70f5d1eb35b24b6e2d91">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'job'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aad1bc73bd8052820705590bf853e34f0"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Reference Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_all_by_analysis_id_status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : (optional) int $analysis_id
+ Arg [2] : (optional) string $status
+ Arg [3] : (optional) int $retry_at_least
+ Example :</pre><div class="fragment"><div class="line">$all_failed_jobs = $adaptor->fetch_all_by_analysis_id_status(undef, <span class="stringliteral">'FAILED'</span>);</div>
+<div class="line"> $analysis_done_jobs = $adaptor->fetch_all_by_analysis_id_status($analysis->dbID, <span class="stringliteral">'DONE'</span>);</div>
+</div><!-- fragment --> <pre> Description: Returns a list of all jobs filtered by given analysis_id (if specified) and given status (if specified).
+ Returntype : reference to list of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> objects</pre><pre> </pre><div id="codesection-fetch_all_by_analysis_id_status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_all_by_analysis_id_status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_all_by_analysis_id_status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_all_by_analysis_id_status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#aad1bc73bd8052820705590bf853e34f0">fetch_all_by_analysis_id_status</a> {</div>
+<div class="line"> my ($self, $analysis_id, $status, $retry_count_at_least) = @_;</div>
+<div class="line"></div>
+<div class="line"> my @constraints = ();</div>
+<div class="line"> push @constraints, <span class="stringliteral">"analysis_id=$analysis_id"</span> <span class="keywordflow">if</span> ($analysis_id);</div>
+<div class="line"> push @constraints, <span class="stringliteral">"status='$status'"</span> <span class="keywordflow">if</span> ($status);</div>
+<div class="line"> push @constraints, <span class="stringliteral">"retry_count >= $retry_count_at_least"</span> <span class="keywordflow">if</span> ($retry_count_at_least);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_all( join(<span class="stringliteral">" AND "</span>, @constraints) );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae84a1895b984f71659306509aac7b3d3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_all_incomplete_jobs_by_worker_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_all_incomplete_jobs_by_worker_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_all_incomplete_jobs_by_worker_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_all_incomplete_jobs_by_worker_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_all_incomplete_jobs_by_worker_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ae84a1895b984f71659306509aac7b3d3">fetch_all_incomplete_jobs_by_worker_id</a> {</div>
+<div class="line"> my ($self, $worker_id) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $constraint = <span class="stringliteral">"status IN ('CLAIMED','PRE_CLEANUP','FETCH_INPUT','RUN','WRITE_OUTPUT','POST_CLEANUP') AND worker_id='$worker_id'"</span>;</div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_all($constraint);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab3ffe9d373143c197120510bbd7f85d7"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_by_url_query </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_by_url_query" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_by_url_query-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_by_url_query-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_by_url_query-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ab3ffe9d373143c197120510bbd7f85d7">fetch_by_url_query</a> {</div>
+<div class="line"> my ($self, $field_name, $field_value) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($field_name eq <span class="stringliteral">'dbID'</span> and $field_value) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_by_dbID($field_value);</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span>;</div>
+<div class="line"></div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a33703ebaa739dc4c4924cad07e2abd25"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_input_ids_for_job_ids </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_input_ids_for_job_ids" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input_ids_for_job_ids-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input_ids_for_job_ids-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input_ids_for_job_ids-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a33703ebaa739dc4c4924cad07e2abd25">fetch_input_ids_for_job_ids</a> {</div>
+<div class="line"> my ($self, $job_ids_csv, $id_scale, $id_offset) = @_;</div>
+<div class="line"> $id_scale ||= 1;</div>
+<div class="line"> $id_offset ||= 0;</div>
+<div class="line"></div>
+<div class="line"> my %input_ids = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $job_ids_csv ) {</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"SELECT job_id, input_id FROM job WHERE job_id in ($job_ids_csv)"</span>;</div>
+<div class="line"> my $sth = $self->prepare( $sql );</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>(my ($job_id, $input_id) = $sth->fetchrow_array() ) {</div>
+<div class="line"> <span class="keywordflow">if</span>($input_id =~ /^_ext(?:\w+)_data_id (\d+)$/) {</div>
+<div class="line"> $input_id = $self->db->get_AnalysisDataAdaptor->fetch_by_analysis_data_id_TO_data($1);</div>
+<div class="line"> }</div>
+<div class="line"> $input_ids{$job_id * $id_scale + $id_offset} = $input_id;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> \%input_ids;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a171ed08ff5a07ce88413d1257093f7e5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::fetch_some_by_analysis_id_limit </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_some_by_analysis_id_limit" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_some_by_analysis_id_limit-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_some_by_analysis_id_limit-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_some_by_analysis_id_limit-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a171ed08ff5a07ce88413d1257093f7e5">fetch_some_by_analysis_id_limit</a> {</div>
+<div class="line"> my ($self, $analysis_id, $limit) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_all( <span class="stringliteral">"analysis_id = '$analysis_id' LIMIT $limit"</span> );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a64c5703becb2a1989bc85e449d961aba"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::gc_dataflow </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: perform automatic dataflow from a dead job that overused resources if a corresponding dataflow rule was provided
+ Should only be called once during garbage collection phase, when the job is definitely 'abandoned' and not being worked on.</pre><pre> </pre><div id="codesection-gc_dataflow" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-gc_dataflow-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-gc_dataflow-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-gc_dataflow-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a64c5703becb2a1989bc85e449d961aba">gc_dataflow</a> {</div>
+<div class="line"> my ($self, $analysis, $job_id, $branch_name) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $branch_code = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a529c8c386c3e60cb1a737231775bf77c">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor::branch_name_2_code</a>($branch_name);</div>
+<div class="line"></div>
+<div class="line"> unless( $self->db->get_DataflowRuleAdaptor->count_all_by_from_analysis_id_AND_branch_code($analysis->dbID, $branch_code) ) {</div>
+<div class="line"> <span class="keywordflow">return</span> 0; # just <span class="keywordflow">return</span> <span class="keywordflow">if</span> no corresponding <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a64c5703becb2a1989bc85e449d961aba">gc_dataflow</a> rule has been defined</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $job = $self->fetch_by_dbID($job_id);</div>
+<div class="line"></div>
+<div class="line"> $job->param_init( 0, $analysis->parameters(), $job->input_id() ); # input_id_templates still supported, however to a limited extent</div>
+<div class="line"></div>
+<div class="line"> $job->dataflow_output_id( $job->input_id() , $branch_name );</div>
+<div class="line"></div>
+<div class="line"> $job->update_status(<span class="stringliteral">'PASSED_ON'</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $semaphored_job_id = $job->semaphored_job_id) {</div>
+<div class="line"> $self->decrease_semaphore_count_for_jobid( $semaphored_job_id ); # step-unblock the semaphore</div>
+<div class="line"> }</div>
+<div class="line"> </div>
+<div class="line"> <span class="keywordflow">return</span> 1;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa023b41587da0be31418d3d871df7cdc"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::grab_jobs_for_worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> object $worker
+ Example:
+ my $jobs = $job_adaptor->grab_jobs_for_worker( $worker );
+ Description:
+ For the specified worker, it will search available jobs,
+ and using the how_many_this_batch parameter, claim/fetch that
+ number of jobs, and then return them.
+ Returntype :
+ reference to array of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> objects
+ Caller : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab6456d819b72b807884df4b49ea30492">Bio::EnsEMBL::Hive::Worker::run</a></pre><pre> </pre><div id="codesection-grab_jobs_for_worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-grab_jobs_for_worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-grab_jobs_for_worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-grab_jobs_for_worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#aa023b41587da0be31418d3d871df7cdc">grab_jobs_for_worker</a> {</div>
+<div class="line"> my ($self, $worker, $how_many_this_batch, $workers_rank) = @_;</div>
+<div class="line"> </div>
+<div class="line"> my $analysis_id = $worker->analysis_id();</div>
+<div class="line"> my $worker_id = $worker->dbID();</div>
+<div class="line"> my $offset = $how_many_this_batch*$workers_rank;</div>
+<div class="line"></div>
+<div class="line"> my $prefix_sql = ($self->dbc->driver eq <span class="stringliteral">'mysql'</span>) ? qq{</div>
+<div class="line"> UPDATE job j</div>
+<div class="line"> JOIN (</div>
+<div class="line"> SELECT job_id</div>
+<div class="line"> FROM job</div>
+<div class="line"> WHERE analysis_id=<span class="stringliteral">'$analysis_id'</span></div>
+<div class="line"> AND status=<span class="stringliteral">'READY'</span></div>
+<div class="line"> } : qq{</div>
+<div class="line"> UPDATE job</div>
+<div class="line"> SET worker_id=<span class="stringliteral">'$worker_id'</span>, status=<span class="stringliteral">'CLAIMED'</span></div>
+<div class="line"> WHERE job_id in (</div>
+<div class="line"> SELECT job_id</div>
+<div class="line"> FROM job</div>
+<div class="line"> WHERE analysis_id=<span class="stringliteral">'$analysis_id'</span></div>
+<div class="line"> AND status=<span class="stringliteral">'READY'</span></div>
+<div class="line"> };</div>
+<div class="line"> my $virgin_sql = qq{ AND retry_count=0 };</div>
+<div class="line"> my $limit_sql = qq{ LIMIT $how_many_this_batch };</div>
+<div class="line"> my $offset_sql = qq{ OFFSET $offset };</div>
+<div class="line"> my $suffix_sql = ($self->dbc->driver eq <span class="stringliteral">'mysql'</span>) ? qq{</div>
+<div class="line"> ) as x</div>
+<div class="line"> USING (job_id)</div>
+<div class="line"> SET j.worker_id='$worker_id', j.status='CLAIMED'</div>
+<div class="line"> WHERE j.status='READY'</div>
+<div class="line"> } : qq{</div>
+<div class="line"> )</div>
+<div class="line"> AND status=<span class="stringliteral">'READY'</span></div>
+<div class="line"> };</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # we have to be explicitly numeric here because of '0E0' value returned by DBI if "no rows have been affected":</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>( (my $claim_count = $self->dbc->do( $prefix_sql . $virgin_sql . $limit_sql . $offset_sql . $suffix_sql)) == 0 ) {</div>
+<div class="line"> <span class="keywordflow">if</span>( ($claim_count = $self->dbc->do( $prefix_sql . $limit_sql . $offset_sql . $suffix_sql)) == 0 ) {</div>
+<div class="line"> $claim_count = $self->dbc->do( $prefix_sql . $limit_sql . $suffix_sql);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_all_by_worker_id_AND_status($worker_id, <span class="stringliteral">'CLAIMED'</span>) ;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac693f76b13041b3709e5d6a11ac03820"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::increase_semaphore_count_for_jobid </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-increase_semaphore_count_for_jobid" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-increase_semaphore_count_for_jobid-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-increase_semaphore_count_for_jobid-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-increase_semaphore_count_for_jobid-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ac693f76b13041b3709e5d6a11ac03820">increase_semaphore_count_for_jobid</a> { # used in semaphore propagation</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $jobid = shift @_ or <span class="keywordflow">return</span>;</div>
+<div class="line"> my $inc = shift @_ || 1;</div>
+<div class="line"></div>
+<div class="line"> my $sql = qq{</div>
+<div class="line"> UPDATE job</div>
+<div class="line"> SET semaphore_count=semaphore_count+?</div>
+<div class="line"> WHERE job_id=?</div>
+<div class="line"> };</div>
+<div class="line"> </div>
+<div class="line"> $self->dbc->protected_prepare_execute( $sql, $inc, $jobid );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="acaa839ac5ee54ada4e4e555205925592"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::object_class </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-object_class" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-object_class-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-object_class-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-object_class-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#acaa839ac5ee54ada4e4e555205925592">object_class</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'Bio::EnsEMBL::Hive::AnalysisJob'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a375c57130791087ff6781f4cc6cc9b9e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::release_and_age_job </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-release_and_age_job" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-release_and_age_job-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-release_and_age_job-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-release_and_age_job-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a375c57130791087ff6781f4cc6cc9b9e">release_and_age_job</a> {</div>
+<div class="line"> my ($self, $job_id, $max_retry_count, $may_retry, $runtime_msec) = @_;</div>
+<div class="line"> $may_retry ||= 0;</div>
+<div class="line"> $runtime_msec = <span class="stringliteral">"NULL"</span> unless(defined $runtime_msec);</div>
+<div class="line"><span class="preprocessor"> # NB: The order of updated fields IS important. Here we first find out the new status and then increment the retry_count:</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # FIXME: would it be possible to retain worker_id for READY jobs in order to temporarily keep track of the previous (failed) worker?</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span> $self->dbc->do( </div>
+<div class="line"> <span class="stringliteral">"UPDATE job "</span></div>
+<div class="line"> .( ($self->dbc->driver eq <span class="stringliteral">'pgsql'</span>)</div>
+<div class="line"> ? <span class="stringliteral">"SET status = CAST(CASE WHEN $may_retry AND (retry_count<$max_retry_count) THEN 'READY' ELSE 'FAILED' END AS jw_status), "</span></div>
+<div class="line"> : <span class="stringliteral">"SET status = CASE WHEN $may_retry AND (retry_count<$max_retry_count) THEN 'READY' ELSE 'FAILED' END, "</span></div>
+<div class="line"> ).qq{</div>
+<div class="line"> retry_count=retry_count+1,</div>
+<div class="line"> runtime_msec=$runtime_msec</div>
+<div class="line"> WHERE job_id=$job_id</div>
+<div class="line"> AND status in (<span class="stringliteral">'CLAIMED'</span>,<span class="stringliteral">'PRE_CLEANUP'</span>,<span class="stringliteral">'FETCH_INPUT'</span>,<span class="stringliteral">'RUN'</span>,<span class="stringliteral">'WRITE_OUTPUT'</span>,<span class="stringliteral">'POST_CLEANUP'</span>)</div>
+<div class="line"> } );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a25ddbb1f2f0fada5fc7c9078c887f7d8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::release_undone_jobs_from_worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> object
+ Arg [2] : optional message to be recorded in 'job_message' table
+ Example :</pre><div class="fragment"></div><!-- fragment --> <pre> Description: If a worker has died some of its jobs need to be reset back to 'READY'
+ so they can be rerun.
+ Jobs in state CLAIMED as simply reset back to READY.
+ If jobs was 'in progress' (PRE_CLEANUP, FETCH_INPUT, RUN, WRITE_OUTPUT, POST_CLEANUP)
+ the retry_count is increased and the status set back to READY.
+ If the retry_count >= $max_retry_count (3 by default) the job is set
+ to 'FAILED' and not rerun again.
+ Exceptions : $worker must be defined
+ Caller : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></pre><pre> </pre><div id="codesection-release_undone_jobs_from_worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-release_undone_jobs_from_worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-release_undone_jobs_from_worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-release_undone_jobs_from_worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a25ddbb1f2f0fada5fc7c9078c887f7d8">release_undone_jobs_from_worker</a> {</div>
+<div class="line"> my ($self, $worker, $msg) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $max_retry_count = $worker->analysis->max_retry_count();</div>
+<div class="line"> my $worker_id = $worker->dbID();</div>
+<div class="line"> my $analysis = $worker->analysis();</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> #first just reset the claimed jobs, these don't need a retry_count index increment:</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # (previous worker_id does not matter, because that worker has never had a chance to run the job)</span></div>
+<div class="line"><span class="preprocessor"></span> $self->dbc->do( qq{</div>
+<div class="line"> UPDATE job</div>
+<div class="line"> SET status=<span class="stringliteral">'READY'</span>, worker_id=NULL</div>
+<div class="line"> WHERE worker_id=<span class="stringliteral">'$worker_id'</span></div>
+<div class="line"> AND status=<span class="stringliteral">'CLAIMED'</span></div>
+<div class="line"> } );</div>
+<div class="line"></div>
+<div class="line"> my $sth = $self->prepare( qq{</div>
+<div class="line"> SELECT job_id</div>
+<div class="line"> FROM job</div>
+<div class="line"> WHERE worker_id=<span class="stringliteral">'$worker_id'</span></div>
+<div class="line"> AND status in (<span class="stringliteral">'PRE_CLEANUP'</span>,<span class="stringliteral">'FETCH_INPUT'</span>,<span class="stringliteral">'RUN'</span>,<span class="stringliteral">'WRITE_OUTPUT'</span>,<span class="stringliteral">'POST_CLEANUP'</span>)</div>
+<div class="line"> } );</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"></div>
+<div class="line"> my $cod = $worker->cause_of_death();</div>
+<div class="line"> $msg ||= <span class="stringliteral">"GarbageCollector: The worker died because of $cod"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $resource_overusage = ($cod eq <span class="stringliteral">'MEMLIMIT'</span>) || ($cod eq <span class="stringliteral">'RUNLIMIT'</span> and $worker->work_done()==0);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>(my ($job_id) = $sth->fetchrow_array()) {</div>
+<div class="line"></div>
+<div class="line"> my $passed_on = 0; # the flag indicating that the garbage_collection was attempted and was successful</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $resource_overusage ) {</div>
+<div class="line"> <span class="keywordflow">if</span>($passed_on = $self->gc_dataflow( $analysis, $job_id, $cod )) {</div>
+<div class="line"> $msg .= <span class="stringliteral">', performing gc_dataflow'</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> unless($passed_on) {</div>
+<div class="line"> <span class="keywordflow">if</span>($passed_on = $self->gc_dataflow( $analysis, $job_id, <span class="stringliteral">'ANYFAILURE'</span> )) {</div>
+<div class="line"> $msg .= <span class="stringliteral">", performing 'ANYFAILURE' gc_dataflow"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->db()->get_LogMessageAdaptor()->store_job_message($job_id, $msg, not $passed_on );</div>
+<div class="line"></div>
+<div class="line"> unless($passed_on) {</div>
+<div class="line"> $self->release_and_age_job( $job_id, $max_retry_count, not $resource_overusage );</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> $sth->finish();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a122b718f7e51f923fb50a1c01cb69805"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::reset_jobs_for_analysis_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : int $analysis_id
+ Arg [2] : bool $all (false by default)
+ Description: Resets either all FAILED jobs of an analysis (default)
+ or ALL jobs of an analysis to 'READY' and their retry_count to 0.
+ Caller : <a class="el" href="beekeeper_8pl.html">beekeeper.pl</a></pre><pre> </pre><div id="codesection-reset_jobs_for_analysis_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-reset_jobs_for_analysis_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-reset_jobs_for_analysis_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-reset_jobs_for_analysis_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a122b718f7e51f923fb50a1c01cb69805">reset_jobs_for_analysis_id</a> {</div>
+<div class="line"> my ($self, $analysis_id, $input_statuses) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $status_filter = <span class="stringliteral">''</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(ref($input_statuses) eq <span class="stringliteral">'ARRAY'</span>) {</div>
+<div class="line"> $status_filter = <span class="stringliteral">'AND status IN ('</span>.join(<span class="stringliteral">', '</span>, map { <span class="stringliteral">"'$_'"</span> } @$input_statuses).<span class="charliteral">')'</span>;</div>
+<div class="line"> } elsif(!$input_statuses) {</div>
+<div class="line"> $status_filter = <span class="stringliteral">"AND status='FAILED'"</span>; # temporarily keep it here <span class="keywordflow">for</span> compatibility</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $sql = qq{</div>
+<div class="line"> UPDATE job</div>
+<div class="line"> SET retry_count = CASE WHEN (status=<span class="stringliteral">'READY'</span> OR status=<span class="stringliteral">'CLAIMED'</span>) THEN 0 ELSE 1 END,</div>
+<div class="line"> }. ( ($self->dbc->driver eq 'pgsql')</div>
+<div class="line"> ? "status = CAST(CASE WHEN semaphore_count>0 THEN 'SEMAPHORED' ELSE 'READY' END AS jw_status) "</div>
+<div class="line"> : "status = CASE WHEN semaphore_count>0 THEN 'SEMAPHORED' ELSE 'READY' END "</div>
+<div class="line"> ).qq{</div>
+<div class="line"> WHERE analysis_id=?</div>
+<div class="line"> } . $status_filter;</div>
+<div class="line"></div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute($analysis_id);</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"></div>
+<div class="line"> $self->db->get_AnalysisStatsAdaptor->update_status($analysis_id, <span class="stringliteral">'LOADING'</span>);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4dd834ac1243d05989bcb352021ede70"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::reset_or_grab_job_by_dbID </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : int $job_id
+ Arg [2] : int $worker_id (optional)
+ Description: resets a job to to 'READY' (if no $worker_id given) or directly to 'CLAIMED' so it can be run again, and fetches it.
+ NB: Will also reset a previously 'SEMAPHORED' job to READY.
+ The retry_count will be set to 1 for previously run jobs (partially or wholly) to trigger PRE_CLEANUP for them,
+ but will not change retry_count if a job has never *really* started.
+ Returntype : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> or undef</pre><pre> </pre><div id="codesection-reset_or_grab_job_by_dbID" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-reset_or_grab_job_by_dbID-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-reset_or_grab_job_by_dbID-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-reset_or_grab_job_by_dbID-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a4dd834ac1243d05989bcb352021ede70">reset_or_grab_job_by_dbID</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> my $job_id = shift;</div>
+<div class="line"> my $worker_id = shift;</div>
+<div class="line"></div>
+<div class="line"> my $new_status = ($worker_id?<span class="stringliteral">'CLAIMED'</span>:<span class="stringliteral">'READY'</span>);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Note: the order of the fields being updated is critical!</span></div>
+<div class="line"><span class="preprocessor"></span> my $sql = qq{</div>
+<div class="line"> UPDATE job</div>
+<div class="line"> SET retry_count = CASE WHEN (status=<span class="stringliteral">'READY'</span> OR status=<span class="stringliteral">'CLAIMED'</span>) THEN retry_count ELSE 1 END</div>
+<div class="line"> , status=?</div>
+<div class="line"> , worker_id=?</div>
+<div class="line"> WHERE job_id=?</div>
+<div class="line"> };</div>
+<div class="line"> my @values = ($new_status, $worker_id, $job_id);</div>
+<div class="line"></div>
+<div class="line"> my $sth = $self->prepare( $sql );</div>
+<div class="line"> my $return_code = $sth->execute( @values )</div>
+<div class="line"> or die "Could not run\n\t$sql\nwith data:\n\t(".join(',', @values).')';</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"></div>
+<div class="line"> my $job = $self->fetch_by_job_id_AND_status($job_id, $new_status) ;</div>
+<div class="line"></div>
+<div class="line"> return $job;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a601af453349bdbe526fed38bcbbbe6af"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Reference Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::store_jobs_and_adjust_counters </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : arrayref of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> $jobs_to_store
+ Arg [2] : (optional) boolean $push_new_semaphore
+ Example :</pre><div class="fragment"><div class="line">my @output_job_ids = @{ $job_adaptor->store_jobs_and_adjust_counters( \@jobs_to_store ) };</div>
+</div><!-- fragment --> <pre> Description: Attempts to store a list of jobs, returns an arrayref of successfully stored job_ids
+ Returntype : Reference to list of job_dbIDs</pre><pre> </pre><div id="codesection-store_jobs_and_adjust_counters" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-store_jobs_and_adjust_counters-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-store_jobs_and_adjust_counters-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-store_jobs_and_adjust_counters-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a601af453349bdbe526fed38bcbbbe6af">store_jobs_and_adjust_counters</a> {</div>
+<div class="line"> my ($self, $jobs, $push_new_semaphore) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $dbc = $self->dbc;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # NB: our use patterns assume all jobs from the same storing batch share the same semaphored_job_id:</span></div>
+<div class="line"><span class="preprocessor"></span> my $semaphored_job_id = scalar(@$jobs) && $jobs->[0]->semaphored_job_id();</div>
+<div class="line"> my $need_to_increase_semaphore_count = ($semaphored_job_id && !$push_new_semaphore);</div>
+<div class="line"></div>
+<div class="line"> my @output_job_ids = ();</div>
+<div class="line"> my $failed_to_store = 0;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $job (@$jobs) {</div>
+<div class="line"><span class="preprocessor"> # avoid deadlocks when dataflowing under transactional mode (used in Ortheus Runnable for example):</span></div>
+<div class="line"><span class="preprocessor"></span> $dbc->do( <span class="stringliteral">"SELECT 1 FROM job WHERE job_id=$semaphored_job_id FOR UPDATE"</span> ) <span class="keywordflow">if</span>($need_to_increase_semaphore_count and ($dbc->driver ne <span class="stringliteral">'sqlite'</span>));</div>
+<div class="line"></div>
+<div class="line"> my ($job, $stored_this_time) = $self->store( $job, 0 );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($stored_this_time) {</div>
+<div class="line"> <span class="keywordflow">if</span>($need_to_increase_semaphore_count) { # <span class="keywordflow">if</span> we are not creating a <span class="keyword">new</span> semaphore (where dependent jobs have already been counted),</div>
+<div class="line"><span class="preprocessor"> # but rather propagating an existing one (same or other level), we have to up-adjust the counter</span></div>
+<div class="line"><span class="preprocessor"></span> $self->increase_semaphore_count_for_jobid( $semaphored_job_id );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> unless($self->db->hive_use_triggers()) {</div>
+<div class="line"> $dbc->do(qq{</div>
+<div class="line"> UPDATE analysis_stats</div>
+<div class="line"> SET total_job_count=total_job_count+1</div>
+<div class="line"> }</div>
+<div class="line"> .(($job->status eq <span class="stringliteral">'READY'</span>)</div>
+<div class="line"> ? <span class="stringliteral">" ,ready_job_count=ready_job_count+1 "</span></div>
+<div class="line"> : <span class="stringliteral">" ,semaphored_job_count=semaphored_job_count+1 "</span></div>
+<div class="line"> ).(($dbc->driver eq <span class="stringliteral">'pgsql'</span>)</div>
+<div class="line"> ? <span class="stringliteral">" ,status = CAST(CASE WHEN status!='BLOCKED' THEN 'LOADING' ELSE 'BLOCKED' END AS analysis_status) "</span></div>
+<div class="line"> : <span class="stringliteral">" ,status = CASE WHEN status!='BLOCKED' THEN 'LOADING' ELSE 'BLOCKED' END "</span></div>
+<div class="line"> ).<span class="stringliteral">" WHERE analysis_id="</span>.$job->analysis_id</div>
+<div class="line"> );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> push @output_job_ids, $job->dbID();</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $failed_to_store++;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # adjust semaphore_count for jobs that failed to be stored (but have been pre-counted during funnel's creation):</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>($push_new_semaphore and $failed_to_store) {</div>
+<div class="line"> $self->decrease_semaphore_count_for_jobid( $semaphored_job_id, $failed_to_store );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> \@output_job_ids;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a67149e75208ca45c0df928213877ac53"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::store_out_files </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> $job
+ Example :</pre><div class="fragment"></div><!-- fragment --> <pre> Description: update locations of log files, if present
+ Returntype :
+ Exceptions :
+ Caller : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></pre><pre> </pre><div id="codesection-store_out_files" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-store_out_files-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-store_out_files-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-store_out_files-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a67149e75208ca45c0df928213877ac53">store_out_files</a> {</div>
+<div class="line"> my ($self, $job) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($job->stdout_file or $job->stderr_file) {</div>
+<div class="line"> my $insert_sql = <span class="stringliteral">'REPLACE INTO job_file (job_id, retry, worker_id, stdout_file, stderr_file) VALUES (?,?,?,?,?)'</span>;</div>
+<div class="line"> my $sth = $self->dbc()->prepare($insert_sql);</div>
+<div class="line"> $sth->execute($job->dbID(), $job->retry_count(), $job->worker_id(), $job->stdout_file(), $job->stderr_file());</div>
+<div class="line"> $sth->finish();</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> my $sql = <span class="stringliteral">'DELETE from job_file WHERE worker_id='</span>.$job->worker_id.<span class="stringliteral">' AND job_id='</span>.$job->dbID;</div>
+<div class="line"> $self->dbc->do($sql);</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad6424e27663135dc9d7dcd17d3b1d569"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::update_status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : $analysis_id
+ Example :</pre><div class="fragment"></div><!-- fragment --> <pre> Description: updates the job.status in the database
+ Returntype :
+ Exceptions :
+ Caller : general</pre><pre> </pre><div id="codesection-update_status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-update_status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-update_status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-update_status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ad6424e27663135dc9d7dcd17d3b1d569">update_status</a> {</div>
+<div class="line"> my ($self, $job) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"UPDATE job SET status='"</span>.$job->status.<span class="stringliteral">"' "</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($job->status eq <span class="stringliteral">'DONE'</span>) {</div>
+<div class="line"> $sql .= <span class="stringliteral">",completed=CURRENT_TIMESTAMP"</span>;</div>
+<div class="line"> $sql .= <span class="stringliteral">",runtime_msec="</span>.$job->runtime_msec;</div>
+<div class="line"> $sql .= <span class="stringliteral">",query_count="</span>.$job->query_count;</div>
+<div class="line"> } elsif($job->status eq <span class="stringliteral">'PASSED_ON'</span>) {</div>
+<div class="line"> $sql .= <span class="stringliteral">", completed=CURRENT_TIMESTAMP"</span>;</div>
+<div class="line"> } elsif($job->status eq <span class="stringliteral">'READY'</span>) {</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $sql .= <span class="stringliteral">" WHERE job_id='"</span>.$job->dbID.<span class="stringliteral">"' "</span>;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # This particular query is infamous for collisions and 'deadlock' situations; let's wait and retry:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->dbc->protected_prepare_execute( $sql );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_analysis_job_adaptor_8pm.html">AnalysisJobAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">AnalysisJobAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor =
+[
+ [ "balance_semaphores", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ac9e28226315228b396483078e3823515", null ],
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+ [ "decrease_semaphore_count_for_jobid", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a1518bf5c281727593960180483f8554b", null ],
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+ [ "fetch_by_url_query", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ab3ffe9d373143c197120510bbd7f85d7", null ],
+ [ "fetch_input_ids_for_job_ids", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a33703ebaa739dc4c4924cad07e2abd25", null ],
+ [ "fetch_some_by_analysis_id_limit", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a171ed08ff5a07ce88413d1257093f7e5", null ],
+ [ "gc_dataflow", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a64c5703becb2a1989bc85e449d961aba", null ],
+ [ "grab_jobs_for_worker", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#aa023b41587da0be31418d3d871df7cdc", null ],
+ [ "increase_semaphore_count_for_jobid", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ac693f76b13041b3709e5d6a11ac03820", null ],
+ [ "object_class", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#acaa839ac5ee54ada4e4e555205925592", null ],
+ [ "release_and_age_job", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a375c57130791087ff6781f4cc6cc9b9e", null ],
+ [ "release_undone_jobs_from_worker", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a25ddbb1f2f0fada5fc7c9078c887f7d8", null ],
+ [ "reset_jobs_for_analysis_id", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a122b718f7e51f923fb50a1c01cb69805", null ],
+ [ "reset_or_grab_job_by_dbID", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a4dd834ac1243d05989bcb352021ede70", null ],
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+];
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+<div class="title">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor Member List</div> </div>
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+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a98976d888957cc7231fcc50e44f21408">decrease_required_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a15fd023779f6e61df20d84d70dc3e28f">decrease_running_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a66f32625d1fbafc4fafbbc23ac11b442">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a7d096d983b7596fa83094ebbb8ebb06a">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#ae2e16bd96ffd64af54c59ba31f6becb1">fetch_all_by_suitability_rc_id_meadow_type</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a08e32841d6e713fc8b4eada7a3057d8d">increase_required_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#aff5f1a7e1f8579cd228352678cce7b78">increase_running_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a57f38be49bb6727b4e1dd853b1ad77b3">interval_update_work_done</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a9670adf2613b9d268ca2195c33099df5">object_class</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#aed7915b07ea5296ca56e90b46f08553b">refresh</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#ab81f838278b0c4e6791cac46713939fa">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="entry"></td></tr>
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+<tr class="memitem:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> ()</td></tr>
+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$analysisStatsAdaptor = $db_adaptor->get_AnalysisStatsAdaptor;</div>
+<div class="line">$analysisStatsAdaptor = $analysisStats->adaptor;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Module to encapsulate all db access for persistent class AnalysisStats.
+ There should be just one per application and database connection.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a98976d888957cc7231fcc50e44f21408"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::decrease_required_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-decrease_required_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-decrease_required_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-decrease_required_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-decrease_required_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a98976d888957cc7231fcc50e44f21408">decrease_required_workers</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> my $analysis_id = shift;</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"UPDATE analysis_stats SET num_required_workers=num_required_workers-1 "</span>.</div>
+<div class="line"> <span class="stringliteral">"WHERE analysis_id='$analysis_id' "</span>;</div>
+<div class="line"></div>
+<div class="line"> $self->dbc->do($sql);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a15fd023779f6e61df20d84d70dc3e28f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::decrease_running_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-decrease_running_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-decrease_running_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-decrease_running_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-decrease_running_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a15fd023779f6e61df20d84d70dc3e28f">decrease_running_workers</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> my $analysis_id = shift;</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"UPDATE analysis_stats SET num_running_workers = num_running_workers - 1 "</span>.</div>
+<div class="line"> <span class="stringliteral">" WHERE analysis_id='$analysis_id'"</span>;</div>
+<div class="line"></div>
+<div class="line"> $self->dbc->do($sql);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a66f32625d1fbafc4fafbbc23ac11b442"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::default_input_column_mapping </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_input_column_mapping" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_input_column_mapping-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_input_column_mapping-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_input_column_mapping-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a66f32625d1fbafc4fafbbc23ac11b442">default_input_column_mapping</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $driver = $self->dbc->driver();</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'last_update'</span> => {</div>
+<div class="line"> <span class="stringliteral">'mysql'</span> => <span class="stringliteral">"UNIX_TIMESTAMP()-UNIX_TIMESTAMP(last_update) seconds_since_last_update "</span>,</div>
+<div class="line"> <span class="stringliteral">'sqlite'</span> => <span class="stringliteral">"strftime('%s','now')-strftime('%s',last_update) seconds_since_last_update "</span>,</div>
+<div class="line"> <span class="stringliteral">'pgsql'</span> => <span class="stringliteral">"EXTRACT(EPOCH FROM CURRENT_TIMESTAMP - last_update) seconds_since_last_update "</span>,</div>
+<div class="line"> }->{$driver},</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7d096d983b7596fa83094ebbb8ebb06a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a7d096d983b7596fa83094ebbb8ebb06a">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'analysis_stats'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae2e16bd96ffd64af54c59ba31f6becb1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::fetch_all_by_suitability_rc_id_meadow_type </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_all_by_suitability_rc_id_meadow_type" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_all_by_suitability_rc_id_meadow_type-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_all_by_suitability_rc_id_meadow_type-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_all_by_suitability_rc_id_meadow_type-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#ae2e16bd96ffd64af54c59ba31f6becb1">fetch_all_by_suitability_rc_id_meadow_type</a> {</div>
+<div class="line"> my ($self, $resource_class_id, $meadow_type) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $join_and_filter_sql = <span class="stringliteral">"JOIN analysis_base USING (analysis_id) WHERE "</span></div>
+<div class="line"> .( $resource_class_id ? <span class="stringliteral">"resource_class_id=$resource_class_id AND "</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> .( $meadow_type ? <span class="stringliteral">"(meadow_type IS NULL OR meadow_type='$meadow_type') AND "</span> : <span class="stringliteral">''</span>);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # the ones that clearly have work to do:</span></div>
+<div class="line"><span class="preprocessor"></span> my $primary_sql = <span class="stringliteral">"num_required_workers>0 AND status in ('READY', 'WORKING') "</span></div>
+<div class="line"> .<span class="stringliteral">"ORDER BY priority DESC, "</span>.( ($self->dbc->driver eq <span class="stringliteral">'mysql'</span>) ? <span class="stringliteral">'RAND()'</span> : <span class="stringliteral">'RANDOM()'</span> );</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # the ones that may have work to do after a sync:</span></div>
+<div class="line"><span class="preprocessor"></span> my $secondary_sql = <span class="stringliteral">"status in ('LOADING', 'BLOCKED', 'ALL_CLAIMED', 'SYNCHING') "</span></div>
+<div class="line"> .<span class="stringliteral">"ORDER BY last_update"</span>; # FIXME: could mix in a.priority <span class="keywordflow">if</span> sync is not too expensive?</div>
+<div class="line"></div>
+<div class="line"> my $primary_results = $self->fetch_all( $join_and_filter_sql . $primary_sql );</div>
+<div class="line"> my $secondary_results = $self->fetch_all( $join_and_filter_sql . $secondary_sql );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> [ @$primary_results, @$secondary_results ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a08e32841d6e713fc8b4eada7a3057d8d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::increase_required_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-increase_required_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-increase_required_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-increase_required_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-increase_required_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a08e32841d6e713fc8b4eada7a3057d8d">increase_required_workers</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> my $analysis_id = shift;</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"UPDATE analysis_stats SET num_required_workers=num_required_workers+1 "</span>.</div>
+<div class="line"> <span class="stringliteral">"WHERE analysis_id='$analysis_id' "</span>;</div>
+<div class="line"></div>
+<div class="line"> $self->dbc->do($sql);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aff5f1a7e1f8579cd228352678cce7b78"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::increase_running_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-increase_running_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-increase_running_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-increase_running_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-increase_running_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#aff5f1a7e1f8579cd228352678cce7b78">increase_running_workers</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> my $analysis_id = shift;</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"UPDATE analysis_stats SET num_running_workers = num_running_workers + 1 "</span>.</div>
+<div class="line"> <span class="stringliteral">" WHERE analysis_id='$analysis_id'"</span>;</div>
+<div class="line"></div>
+<div class="line"> $self->dbc->do($sql);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a57f38be49bb6727b4e1dd853b1ad77b3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::interval_update_work_done </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : int $analysis_id
+ Arg [2] : int $jobs_done_in_interval
+ Arg [3] : int $interval_msec
+ Arg [4] : int $fetching_msec
+ Arg [5] : int $running_msec
+ Arg [6] : int $writing_msec
+ Arg [7] : real $weight_factor [optional]
+ Example :</pre><div class="fragment"><div class="line">$statsDBA->interval_update_work_done($analysis_id, $jobs_done, $interval_msec, $fetching_msec, $running_msec, $writing_msec);</div>
+</div><!-- fragment --> <pre> Description : does a database update to recalculate the avg_msec_per_job and done_job_count
+ does an interval equation by multiplying out the previous done_job_count with the
+ previous avg_msec_per_job and then expanding by new interval values to give a better average.
+ Caller : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></pre><pre> </pre><div id="codesection-interval_update_work_done" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-interval_update_work_done-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-interval_update_work_done-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-interval_update_work_done-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a57f38be49bb6727b4e1dd853b1ad77b3">interval_update_work_done</a> {</div>
+<div class="line"> my ($self, $analysis_id, $job_count, $interval_msec, $fetching_msec, $running_msec, $writing_msec, $weight_factor) = @_;</div>
+<div class="line"></div>
+<div class="line"> $weight_factor ||= 3; # makes it more sensitive to the dynamics of the farm</div>
+<div class="line"></div>
+<div class="line"> my $sql = $self->db->hive_use_triggers()</div>
+<div class="line"> ? qq{</div>
+<div class="line"> UPDATE analysis_stats SET</div>
+<div class="line"> avg_msec_per_job = (((done_job_count*avg_msec_per_job)/$weight_factor + $interval_msec) / (done_job_count/$weight_factor + $job_count)), </div>
+<div class="line"> avg_input_msec_per_job = (((done_job_count*avg_input_msec_per_job)/$weight_factor + $fetching_msec) / (done_job_count/$weight_factor + $job_count)), </div>
+<div class="line"> avg_run_msec_per_job = (((done_job_count*avg_run_msec_per_job)/$weight_factor + $running_msec) / (done_job_count/$weight_factor + $job_count)), </div>
+<div class="line"> avg_output_msec_per_job = (((done_job_count*avg_output_msec_per_job)/$weight_factor + $writing_msec) / (done_job_count/$weight_factor + $job_count))</div>
+<div class="line"> WHERE analysis_id= $analysis_id</div>
+<div class="line"> }</div>
+<div class="line"> : qq{</div>
+<div class="line"> UPDATE analysis_stats SET</div>
+<div class="line"> avg_msec_per_job = (((done_job_count*avg_msec_per_job)/$weight_factor + $interval_msec) / (done_job_count/$weight_factor + $job_count)), </div>
+<div class="line"> avg_input_msec_per_job = (((done_job_count*avg_input_msec_per_job)/$weight_factor + $fetching_msec) / (done_job_count/$weight_factor + $job_count)), </div>
+<div class="line"> avg_run_msec_per_job = (((done_job_count*avg_run_msec_per_job)/$weight_factor + $running_msec) / (done_job_count/$weight_factor + $job_count)), </div>
+<div class="line"> avg_output_msec_per_job = (((done_job_count*avg_output_msec_per_job)/$weight_factor + $writing_msec) / (done_job_count/$weight_factor + $job_count)), </div>
+<div class="line"> ready_job_count = ready_job_count - $job_count, </div>
+<div class="line"> done_job_count = done_job_count + $job_count </div>
+<div class="line"> WHERE analysis_id= $analysis_id</div>
+<div class="line"> };</div>
+<div class="line"></div>
+<div class="line"> $self->dbc->do($sql);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9670adf2613b9d268ca2195c33099df5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::object_class </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-object_class" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-object_class-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-object_class-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-object_class-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a9670adf2613b9d268ca2195c33099df5">object_class</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'Bio::EnsEMBL::Hive::AnalysisStats'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aed7915b07ea5296ca56e90b46f08553b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a> Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::refresh </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a> object
+ Description: reload the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">AnalysisStats</a> object from the database
+ Returntype : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a> object - same one with reloaded data</pre><pre> </pre><div id="codesection-refresh" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-refresh-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-refresh-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-refresh-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#aed7915b07ea5296ca56e90b46f08553b">refresh</a> {</div>
+<div class="line"> my ($self, $stats) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $new_stats = $self->fetch_by_analysis_id( $stats->analysis_id ); # fetch into a separate <span class="keywordtype">object</span></div>
+<div class="line"></div>
+<div class="line"> %$stats = %$new_stats; # copy the data over</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $stats;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab81f838278b0c4e6791cac46713939fa"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::update </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a> object
+ Example :</pre><div class="fragment"></div><!-- fragment --> <pre> Description:
+ Returntype : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a>
+ Exceptions :
+ Caller :</pre><pre> </pre><div id="codesection-update" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-update-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-update-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-update-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#ab81f838278b0c4e6791cac46713939fa">update</a> {</div>
+<div class="line"> my ($self, $stats) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $hive_capacity = $stats->hive_capacity;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span> ($stats->behaviour eq <span class="stringliteral">"DYNAMIC"</span>) {</div>
+<div class="line"></div>
+<div class="line"> my $max_hive_capacity = $stats->avg_input_msec_per_job</div>
+<div class="line"> ? int($stats->input_capacity * $stats->avg_msec_per_job / $stats->avg_input_msec_per_job)</div>
+<div class="line"> : $hive_capacity;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span> ($stats->avg_output_msec_per_job) {</div>
+<div class="line"> my $max_hive_capacity2 = int($stats->output_capacity * $stats->avg_msec_per_job / $stats->avg_output_msec_per_job);</div>
+<div class="line"> <span class="keywordflow">if</span> ($max_hive_capacity2 < $max_hive_capacity) {</div>
+<div class="line"> $max_hive_capacity = $max_hive_capacity2;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $stats->hive_capacity( <span class="keywordtype">int</span>( ($hive_capacity+$max_hive_capacity+1)/2 ) );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"UPDATE analysis_stats SET status='"</span>.$stats->status.<span class="stringliteral">"' "</span>;</div>
+<div class="line"> $sql .= <span class="stringliteral">",batch_size="</span> . $stats->batch_size();</div>
+<div class="line"> $sql .= <span class="stringliteral">",hive_capacity="</span> . (defined($stats->hive_capacity()) ? $stats->hive_capacity() : <span class="stringliteral">'NULL'</span>);</div>
+<div class="line"></div>
+<div class="line"> $sql .= <span class="stringliteral">",avg_msec_per_job="</span> . $stats->avg_msec_per_job();</div>
+<div class="line"> $sql .= <span class="stringliteral">",avg_input_msec_per_job="</span> . $stats->avg_input_msec_per_job();</div>
+<div class="line"> $sql .= <span class="stringliteral">",avg_run_msec_per_job="</span> . $stats->avg_run_msec_per_job();</div>
+<div class="line"> $sql .= <span class="stringliteral">",avg_output_msec_per_job="</span> . $stats->avg_output_msec_per_job();</div>
+<div class="line"></div>
+<div class="line"> unless( $self->db->hive_use_triggers() ) {</div>
+<div class="line"> $sql .= <span class="stringliteral">",total_job_count="</span> . $stats->total_job_count();</div>
+<div class="line"> $sql .= <span class="stringliteral">",semaphored_job_count="</span> . $stats->semaphored_job_count();</div>
+<div class="line"> $sql .= <span class="stringliteral">",ready_job_count="</span> . $stats->ready_job_count();</div>
+<div class="line"> $sql .= <span class="stringliteral">",done_job_count="</span> . $stats->done_job_count();</div>
+<div class="line"> $sql .= <span class="stringliteral">",failed_job_count="</span> . $stats->failed_job_count();</div>
+<div class="line"></div>
+<div class="line"> $stats->num_running_workers( $self->db->get_Queen->count_running_workers( $stats->analysis_id() ) );</div>
+<div class="line"> $sql .= <span class="stringliteral">",num_running_workers="</span> . $stats->num_running_workers();</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $sql .= <span class="stringliteral">",num_required_workers="</span> . $stats->num_required_workers();</div>
+<div class="line"> $sql .= <span class="stringliteral">",last_update=CURRENT_TIMESTAMP"</span>;</div>
+<div class="line"> $sql .= <span class="stringliteral">",sync_lock='0'"</span>;</div>
+<div class="line"> $sql .= <span class="stringliteral">" WHERE analysis_id='"</span>.$stats->analysis_id.<span class="stringliteral">"' "</span>;</div>
+<div class="line"></div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"> $sth = $self->prepare(<span class="stringliteral">"INSERT INTO analysis_stats_monitor SELECT CURRENT_TIMESTAMP, analysis_stats.* from analysis_stats WHERE analysis_id = "</span>.$stats->analysis_id);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"> $stats->seconds_since_last_update(0); #not exact but good enough :)</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac0868a1d8302c76a87eb04f1975b89c7"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor::update_status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-update_status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-update_status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-update_status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-update_status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#ac0868a1d8302c76a87eb04f1975b89c7">update_status</a> {</div>
+<div class="line"> my ($self, $analysis_id, $status) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"UPDATE analysis_stats SET status='$status' "</span>;</div>
+<div class="line"> $sql .= <span class="stringliteral">" WHERE analysis_id='$analysis_id' "</span>;</div>
+<div class="line"></div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"> $sth->finish;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_analysis_stats_adaptor_8pm.html">AnalysisStatsAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">AnalysisStatsAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor =
+[
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+  <span id="projectnumber">1.9</span>
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+<div class="title">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae3e95ef6cee275aa2ace188e45da854a">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+  <span id="projectnumber">1.9</span>
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+<div class="title">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor Class Reference</div> </div>
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+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor_inherit__map" alt="Inheritance graph"/></div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor_coll__map">
+</map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:ae3e95ef6cee275aa2ace188e45da854a"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae3e95ef6cee275aa2ace188e45da854a">default_table_name</a> ()</td></tr>
+<tr class="separator:ae3e95ef6cee275aa2ace188e45da854a"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a129b813103eead72607723d43d3a6567"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a> ()</td></tr>
+<tr class="separator:a129b813103eead72607723d43d3a6567"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac73267d0e33aad126c188108f7e7c468"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a> ()</td></tr>
+<tr class="separator:ac73267d0e33aad126c188108f7e7c468"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2f77cbefb20d4b4e3a40cf75ce420036"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a> ()</td></tr>
+<tr class="separator:a2f77cbefb20d4b4e3a40cf75ce420036"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1f8bbd7bad6d23b679d4c07ab4121085"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a> ()</td></tr>
+<tr class="separator:a1f8bbd7bad6d23b679d4c07ab4121085"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac7e056384281180e1b314889fc7c317f"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a> ()</td></tr>
+<tr class="separator:ac7e056384281180e1b314889fc7c317f"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9ee7f9cfe42ad4993d0b544acfb4e1f5"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a> ()</td></tr>
+<tr class="separator:a9ee7f9cfe42ad4993d0b544acfb4e1f5"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:acd1bde351fcbdfddf8fa9896c8716514"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a> ()</td></tr>
+<tr class="separator:acd1bde351fcbdfddf8fa9896c8716514"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ada55ab8c29c95535953efb0ca8c1d805"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a> ()</td></tr>
+<tr class="separator:ada55ab8c29c95535953efb0ca8c1d805"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae98ea2fa8c6a85c6df918b9816bd6cbf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a> ()</td></tr>
+<tr class="separator:ae98ea2fa8c6a85c6df918b9816bd6cbf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae47ff32866fc8b69d8463680b5ead1d2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a> ()</td></tr>
+<tr class="separator:ae47ff32866fc8b69d8463680b5ead1d2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7da3298fc1c03c9e7e07123fb710e9a5"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a> ()</td></tr>
+<tr class="separator:a7da3298fc1c03c9e7e07123fb710e9a5"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a348c46fdc789f2eb970dfcc5260aaa28"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a> ()</td></tr>
+<tr class="separator:a348c46fdc789f2eb970dfcc5260aaa28"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5675f57702aa4cae6bfc1e39eb420bde"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a> ()</td></tr>
+<tr class="separator:a5675f57702aa4cae6bfc1e39eb420bde"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a18c6bfae797d67669e16242c2390c379"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a> ()</td></tr>
+<tr class="separator:a18c6bfae797d67669e16242c2390c379"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aadc8dac52ad2c57bff954060d60af436"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a> ()</td></tr>
+<tr class="separator:aadc8dac52ad2c57bff954060d60af436"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a29854e14eb6854bc6871db82fdb89d1f"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a> ()</td></tr>
+<tr class="separator:a29854e14eb6854bc6871db82fdb89d1f"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1e7b244d27dcc1244453f725d81d3e54"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a> ()</td></tr>
+<tr class="separator:a1e7b244d27dcc1244453f725d81d3e54"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab19a4a6d447c8661574a97ae159234f3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a> ()</td></tr>
+<tr class="separator:ab19a4a6d447c8661574a97ae159234f3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab8f4cc3813b7d1ad259b02e4a24112f2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> ()</td></tr>
+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23e67bcbf6294126212da34c0c5a2a90"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a> ()</td></tr>
+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeac6bf08072f89a153165ea39b8ed7a1"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> ()</td></tr>
+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ The base class for all other Object- or NakedTable- adaptors.
+ Performs the low-level SQL needed to retrieve and store data in tables.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a348c46fdc789f2eb970dfcc5260aaa28"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::_table_info_loader </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_table_info_loader" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_table_info_loader-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_table_info_loader-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_table_info_loader-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $dbc = $self->dbc();</div>
+<div class="line"> my $dbh = $dbc->db_handle();</div>
+<div class="line"> my $driver = $dbc->driver();</div>
+<div class="line"> my $dbname = $dbc->dbname();</div>
+<div class="line"> my $table_name = $self->table_name();</div>
+<div class="line"></div>
+<div class="line"> my %<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a> = ();</div>
+<div class="line"> my %name2type = ();</div>
+<div class="line"> my $autoinc_id = <span class="stringliteral">''</span>;</div>
+<div class="line"> my @<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a> = $dbh->primary_key(undef, undef, $table_name);</div>
+<div class="line"></div>
+<div class="line"> my $sth = $dbh->column_info(undef, undef, $table_name, <span class="charliteral">'%'</span>);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"> <span class="keywordflow">while</span> (my $row = $sth->fetchrow_hashref()) {</div>
+<div class="line"> my ($position, $column_name, $column_type, $is_ai) = @$row{<span class="stringliteral">'ORDINAL_POSITION'</span>,<span class="stringliteral">'COLUMN_NAME'</span>, <span class="stringliteral">'TYPE_NAME'</span>, <span class="stringliteral">'mysql_is_auto_increment'</span>};</div>
+<div class="line"></div>
+<div class="line"> $column_set{$column_name} = 1;</div>
+<div class="line"> $name2type{$column_name} = $column_type;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $is_ai # careful! This is only supported by DBD::mysql and will not work with other drivers</div>
+<div class="line"> or ($column_name eq $table_name.<span class="stringliteral">'_id'</span>)</div>
+<div class="line"> or ($table_name eq <span class="stringliteral">'analysis_base'</span> and $column_name eq <span class="stringliteral">'analysis_id'</span>) ) { # a special <span class="keywordflow">case</span> (historical)</div>
+<div class="line"> $autoinc_id = $column_name; # careful! This is only supported by DBD::mysql and will not work with other drivers</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"></div>
+<div class="line"> $self->column_set( \%<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a> );</div>
+<div class="line"> $self->primary_key( \@primary_key );</div>
+<div class="line"> $self->autoinc_id( $autoinc_id );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7da3298fc1c03c9e7e07123fb710e9a5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::autoinc_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-autoinc_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-autoinc_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-autoinc_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-autoinc_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) { # setter</div>
+<div class="line"> $self->{_autoinc_id} = shift @_;</div>
+<div class="line"> } elsif( !defined( $self->{_autoinc_id} ) ) {</div>
+<div class="line"> $self->_table_info_loader();</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_autoinc_id};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4805f85a21ec6b85814f32312ee36711"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::AUTOLOAD </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-AUTOLOAD" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-AUTOLOAD-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-AUTOLOAD-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-AUTOLOAD-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> {</div>
+<div class="line"> our $AUTOLOAD;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($AUTOLOAD =~ /::fetch(_all)?(?:_by_(\w+?))?(?:_HASHED_FROM_(\w+?))?(?:_TO_(\w+?))?$/) {</div>
+<div class="line"> my $all = $1;</div>
+<div class="line"> my $filter_string = $2;</div>
+<div class="line"> my $key_string = $3;</div>
+<div class="line"> my $value_column = $4;</div>
+<div class="line"></div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> my $column_set = $self->column_set();</div>
+<div class="line"></div>
+<div class="line"> my $filter_components = $filter_string && [ split(/_AND_/i, $filter_string) ];</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $column_name ( @$filter_components ) {</div>
+<div class="line"> unless($column_set->{$column_name}) {</div>
+<div class="line"> die <span class="stringliteral">"unknown column '$column_name'"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> my $key_components = $key_string && [ split(/_AND_/i, $key_string) ];</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $column_name ( @$key_components ) {</div>
+<div class="line"> unless($column_set->{$column_name}) {</div>
+<div class="line"> die <span class="stringliteral">"unknown column '$column_name'"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">if</span>($value_column && !$column_set->{$value_column}) {</div>
+<div class="line"> die <span class="stringliteral">"unknown column '$value_column'"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"># warn "Setting up '$AUTOLOAD' method\n";</span></div>
+<div class="line"><span class="preprocessor"></span> $AUTOLOAD = sub {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_all(</div>
+<div class="line"> join(<span class="stringliteral">' AND '</span>, map { <span class="stringliteral">"$filter_components->[$_]='$_[$_]'"</span> } 0..scalar(@$filter_components)-1),</div>
+<div class="line"> !$all,</div>
+<div class="line"> $key_components,</div>
+<div class="line"> $value_column</div>
+<div class="line"> );</div>
+<div class="line"> };</div>
+<div class="line"> <span class="keywordflow">goto</span> &$AUTOLOAD; # restart the <span class="keyword">new</span> method</div>
+<div class="line"></div>
+<div class="line"> } elsif($AUTOLOAD =~ /::count_all_by_(\w+)$/) {</div>
+<div class="line"> my $filter_string = $1;</div>
+<div class="line"></div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> my $column_set = $self->column_set();</div>
+<div class="line"></div>
+<div class="line"> my $filter_components = $filter_string && [ split(/_AND_/i, $filter_string) ];</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $column_name ( @$filter_components ) {</div>
+<div class="line"> unless($column_set->{$column_name}) {</div>
+<div class="line"> die <span class="stringliteral">"unknown column '$column_name'"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"># warn "Setting up '$AUTOLOAD' method\n";</span></div>
+<div class="line"><span class="preprocessor"></span> $AUTOLOAD = sub {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> <span class="keywordflow">return</span> $self->count_all(</div>
+<div class="line"> join(<span class="stringliteral">' AND '</span>, map { <span class="stringliteral">"$filter_components->[$_]='$_[$_]'"</span> } 0..scalar(@$filter_components)-1),</div>
+<div class="line"> );</div>
+<div class="line"> };</div>
+<div class="line"> <span class="keywordflow">goto</span> &$AUTOLOAD; # restart the <span class="keyword">new</span> method</div>
+<div class="line"></div>
+<div class="line"> } elsif($AUTOLOAD =~ /::remove_all_by_(\w+)$/) {</div>
+<div class="line"> my $filter_name = $1;</div>
+<div class="line"></div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> my $column_set = $self->column_set();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($column_set->{$filter_name}) {</div>
+<div class="line"><span class="preprocessor"># warn "Setting up '$AUTOLOAD' method\n";</span></div>
+<div class="line"><span class="preprocessor"></span> $AUTOLOAD = sub { my ($self, $filter_value) = @_; <span class="keywordflow">return</span> $self->remove_all(<span class="stringliteral">"$filter_name='$filter_value'"</span>); };</div>
+<div class="line"> <span class="keywordflow">goto</span> &$AUTOLOAD; # restart the <span class="keyword">new</span> method</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> die <span class="stringliteral">"unknown column '$filter_name'"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> } elsif($AUTOLOAD =~ /::update_(\w+)$/) {</div>
+<div class="line"> my @columns_to_update = split(/_AND_/i, $1);</div>
+<div class="line"><span class="preprocessor"># warn "Setting up '$AUTOLOAD' method\n";</span></div>
+<div class="line"><span class="preprocessor"></span> $AUTOLOAD = sub { my ($self, $object) = @_; <span class="keywordflow">return</span> $self->update($object, @columns_to_update); };</div>
+<div class="line"> <span class="keywordflow">goto</span> &$AUTOLOAD; # restart the <span class="keyword">new</span> method</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"sub '$AUTOLOAD' not implemented"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a73ed3c029cb8e6ba86cfd3159de577b2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::check_object_present_in_db </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-check_object_present_in_db" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-check_object_present_in_db-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-check_object_present_in_db-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-check_object_present_in_db-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> { # <span class="keywordflow">return</span> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>/undef <span class="keywordflow">if</span> the table has <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a> or just 1/undef <span class="keywordflow">if</span> not</div>
+<div class="line"> my ( $self, $object ) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $table_name = $self->table_name();</div>
+<div class="line"> my $column_set = $self->column_set();</div>
+<div class="line"> my $autoinc_id = $self->autoinc_id();</div>
+<div class="line"></div>
+<div class="line"> my $non_autoinc_columns = [ grep { $_ ne $autoinc_id } keys %$column_set ];</div>
+<div class="line"> my $non_autoinc_values = $self->slicer( $object, $non_autoinc_columns );</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">'SELECT '</span>.($autoinc_id or 1).<span class="stringliteral">" FROM $table_name WHERE "</span>.</div>
+<div class="line"> # we look <span class="keywordflow">for</span> identical contents, so must skip the <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a> columns when fetching:</div>
+<div class="line"> join(<span class="stringliteral">' AND '</span>, map { my $v=$non_autoinc_values->[$_]; <span class="stringliteral">"$non_autoinc_columns->[$_] "</span>.(defined($v) ? <span class="stringliteral">"='$v'"</span> : <span class="stringliteral">'IS NULL'</span>) } (0..@$non_autoinc_columns-1) );</div>
+<div class="line"></div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"></div>
+<div class="line"> my ($return_value) = $sth->fetchrow_array();</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $return_value;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ada55ab8c29c95535953efb0ca8c1d805"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::column_set </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-column_set" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-column_set-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-column_set-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-column_set-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) { # setter</div>
+<div class="line"> $self->{_column_set} = shift @_;</div>
+<div class="line"> } elsif( !defined( $self->{_column_set} ) ) {</div>
+<div class="line"> $self->_table_info_loader();</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_column_set};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a5675f57702aa4cae6bfc1e39eb420bde"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::count_all </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-count_all" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-count_all-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-count_all-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-count_all-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a> {</div>
+<div class="line"> my ($self, $constraint) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $table_name = $self->table_name();</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"SELECT COUNT(*) FROM $table_name"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($constraint) {</div>
+<div class="line"><span class="preprocessor"> # in case $constraint contains any kind of JOIN (regular, LEFT, RIGHT, etc) do not put WHERE in front:</span></div>
+<div class="line"><span class="preprocessor"></span> $sql .= (($constraint=~/\bJOIN\b/i) ? <span class="charliteral">' '</span> : <span class="stringliteral">' WHERE '</span>) . $constraint;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # warn "SQL: $sql\n";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute; </div>
+<div class="line"> my ($count) = $sth->fetchrow_array();</div>
+<div class="line"> $sth->finish; </div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $count;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2f77cbefb20d4b4e3a40cf75ce420036"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::default_input_column_mapping </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_input_column_mapping" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_input_column_mapping-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_input_column_mapping-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_input_column_mapping-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"><span class="preprocessor"> # 'original_column1' => "original_column1*10 AS c1_times_ten",</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # 'original_column2' => "original_column2+1 AS c2_plus_one",</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # ...</span></div>
+<div class="line"><span class="preprocessor"></span> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a129b813103eead72607723d43d3a6567"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::default_insertion_method </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_insertion_method" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_insertion_method-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_insertion_method-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_insertion_method-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'INSERT_IGNORE'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac73267d0e33aad126c188108f7e7c468"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::default_overflow_limit </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_overflow_limit" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_overflow_limit-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_overflow_limit-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_overflow_limit-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"><span class="preprocessor"> # 'overflow_column1_name' => column1_size,</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # 'overflow_column2_name' => column2_size,</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # ...</span></div>
+<div class="line"><span class="preprocessor"></span> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae3e95ef6cee275aa2ace188e45da854a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae3e95ef6cee275aa2ace188e45da854a">default_table_name</a> {</div>
+<div class="line"> die <span class="stringliteral">"Please define table_name either by setting it via table_name() method or by redefining default_table_name() in your adaptor class"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aeac6bf08072f89a153165ea39b8ed7a1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::DESTROY </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-DESTROY" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-DESTROY-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-DESTROY-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-DESTROY-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> { } # to simplify <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a18c6bfae797d67669e16242c2390c379"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::fetch_all </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_all" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_all-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_all-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_all-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a> {</div>
+<div class="line"> my ($self, $constraint, $one_per_key, $key_list, $value_column) = @_;</div>
+<div class="line"> </div>
+<div class="line"> my $table_name = $self->table_name();</div>
+<div class="line"> my $input_column_mapping = $self->input_column_mapping();</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">'SELECT '</span> . join(<span class="stringliteral">', '</span>, map { $input_column_mapping->{$_} <span class="comment">// "$table_name.$_" } keys %{$self->column_set()}) . " FROM $table_name";</span></div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($constraint) { </div>
+<div class="line"><span class="preprocessor"> # in case $constraint contains any kind of JOIN (regular, LEFT, RIGHT, etc) do not put WHERE in front:</span></div>
+<div class="line"><span class="preprocessor"></span> $sql .= (($constraint=~/\bJOIN\b/i or $constraint=~/^LIMIT|ORDER|GROUP/) ? <span class="charliteral">' '</span> : <span class="stringliteral">' WHERE '</span>) . $constraint;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # warn "SQL: $sql\n";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute; </div>
+<div class="line"></div>
+<div class="line"> my @overflow_columns = keys %{ $self->overflow_limit() };</div>
+<div class="line"> my $overflow_adaptor = scalar(@overflow_columns) && $self->db->get_AnalysisDataAdaptor();</div>
+<div class="line"></div>
+<div class="line"> my $result_struct; # will be autovivified to the correct data structure</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>(my $hashref = $sth->fetchrow_hashref) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $overflow_key (@overflow_columns) {</div>
+<div class="line"> <span class="keywordflow">if</span>($hashref->{$overflow_key} =~ /^_ext(?:\w+)_data_id (\d+)$/) {</div>
+<div class="line"> $hashref->{$overflow_key} = $overflow_adaptor->fetch_by_analysis_data_id_TO_data($1);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $pptr = \$result_struct;</div>
+<div class="line"> <span class="keywordflow">if</span>($key_list) {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $syll (@$key_list) {</div>
+<div class="line"> $pptr = \$$pptr->{$hashref->{$syll}}; # <span class="keyword">using</span> pointer-to-pointer to enforce same-level vivification</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> my $object = $value_column</div>
+<div class="line"> ? $hashref->{$value_column}</div>
+<div class="line"> : $self->objectify($hashref);</div>
+<div class="line"> <span class="keywordflow">if</span>($one_per_key) {</div>
+<div class="line"> $$pptr = $object;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> push @$$pptr, $object;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> $sth->finish; </div>
+<div class="line"></div>
+<div class="line"> unless(defined($result_struct)) {</div>
+<div class="line"> <span class="keywordflow">if</span>($key_list and scalar(@$key_list)) {</div>
+<div class="line"> $result_struct = {};</div>
+<div class="line"> } elsif(!$one_per_key) {</div>
+<div class="line"> $result_struct = [];</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $result_struct; # either listref or hashref is returned, depending on the call parameters</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a29854e14eb6854bc6871db82fdb89d1f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::fetch_by_dbID </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_by_dbID" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_by_dbID-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_by_dbID-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_by_dbID-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a> {</div>
+<div class="line"> my $self = shift @_; # the rest in @_ should be primary_key column values</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_all( $self->primary_key_constraint( \@_ ), 1 );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac7e056384281180e1b314889fc7c317f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::input_column_mapping </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-input_column_mapping" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-input_column_mapping-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-input_column_mapping-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-input_column_mapping-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) { # setter</div>
+<div class="line"> $self->{_input_column_mapping} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_input_column_mapping} || $self->default_input_column_mapping();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="acd1bde351fcbdfddf8fa9896c8716514"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::insertion_method </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-insertion_method" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-insertion_method-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-insertion_method-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-insertion_method-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) { # setter</div>
+<div class="line"> $self->{_insertion_method} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_insertion_method} || $self->default_insertion_method();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1f8bbd7bad6d23b679d4c07ab4121085"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::overflow_limit </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-overflow_limit" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-overflow_limit-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-overflow_limit-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-overflow_limit-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) { # setter</div>
+<div class="line"> $self->{_overflow_limit} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_overflow_limit} || $self->default_overflow_limit();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae98ea2fa8c6a85c6df918b9816bd6cbf"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::primary_key </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-primary_key" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-primary_key-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-primary_key-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-primary_key-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub primary_key { # not necessarily <span class="keyword">auto</span>-incrementing</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) { # setter</div>
+<div class="line"> $self->{_primary_key} = shift @_;</div>
+<div class="line"> } elsif( !defined( $self->{_primary_key} ) ) {</div>
+<div class="line"> $self->_table_info_loader();</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_primary_key};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aadc8dac52ad2c57bff954060d60af436"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::primary_key_constraint </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-primary_key_constraint" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-primary_key_constraint-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-primary_key_constraint-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-primary_key_constraint-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $sliceref = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $primary_key = $self->primary_key(); # Attention: the order of primary_key columns of your call should match the order in the table definition!</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@$primary_key) {</div>
+<div class="line"> <span class="keywordflow">return</span> join (<span class="stringliteral">' AND '</span>, map { $primary_key->[$_].<span class="stringliteral">"='"</span>.$sliceref->[$_].<span class="stringliteral">"'"</span> } (0..scalar(@$primary_key)-1));</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> my $table_name = $self->table_name();</div>
+<div class="line"> die <span class="stringliteral">"Table '$table_name' doesn't have a primary_key"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab19a4a6d447c8661574a97ae159234f3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::remove </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-remove" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-remove-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-remove-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-remove-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">remove</span> { # <span class="keyword">remove</span> the <span class="keywordtype">object</span> by primary_key</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $object = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $primary_key_constraint = $self->primary_key_constraint( $self->slicer($object, $self->primary_key()) );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->remove_all( $primary_key_constraint );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1e7b244d27dcc1244453f725d81d3e54"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::remove_all </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-remove_all" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-remove_all-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-remove_all-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-remove_all-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a> { # <span class="keyword">remove</span> entries by a constraint</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $constraint = shift @_ || 1;</div>
+<div class="line"></div>
+<div class="line"> my $table_name = $self->table_name();</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"DELETE FROM $table_name WHERE $constraint"</span>;</div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"> $sth->finish();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a23e67bcbf6294126212da34c0c5a2a90"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::store </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-store" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-store-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-store-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-store-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a> {</div>
+<div class="line"> my ($self, $object_or_list, $check_presence_in_db_first) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $objects = (ref($object_or_list) eq 'ARRAY') <span class="preprocessor"># ensure we get an array of objects to store</span></div>
+<div class="line"><span class="preprocessor"></span> ? $object_or_list</div>
+<div class="line"> : [ $object_or_list ];</div>
+<div class="line"> <span class="keywordflow">return</span> unless(scalar(@$objects));</div>
+<div class="line"></div>
+<div class="line"> my $table_name = $self->table_name();</div>
+<div class="line"> my $autoinc_id = $self->autoinc_id();</div>
+<div class="line"> my $all_storable_columns = [ grep { $_ ne $autoinc_id } keys %{ $self->column_set() } ];</div>
+<div class="line"> my $driver = $self->dbc->driver();</div>
+<div class="line"> my $insertion_method = $self->insertion_method; # INSERT, INSERT_IGNORE or REPLACE</div>
+<div class="line"> $insertion_method =~ s/_/ /g;</div>
+<div class="line"> <span class="keywordflow">if</span>($driver eq <span class="stringliteral">'sqlite'</span>) {</div>
+<div class="line"> $insertion_method =~ s/INSERT IGNORE/INSERT OR IGNORE/ig;</div>
+<div class="line"> } elsif($driver eq <span class="stringliteral">'pgsql'</span>) { # FIXME! temporary hack</div>
+<div class="line"> $insertion_method = <span class="stringliteral">'INSERT'</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my %hashed_sth = (); # <span class="keywordflow">do</span> not prepare statements until there is a real need</div>
+<div class="line"></div>
+<div class="line"> my $stored_this_time = 0;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $object (@$objects) {</div>
+<div class="line"> <span class="keywordflow">if</span>($check_presence_in_db_first and my $present = $self->check_object_present_in_db($object)) {</div>
+<div class="line"> $self->mark_stored($object, $present);</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> my ($columns_being_stored, $column_key) = (ref($object) eq 'HASH') ? $self->keys_to_columns($object) : ($all_storable_columns, '*all*');</div>
+<div class="line"> <span class="preprocessor"># warn "COLUMN_KEY='$column_key'\n";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my $this_sth;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # only prepare (once!) if we get here:</span></div>
+<div class="line"><span class="preprocessor"></span> unless($this_sth = $hashed_sth{$column_key}) {</div>
+<div class="line"><span class="preprocessor"> # By using question marks we can insert true NULLs by setting corresponding values to undefs:</span></div>
+<div class="line"><span class="preprocessor"></span> my $sql = <span class="stringliteral">"$insertion_method INTO $table_name ("</span>.join(<span class="stringliteral">', '</span>, @$columns_being_stored).<span class="stringliteral">') VALUES ('</span>.join(<span class="charliteral">','</span>, ((<span class="charliteral">'?'</span>) x scalar(@$columns_being_stored))).<span class="charliteral">')'</span>;</div>
+<div class="line"><span class="preprocessor"> # warn "STORE: $sql\n";</span></div>
+<div class="line"><span class="preprocessor"></span> $this_sth = $hashed_sth{$column_key} = $self->prepare( $sql ) or die <span class="stringliteral">"Could not prepare statement: $sql"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # warn "STORED_COLUMNS: ".join(', ', map { "`$_`" } @$columns_being_stored)."\n";</span></div>
+<div class="line"><span class="preprocessor"></span> my $values_being_stored = $self->slicer( $object, $columns_being_stored );</div>
+<div class="line"><span class="preprocessor"> # warn "STORED_VALUES: ".join(', ', map { "'$_'" } @$values_being_stored)."\n";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my $return_code = $this_sth->execute( @$values_being_stored )</div>
+<div class="line"><span class="preprocessor"> # using $return_code in boolean context allows to skip the value '0E0' ('no rows affected') that Perl treats as zero but regards as true:</span></div>
+<div class="line"><span class="preprocessor"></span> or die <span class="stringliteral">"Could not store fields\n\t{$column_key}\nwith data:\n\t("</span>.join(<span class="charliteral">','</span>, @$values_being_stored).<span class="charliteral">')'</span>;</div>
+<div class="line"> <span class="keywordflow">if</span>($return_code > 0) { # <--- <span class="keywordflow">for</span> the same reason we have to be explicitly numeric here</div>
+<div class="line"> my $liid = $autoinc_id && $self->dbc->db_handle->last_insert_id(undef, undef, $table_name, $autoinc_id);</div>
+<div class="line"> $self->mark_stored($object, $liid );</div>
+<div class="line"> ++$stored_this_time;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $sth (values %hashed_sth) {</div>
+<div class="line"> $sth->finish();</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ($object_or_list, $stored_this_time);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9ee7f9cfe42ad4993d0b544acfb4e1f5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) { # setter</div>
+<div class="line"> $self->{_table_name} = shift @_;</div>
+<div class="line"> $self->_table_info_loader();</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_table_name} || $self->default_table_name();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae47ff32866fc8b69d8463680b5ead1d2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::updatable_column_list </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-updatable_column_list" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-updatable_column_list-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-updatable_column_list-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-updatable_column_list-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a> { # it<span class="stringliteral">'s just a cashed view, you cannot set it directly</span></div>
+<div class="line"><span class="stringliteral"> my $self = shift @_;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> unless($self->{_updatable_column_list}) {</span></div>
+<div class="line"><span class="stringliteral"> my %primary_key_set = map { $_ => 1 } @{$self->primary_key()};</span></div>
+<div class="line"><span class="stringliteral"> my $column_set = $self->column_set();</span></div>
+<div class="line"><span class="stringliteral"> $self->{_updatable_column_list} = [ grep { not $primary_key_set{$_} } keys %$column_set ];</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> return $self->{_updatable_column_list};</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab8f4cc3813b7d1ad259b02e4a24112f2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor::update </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-update" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-update-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-update-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-update-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> { # <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> (some or all) non_primary columns from the primary</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $object = shift @_; # the rest in @_ should be the column names to be updated</div>
+<div class="line"></div>
+<div class="line"> my $table_name = $self->table_name();</div>
+<div class="line"> my $primary_key_constraint = $self->primary_key_constraint( $self->slicer($object, $self->primary_key()) );</div>
+<div class="line"> my $columns_to_update = scalar(@_) ? \@_ : $self->updatable_column_list();</div>
+<div class="line"> my $values_to_update = $self->slicer( $object, $columns_to_update );</div>
+<div class="line"></div>
+<div class="line"> unless(@$columns_to_update) {</div>
+<div class="line"> die <span class="stringliteral">"There are no dependent columns to update, as everything seems to belong to the primary key"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"UPDATE $table_name SET "</span>.join(<span class="stringliteral">', '</span>, map { <span class="stringliteral">"$_=?"</span> } @$columns_to_update).<span class="stringliteral">" WHERE $primary_key_constraint"</span>;</div>
+<div class="line"><span class="preprocessor"> # warn "SQL: $sql\n";</span></div>
+<div class="line"><span class="preprocessor"></span> my $sth = $self->prepare($sql);</div>
+<div class="line"><span class="preprocessor"> # warn "VALUES_TO_UPDATE: ".join(', ', map { "'$_'" } @$values_to_update)."\n";</span></div>
+<div class="line"><span class="preprocessor"></span> $sth->execute( @$values_to_update);</div>
+<div class="line"></div>
+<div class="line"> $sth->finish();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_base_adaptor_8pm.html">BaseAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">BaseAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::DBAdaptor:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor_inherit__map" alt="Inheritance graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor_inherit__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor_inherit__map">
+</map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::DBSQL::DBAdaptor:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor_coll__map">
+</map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:abf2b541c5d7e3b124323a34356e3ace6"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#abf2b541c5d7e3b124323a34356e3ace6">new</a> ()</td></tr>
+<tr class="separator:abf2b541c5d7e3b124323a34356e3ace6"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a704db480f27205d0cf17952fd54ffddf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a704db480f27205d0cf17952fd54ffddf">dbc</a> ()</td></tr>
+<tr class="separator:a704db480f27205d0cf17952fd54ffddf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5169045d2592861884a452dec9f3dd06"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a5169045d2592861884a452dec9f3dd06">hive_use_triggers</a> ()</td></tr>
+<tr class="separator:a5169045d2592861884a452dec9f3dd06"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a364f93a3a3019a023c09f7fd02313970"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a364f93a3a3019a023c09f7fd02313970">hive_use_param_stack</a> ()</td></tr>
+<tr class="separator:a364f93a3a3019a023c09f7fd02313970"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0baccc85ec9695e7ffa80c16d54cb9d9"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a0baccc85ec9695e7ffa80c16d54cb9d9">get_available_adaptors</a> ()</td></tr>
+<tr class="separator:a0baccc85ec9695e7ffa80c16d54cb9d9"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$db = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#abf2b541c5d7e3b124323a34356e3ace6">new</a>(</div>
+<div class="line"> -user => <span class="stringliteral">'root'</span>,</div>
+<div class="line"> -dbname => <span class="stringliteral">'pog'</span>,</div>
+<div class="line"> -host => <span class="stringliteral">'caldy'</span>,</div>
+<div class="line"> -driver => <span class="stringliteral">'mysql'</span>,</div>
+<div class="line">);</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This object represents the handle for a Hive system enabled database
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a704db480f27205d0cf17952fd54ffddf"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::DBAdaptor::dbc </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-dbc" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dbc-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dbc-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dbc-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a704db480f27205d0cf17952fd54ffddf">dbc</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $dbc = $self->SUPER::dbc( @_ );</div>
+<div class="line"> bless $dbc, <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::DBConnection'</span> <span class="keywordflow">if</span>( $dbc );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $dbc;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0baccc85ec9695e7ffa80c16d54cb9d9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::DBAdaptor::get_available_adaptors </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_available_adaptors" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_available_adaptors-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_available_adaptors-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_available_adaptors-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a0baccc85ec9695e7ffa80c16d54cb9d9">get_available_adaptors</a> {</div>
+<div class="line"> </div>
+<div class="line"> my %pairs = (</div>
+<div class="line"><span class="preprocessor"> # Core adaptors extended with Hive stuff:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'MetaContainer'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::MetaContainer'</span>,</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # "new" Hive adaptors (sharing the same fetching/storing code inherited from the BaseAdaptor class) :</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'AnalysisCtrlRule'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'DataflowRule'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'ResourceDescription'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'ResourceClass'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'LogMessage'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'NakedTable'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'Analysis'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'Queen'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::Queen'</span>,</div>
+<div class="line"> <span class="stringliteral">'AnalysisData'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'Accumulator'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'Meta'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor'</span>,</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # "old" Hive adaptors (having their own fetching/storing code) :</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'AnalysisJob'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'AnalysisStats'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor'</span>,</div>
+<div class="line"> );</div>
+<div class="line"> <span class="keywordflow">return</span> \%pairs;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a364f93a3a3019a023c09f7fd02313970"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::DBAdaptor::hive_use_param_stack </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-hive_use_param_stack" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-hive_use_param_stack-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-hive_use_param_stack-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-hive_use_param_stack-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a364f93a3a3019a023c09f7fd02313970">hive_use_param_stack</a> { # getter only, not setter</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> unless( defined($self->{<span class="stringliteral">'_hive_use_param_stack'</span>}) ) {</div>
+<div class="line"> my $hive_use_param_stack = $self->get_MetaAdaptor->fetch_value_by_key( <span class="stringliteral">'hive_use_param_stack'</span> );</div>
+<div class="line"> $self->{<span class="stringliteral">'_hive_use_param_stack'</span>} = $hive_use_param_stack || 0;</div>
+<div class="line"> } </div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_hive_use_param_stack'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a5169045d2592861884a452dec9f3dd06"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::DBAdaptor::hive_use_triggers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-hive_use_triggers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-hive_use_triggers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-hive_use_triggers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-hive_use_triggers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a5169045d2592861884a452dec9f3dd06">hive_use_triggers</a> { # getter only, not setter</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> unless( defined($self->{<span class="stringliteral">'_hive_use_triggers'</span>}) ) {</div>
+<div class="line"> my $hive_use_triggers = $self->get_MetaAdaptor->fetch_value_by_key( <span class="stringliteral">'hive_use_triggers'</span> );</div>
+<div class="line"> $self->{<span class="stringliteral">'_hive_use_triggers'</span>} = $hive_use_triggers || 0;</div>
+<div class="line"> } </div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_hive_use_triggers'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="abf2b541c5d7e3b124323a34356e3ace6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::DBAdaptor::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my ($class, @args) = @_;</div>
+<div class="line"></div>
+<div class="line"> my ($url, $reg_conf, $reg_type, $reg_alias, $no_sql_schema_version_check)</div>
+<div class="line"> = rearrange([<span class="stringliteral">'URL'</span>, <span class="stringliteral">'REG_CONF'</span>, <span class="stringliteral">'REG_TYPE'</span>, <span class="stringliteral">'REG_ALIAS'</span>, <span class="stringliteral">'NO_SQL_SCHEMA_VERSION_CHECK'</span>], @args);</div>
+<div class="line"></div>
+<div class="line"> $url .= <span class="stringliteral">';nosqlvc=1'</span> <span class="keywordflow">if</span>($url && $no_sql_schema_version_check);</div>
+<div class="line"></div>
+<div class="line"> my $self;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($url) {</div>
+<div class="line"> $self = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">fetch</a>($url)</div>
+<div class="line"> or die <span class="stringliteral">"Unable to connect to DBA using url='$url'\n"</span>;</div>
+<div class="line"> } elsif($reg_alias) {</div>
+<div class="line"> Bio::EnsEMBL::Registry->load_all($reg_conf) <span class="keywordflow">if</span>($reg_conf);</div>
+<div class="line"></div>
+<div class="line"> $reg_type ||= <span class="stringliteral">'hive'</span>;</div>
+<div class="line"></div>
+<div class="line"> $self = Bio::EnsEMBL::Registry->get_DBAdaptor($reg_alias, $reg_type)</div>
+<div class="line"> or die <span class="stringliteral">"Unable to connect to DBA using reg_conf='$reg_conf', reg_type='$reg_type', reg_alias='$reg_alias'\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($reg_type ne <span class="stringliteral">'hive'</span>) { # ensure we are getting a Hive adaptor even from a non-Hive Registry entry:</div>
+<div class="line"> $self = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#abf2b541c5d7e3b124323a34356e3ace6">new</a>( -dbconn => $self->dbc(), -no_sql_schema_version_check => $no_sql_schema_version_check );</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $self = $class->SUPER::new(@args)</div>
+<div class="line"> or die <span class="stringliteral">"Unable to connect to DBA using parameters ("</span>.join(<span class="stringliteral">', '</span>, @args).<span class="stringliteral">")\n"</span></div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> unless($no_sql_schema_version_check) {</div>
+<div class="line"></div>
+<div class="line"> my $dbc = $self->dbc();</div>
+<div class="line"> $url ||= $dbc->url();</div>
+<div class="line"></div>
+<div class="line"> my $code_sql_schema_version = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a0c2dc02c4e81944f9eb9fa7f670aa753">get_code_sql_schema_version</a>()</div>
+<div class="line"> || die <span class="stringliteral">"DB($url) Could not establish code_sql_schema_version, please check that 'EHIVE_ROOT_DIR' environment variable is set correctly"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $db_sql_schema_version = eval { $self->get_MetaAdaptor->fetch_value_by_key( <span class="stringliteral">'hive_sql_schema_version'</span> ); };</div>
+<div class="line"> <span class="keywordflow">if</span>($@) {</div>
+<div class="line"> <span class="keywordflow">if</span>($@ =~ /hive_meta.*doesn<span class="stringliteral">'t exist/) {</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> die "\nDB($url) The '</span>hive_meta<span class="stringliteral">' table does not seem to exist in the database yet.\nPlease patch the database up to sql_schema_version '</span>$code_sql_schema_version<span class="stringliteral">' and try again.\n";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> die "DB($url) $@";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> } elsif(!$db_sql_schema_version) {</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> die "\nDB($url) The '</span>hive_meta<span class="stringliteral">' table does not contain '</span>hive_sql_schema_version<span class="stringliteral">' entry.\nPlease investigate.\n";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> } elsif($db_sql_schema_version < $code_sql_schema_version) {</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $new_patches = Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor->get_sql_schema_patches( $db_sql_schema_version, $dbc->driver )</span></div>
+<div class="line"><span class="stringliteral"> || die "DB($url) sql_schema_version mismatch: the database'</span>s version is <span class="stringliteral">'$db_sql_schema_version'</span> but the code is already <span class="stringliteral">'$code_sql_schema_version'</span>.\n<span class="stringliteral">"</span></div>
+<div class="line"><span class="stringliteral"> ."</span>Unfortunately we cannot patch the database; you may have to create a <span class="keyword">new</span> database or agree to run older code\n<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $patcher_command = "</span>$ENV{<span class="stringliteral">'EHIVE_ROOT_DIR'</span>}/scripts/db_cmd.pl -url $url<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> die "</span>DB($url) sql_schema_version mismatch: the database's version is '$db_sql_schema_version' but the code is already '$code_sql_schema_version'.\n"</div>
+<div class="line"> ."Please upgrade the database by applying the following patches:\n\n".join("\n", map { <span class="stringliteral">"\t$patcher_command < $_"</span> } @$new_patches).<span class="stringliteral">"\n\nand try again.\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> } elsif($code_sql_schema_version < $db_sql_schema_version) {</div>
+<div class="line"></div>
+<div class="line"> die <span class="stringliteral">"DB($url) sql_schema_version mismatch: the database's version is '$db_sql_schema_version', but your code is still '$code_sql_schema_version'.\n"</span></div>
+<div class="line"> .<span class="stringliteral">"Please update the code and try again.\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_d_b_adaptor_8pm.html">DBAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">DBAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor =
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+];
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="navtree.js"></script>
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+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
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+ class="ui-resizable-handle">
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+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
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+ name="MSearchResults" id="MSearchResults">
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+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::DBConnection Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html#aa5dabd385b717af07205feec2e8fee41">protected_prepare_execute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html#a0d1860ad6f23fb2e1806171d46dbc40a">url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
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diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Bio::EnsEMBL::Hive::DBSQL::DBConnection Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+ name="MSearchResults" id="MSearchResults">
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+
+<div class="header">
+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::DBConnection Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::DBConnection:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection_inherit__map" alt="Inheritance graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection_inherit__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection_inherit__map">
+</map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::DBSQL::DBConnection:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection_coll__map">
+</map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a0d1860ad6f23fb2e1806171d46dbc40a"><td class="memItemLeft" align="right" valign="top">public String </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html#a0d1860ad6f23fb2e1806171d46dbc40a">url</a> ()</td></tr>
+<tr class="separator:a0d1860ad6f23fb2e1806171d46dbc40a"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aa5dabd385b717af07205feec2e8fee41"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html#aa5dabd385b717af07205feec2e8fee41">protected_prepare_execute</a> ()</td></tr>
+<tr class="separator:aa5dabd385b717af07205feec2e8fee41"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">my $url = $dbc->url();</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Extends the functionality of Bio::EnsEMBL::DBSQL::DBConnection with things needed by the Hive
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="aa5dabd385b717af07205feec2e8fee41"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::DBConnection::protected_prepare_execute </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-protected_prepare_execute" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-protected_prepare_execute-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-protected_prepare_execute-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-protected_prepare_execute-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html#aa5dabd385b717af07205feec2e8fee41">protected_prepare_execute</a> { # <span class="keywordflow">try</span> to resolve certain mysql <span class="stringliteral">"Deadlocks"</span> by trying again (a useful workaround even in mysql 5.1.61)</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $sql = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $retries = 3;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> (0..$retries) {</div>
+<div class="line"> eval {</div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute( @_ );</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"> 1;</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0d1860ad6f23fb2e1806171d46dbc40a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public String Bio::EnsEMBL::Hive::DBSQL::DBConnection::url </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : String $environment_variable_name_to_store_password_in (optional)
+ Example :</pre><div class="fragment"><div class="line">$url = $dbc->url;</div>
+</div><!-- fragment --> <pre> Description: Constructs a URL string for this database connection.
+ Returntype : string of format mysql://<user>:<pass><host>:<port>/<dbname>
+ or sqlite:///<dbname>
+ Exceptions : none
+ Caller : general</pre><pre> </pre><div id="codesection-url" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-url-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-url-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-url-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html#a0d1860ad6f23fb2e1806171d46dbc40a">url</a> {</div>
+<div class="line"> my ($self, $psw_env_var_name) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $url = $self->driver . <span class="stringliteral">'://'</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->username) {</div>
+<div class="line"> $url .= $self->username;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $psw_expression = $self->password) {</div>
+<div class="line"> <span class="keywordflow">if</span>($psw_env_var_name) {</div>
+<div class="line"> $ENV{$psw_env_var_name} = $psw_expression;</div>
+<div class="line"> $psw_expression = <span class="stringliteral">'${'</span>.$psw_env_var_name.<span class="charliteral">'}'</span>;</div>
+<div class="line"> }</div>
+<div class="line"> $url .= <span class="charliteral">':'</span>.$psw_expression <span class="keywordflow">if</span>($psw_expression);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $url .= <span class="charliteral">'@'</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->host) {</div>
+<div class="line"> $url .= $self->host;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->port) {</div>
+<div class="line"> $url .= <span class="charliteral">':'</span>.$self->port;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> $url .= <span class="charliteral">'/'</span> . $self->dbname;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $url;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_d_b_connection_8pm.html">DBConnection.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">DBConnection</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+<div class="title">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a529c8c386c3e60cb1a737231775bf77c">branch_name_2_code</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#ac91050686189e4d62b84fc5ac21c9399">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a1ef36bbed301036800367e22c6895f13">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a6001078bcc7bcb8fb45f46c415fb65d8">object_class</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+<tr class="separator:ae47ff32866fc8b69d8463680b5ead1d2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a> ()</td></tr>
+<tr class="separator:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a> ()</td></tr>
+<tr class="separator:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a> ()</td></tr>
+<tr class="separator:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a> ()</td></tr>
+<tr class="separator:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a> ()</td></tr>
+<tr class="separator:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a1e7b244d27dcc1244453f725d81d3e54 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> ()</td></tr>
+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a> ()</td></tr>
+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$dataflow_rule_adaptor = $db_adaptor->get_DataflowRuleAdaptor;</div>
+<div class="line">$dataflow_rule_adaptor = $dataflowRuleObj->adaptor;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Module to encapsulate all db access for persistent class DataflowRule.
+ There should be just one per application and database connection.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a529c8c386c3e60cb1a737231775bf77c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor::branch_name_2_code </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+Description: encodes a branch mnemonic name into numeric code</pre><pre> </pre><div id="codesection-branch_name_2_code" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-branch_name_2_code-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-branch_name_2_code-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-branch_name_2_code-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a529c8c386c3e60cb1a737231775bf77c">branch_name_2_code</a> {</div>
+<div class="line"></div>
+<div class="line"> shift @_ <span class="keywordflow">if</span>(ref($_[0])); # skip the first argument <span class="keywordflow">if</span> it is an object, so it works both as a method and a subroutine</div>
+<div class="line"></div>
+<div class="line"> my ($branch_name_or_code, $no_default) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ($no_default ? undef : 1) unless(defined($branch_name_or_code));</div>
+<div class="line"></div>
+<div class="line"> my $branch_code = ($branch_name_or_code=~/^\-?\d+$/)</div>
+<div class="line"> ? $branch_name_or_code</div>
+<div class="line"> : {</div>
+<div class="line"> <span class="stringliteral">'MAIN'</span> => 1,</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'ANYFAILURE'</span> => 0,</div>
+<div class="line"> <span class="stringliteral">'MEMLIMIT'</span> => -1,</div>
+<div class="line"> <span class="stringliteral">'RUNLIMIT'</span> => -2,</div>
+<div class="line"> }->{$branch_name_or_code};</div>
+<div class="line"> <span class="keywordflow">return</span> defined($branch_code) ? $branch_code : die <span class="stringliteral">"Could not map the branch_name '$branch_name_or_code' to the internal code"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac91050686189e4d62b84fc5ac21c9399"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor::default_insertion_method </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_insertion_method" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_insertion_method-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_insertion_method-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_insertion_method-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#ac91050686189e4d62b84fc5ac21c9399">default_insertion_method</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'INSERT'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1ef36bbed301036800367e22c6895f13"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a1ef36bbed301036800367e22c6895f13">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'dataflow_rule'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
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+</div>
+<a class="anchor" id="a6001078bcc7bcb8fb45f46c415fb65d8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor::object_class </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-object_class" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-object_class-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-object_class-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-object_class-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a6001078bcc7bcb8fb45f46c415fb65d8">object_class</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'Bio::EnsEMBL::Hive::DataflowRule'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_dataflow_rule_adaptor_8pm.html">DataflowRuleAdaptor.pm</a></li>
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+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor =
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+<div class="contents">
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#a9c5a35a90a18728182e12a66503ced26">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b">keys_to_columns</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2a39cbb60a5021d1cd5a4e385da4000f">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#ad90a452430769ce22f854fb0d195e905">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#a4040dc342aa0c6f479a56970e8a6c911">store_job_message</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#ad9ad5fe362cffb2edaa31c3086ad7a40">store_worker_message</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor_coll__map" alt="Collaboration graph"/></div>
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+<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html" title="Bio::EnsEMBL::Hive\l::DBSQL::NakedTableAdaptor" alt="" coords="7,187,205,229"/><area shape="rect" id="node3" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html" title="Bio::EnsEMBL::Hive\l::DBSQL::BaseAdaptor" alt="" coords="27,97,185,138"/></map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a9c5a35a90a18728182e12a66503ced26"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#a9c5a35a90a18728182e12a66503ced26">default_table_name</a> ()</td></tr>
+<tr class="separator:a9c5a35a90a18728182e12a66503ced26"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4040dc342aa0c6f479a56970e8a6c911"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#a4040dc342aa0c6f479a56970e8a6c911">store_job_message</a> ()</td></tr>
+<tr class="separator:a4040dc342aa0c6f479a56970e8a6c911"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad9ad5fe362cffb2edaa31c3086ad7a40"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#ad9ad5fe362cffb2edaa31c3086ad7a40">store_worker_message</a> ()</td></tr>
+<tr class="separator:ad9ad5fe362cffb2edaa31c3086ad7a40"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td></tr>
+<tr class="memitem:a2fd8279544ff4bd78e9b3fd09495542c inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">slicer</a> ()</td></tr>
+<tr class="separator:a2fd8279544ff4bd78e9b3fd09495542c inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad90a452430769ce22f854fb0d195e905 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#ad90a452430769ce22f854fb0d195e905">objectify</a> ()</td></tr>
+<tr class="separator:ad90a452430769ce22f854fb0d195e905 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2a39cbb60a5021d1cd5a4e385da4000f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2a39cbb60a5021d1cd5a4e385da4000f">mark_stored</a> ()</td></tr>
+<tr class="separator:a2a39cbb60a5021d1cd5a4e385da4000f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a74f3ead3ecf4d1183b667c5da544362b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b">keys_to_columns</a> ()</td></tr>
+<tr class="separator:a74f3ead3ecf4d1183b667c5da544362b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td></tr>
+<tr class="memitem:ae3e95ef6cee275aa2ace188e45da854a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae3e95ef6cee275aa2ace188e45da854a">default_table_name</a> ()</td></tr>
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+<tr class="memitem:a129b813103eead72607723d43d3a6567 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a> ()</td></tr>
+<tr class="separator:a129b813103eead72607723d43d3a6567 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac73267d0e33aad126c188108f7e7c468 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a> ()</td></tr>
+<tr class="separator:ac73267d0e33aad126c188108f7e7c468 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2f77cbefb20d4b4e3a40cf75ce420036 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a> ()</td></tr>
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+<tr class="memitem:a1f8bbd7bad6d23b679d4c07ab4121085 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a> ()</td></tr>
+<tr class="separator:a1f8bbd7bad6d23b679d4c07ab4121085 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac7e056384281180e1b314889fc7c317f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a> ()</td></tr>
+<tr class="separator:ac7e056384281180e1b314889fc7c317f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9ee7f9cfe42ad4993d0b544acfb4e1f5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a> ()</td></tr>
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+<tr class="memitem:acd1bde351fcbdfddf8fa9896c8716514 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a> ()</td></tr>
+<tr class="separator:acd1bde351fcbdfddf8fa9896c8716514 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ada55ab8c29c95535953efb0ca8c1d805 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a> ()</td></tr>
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+<tr class="memitem:ae98ea2fa8c6a85c6df918b9816bd6cbf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a> ()</td></tr>
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+<tr class="memitem:ae47ff32866fc8b69d8463680b5ead1d2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a> ()</td></tr>
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+<tr class="memitem:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a> ()</td></tr>
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+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$dba->get_LogMessageAdaptor->store_job_message($job_id, $msg, $is_error);</div>
+<div class="line"></div>
+<div class="line">$dba->get_LogMessageAdaptor->store_worker_message($worker_id, $msg, $is_error);</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is currently an "objectless" adaptor that helps to store either warning-messages or die-messages generated by jobs
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a9c5a35a90a18728182e12a66503ced26"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#a9c5a35a90a18728182e12a66503ced26">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'log_message'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4040dc342aa0c6f479a56970e8a6c911"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor::store_job_message </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-store_job_message" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-store_job_message-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-store_job_message-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-store_job_message-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#a4040dc342aa0c6f479a56970e8a6c911">store_job_message</a> {</div>
+<div class="line"> my ($self, $job_id, $msg, $is_error) = @_;</div>
+<div class="line"></div>
+<div class="line"> chomp $msg; # we don<span class="stringliteral">'t want that last "\n" in the database</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $table_name = $self->table_name();</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # Note: the timestamp '</span>time<span class="stringliteral">' column will be set automatically</span></div>
+<div class="line"><span class="stringliteral"> my $sql = qq{</span></div>
+<div class="line"><span class="stringliteral"> INSERT INTO $table_name (job_id, worker_id, retry, status, msg, is_error)</span></div>
+<div class="line"><span class="stringliteral"> SELECT job_id, worker_id, retry_count, status, ?, ?</span></div>
+<div class="line"><span class="stringliteral"> FROM job WHERE job_id=?</span></div>
+<div class="line"><span class="stringliteral"> };</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $sth = $self->prepare( $sql );</span></div>
+<div class="line"><span class="stringliteral"> $sth->execute( $msg, $is_error ? 1 : 0, $job_id );</span></div>
+<div class="line"><span class="stringliteral"> $sth->finish();</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad9ad5fe362cffb2edaa31c3086ad7a40"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor::store_worker_message </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-store_worker_message" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-store_worker_message-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-store_worker_message-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-store_worker_message-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#ad9ad5fe362cffb2edaa31c3086ad7a40">store_worker_message</a> {</div>
+<div class="line"> my ($self, $worker_id, $msg, $is_error) = @_;</div>
+<div class="line"></div>
+<div class="line"> chomp $msg; # we don<span class="stringliteral">'t want that last "\n" in the database</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $table_name = $self->table_name();</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # Note: the timestamp '</span>time<span class="stringliteral">' column will be set automatically</span></div>
+<div class="line"><span class="stringliteral"> my $sql = qq{</span></div>
+<div class="line"><span class="stringliteral"> INSERT INTO $table_name (worker_id, status, msg, is_error)</span></div>
+<div class="line"><span class="stringliteral"> SELECT worker_id, status, ?, ?</span></div>
+<div class="line"><span class="stringliteral"> FROM worker WHERE worker_id=?</span></div>
+<div class="line"><span class="stringliteral"> };</span></div>
+<div class="line"><span class="stringliteral"> my $sth = $self->prepare( $sql );</span></div>
+<div class="line"><span class="stringliteral"> $sth->execute( $msg, $is_error ? 1 : 0, $worker_id );</span></div>
+<div class="line"><span class="stringliteral"> $sth->finish();</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_log_message_adaptor_8pm.html">LogMessageAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html">LogMessageAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor =
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+<div class="title">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#afee7422722307560e830dd17c7065993">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#a872fcb522c8b0322daf1033f7e2fa41e">fetch_value_by_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b">keys_to_columns</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2a39cbb60a5021d1cd5a4e385da4000f">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#ad90a452430769ce22f854fb0d195e905">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#a68fb7396bf048cecf23f94e1d616f1a3">store_pair</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor Class Reference</div> </div>
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor:</div>
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+<tr class="memitem:ae98ea2fa8c6a85c6df918b9816bd6cbf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a> ()</td></tr>
+<tr class="separator:ae98ea2fa8c6a85c6df918b9816bd6cbf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ae47ff32866fc8b69d8463680b5ead1d2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a> ()</td></tr>
+<tr class="separator:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a> ()</td></tr>
+<tr class="separator:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a> ()</td></tr>
+<tr class="separator:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a> ()</td></tr>
+<tr class="separator:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a> ()</td></tr>
+<tr class="separator:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a> ()</td></tr>
+<tr class="separator:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a1e7b244d27dcc1244453f725d81d3e54 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a> ()</td></tr>
+<tr class="separator:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> ()</td></tr>
+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a> ()</td></tr>
+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> ()</td></tr>
+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$dba->get_MetaAdaptor->store( \@rows );</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is currently an "objectless" adaptor for storing and fetching Hive-specific metadata
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="afee7422722307560e830dd17c7065993"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#afee7422722307560e830dd17c7065993">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'hive_meta'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a872fcb522c8b0322daf1033f7e2fa41e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor::fetch_value_by_key </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_value_by_key" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_value_by_key-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_value_by_key-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_value_by_key-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#a872fcb522c8b0322daf1033f7e2fa41e">fetch_value_by_key</a> {</div>
+<div class="line"> my ($self, $meta_key) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $pair = $self->fetch_by_meta_key( $meta_key );</div>
+<div class="line"> <span class="keywordflow">return</span> $pair && $pair->{<span class="stringliteral">'meta_value'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a68fb7396bf048cecf23f94e1d616f1a3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor::store_pair </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-store_pair" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-store_pair-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-store_pair-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-store_pair-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#a68fb7396bf048cecf23f94e1d616f1a3">store_pair</a> {</div>
+<div class="line"> my ($self, $meta_key, $meta_value) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->store( { <span class="stringliteral">'meta_key'</span> => $meta_key, <span class="stringliteral">'meta_value'</span> => $meta_value } );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_meta_adaptor_8pm.html">MetaAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
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+ <div id="projectname">ensembl-hive
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+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
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+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::MetaContainer Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a>, including all inherited members.</p>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a9b86c006546292af7280396e0e86ad41">get_param_hash</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b">keys_to_columns</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2a39cbb60a5021d1cd5a4e385da4000f">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#ad90a452430769ce22f854fb0d195e905">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a2f04643ded7a65f9b80887b78b0d40ab">store_pair</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+<title>ensembl-hive: Bio::EnsEMBL::Hive::DBSQL::MetaContainer Class Reference</title>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
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+<div class="header">
+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::MetaContainer Class Reference</div> </div>
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+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::MetaContainer:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::DBSQL::MetaContainer:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container_coll__map" alt="Collaboration graph"/></div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a2b2f74be0c9bbc3330a2bfa1c97c5e99"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a2b2f74be0c9bbc3330a2bfa1c97c5e99">default_table_name</a> ()</td></tr>
+<tr class="separator:a2b2f74be0c9bbc3330a2bfa1c97c5e99"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2f04643ded7a65f9b80887b78b0d40ab"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a2f04643ded7a65f9b80887b78b0d40ab">store_pair</a> ()</td></tr>
+<tr class="separator:a2f04643ded7a65f9b80887b78b0d40ab"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9b86c006546292af7280396e0e86ad41"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a9b86c006546292af7280396e0e86ad41">get_param_hash</a> ()</td></tr>
+<tr class="separator:a9b86c006546292af7280396e0e86ad41"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td></tr>
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+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> ()</td></tr>
+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$meta_container = $db_adaptor->get_MetaContainer;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This module deals with pipeline_wide_parameters' storage and retrieval, and also stores 'schema_version' for compatibility with Core API
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a2b2f74be0c9bbc3330a2bfa1c97c5e99"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::MetaContainer::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a2b2f74be0c9bbc3330a2bfa1c97c5e99">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'meta'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9b86c006546292af7280396e0e86ad41"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::MetaContainer::get_param_hash </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: returns the content of the 'meta' table as a hash</pre><pre> </pre><div id="codesection-get_param_hash" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_param_hash-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_param_hash-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_param_hash-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a9b86c006546292af7280396e0e86ad41">get_param_hash</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $original_value = $self->fetch_all_HASHED_FROM_meta_key_TO_meta_value();</div>
+<div class="line"> my %destringified_hash = map { $_, destringify($original_value->{$_}[0]) } keys %$original_value;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> \%destringified_hash;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2f04643ded7a65f9b80887b78b0d40ab"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::MetaContainer::store_pair </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-store_pair" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-store_pair-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-store_pair-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-store_pair-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a2f04643ded7a65f9b80887b78b0d40ab">store_pair</a> {</div>
+<div class="line"> my ($self, $meta_key, $meta_value) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->store( { <span class="stringliteral">'meta_key'</span> => $meta_key, <span class="stringliteral">'meta_value'</span> => stringify( $meta_value ), <span class="stringliteral">'species_id'</span> => undef } );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_meta_container_8pm.html">MetaContainer.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html">MetaContainer</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container =
+[
+ [ "default_table_name", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a2b2f74be0c9bbc3330a2bfa1c97c5e99", null ],
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+ [ "store_pair", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a2f04643ded7a65f9b80887b78b0d40ab", null ]
+];
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
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+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
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+ <li><a href="index.html"><span>Main Page</span></a></li>
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+ <li>
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+ <span class="left">
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+ alt=""/>
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+ </li>
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+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae3e95ef6cee275aa2ace188e45da854a">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b">keys_to_columns</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2a39cbb60a5021d1cd5a4e385da4000f">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#ad90a452430769ce22f854fb0d195e905">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor:</div>
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+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
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+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a2fd8279544ff4bd78e9b3fd09495542c"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">slicer</a> ()</td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td></tr>
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+<tr class="memitem:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a> ()</td></tr>
+<tr class="separator:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> ()</td></tr>
+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a> ()</td></tr>
+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> ()</td></tr>
+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$naked_table_adaptor = $dba->get_NakedTableAdaptor;</div>
+<div class="line">$naked_table_adaptor = $naked_table->adaptor;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This module together with its data container are used to enable dataflow into arbitrary tables (rather than just 'job' table).
+ Due to the implementation of EnsEMBL Registry code, NakedTable objects know *where* to dataflow, and NakedTableAdaptor knows *how* to dataflow.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a74f3ead3ecf4d1183b667c5da544362b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor::keys_to_columns </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-keys_to_columns" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-keys_to_columns-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-keys_to_columns-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-keys_to_columns-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b">keys_to_columns</a> {</div>
+<div class="line"> my ($self, $object) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $sorted_keys = [ sort keys %$object ];</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ( $sorted_keys, join(<span class="stringliteral">', '</span>, @$sorted_keys) );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2a39cbb60a5021d1cd5a4e385da4000f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor::mark_stored </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-mark_stored" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-mark_stored-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-mark_stored-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-mark_stored-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2a39cbb60a5021d1cd5a4e385da4000f">mark_stored</a> {</div>
+<div class="line"> my ($self, $hashref, $dbID) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $autoinc_id = $self->autoinc_id()) {</div>
+<div class="line"> $hashref->{$autoinc_id} = $dbID;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad90a452430769ce22f854fb0d195e905"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor::objectify </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-objectify" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-objectify-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-objectify-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-objectify-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#ad90a452430769ce22f854fb0d195e905">objectify</a> { # pretend the hashref becomes an object (<span class="keywordflow">if</span> only we could <span class="keyword">inline</span> in Perl!)</div>
+<div class="line"> return pop @_;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2fd8279544ff4bd78e9b3fd09495542c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor::slicer </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-slicer" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-slicer-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-slicer-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-slicer-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">slicer</a> { # take a slice of the hashref (<span class="keywordflow">if</span> only we could <span class="keyword">inline</span> in Perl!)</div>
+<div class="line"> my ($self, $object, $fields) = @_;</div>
+<div class="line"></div>
+<div class="line"> return [ @$object{@$fields} ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_naked_table_adaptor_8pm.html">NakedTableAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">NakedTableAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor =
+[
+ [ "keys_to_columns", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b", null ],
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+  <span id="projectnumber">1.9</span>
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+<div class="title">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor Member List</div> </div>
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+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae3e95ef6cee275aa2ace188e45da854a">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a834186b707376a4ead29771860ab440f">object_class</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
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+<div class="title">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor Class Reference</div> </div>
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+<tr class="memitem:ae98ea2fa8c6a85c6df918b9816bd6cbf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a> ()</td></tr>
+<tr class="separator:ae98ea2fa8c6a85c6df918b9816bd6cbf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae47ff32866fc8b69d8463680b5ead1d2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a> ()</td></tr>
+<tr class="separator:ae47ff32866fc8b69d8463680b5ead1d2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a> ()</td></tr>
+<tr class="separator:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a> ()</td></tr>
+<tr class="separator:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a> ()</td></tr>
+<tr class="separator:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a> ()</td></tr>
+<tr class="separator:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a> ()</td></tr>
+<tr class="separator:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a> ()</td></tr>
+<tr class="separator:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1e7b244d27dcc1244453f725d81d3e54 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a> ()</td></tr>
+<tr class="separator:a1e7b244d27dcc1244453f725d81d3e54 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a> ()</td></tr>
+<tr class="separator:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> ()</td></tr>
+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a> ()</td></tr>
+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> ()</td></tr>
+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$object_adaptor = $dba->get_SpecificObjectAdaptor;</div>
+<div class="line">$object_adaptor = $specific_object->adaptor;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This module defines a parent class for all specific object adaptors.
+ It is not supposed to be instantiated directly.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a90b0359523ef5040fd0e839edd83cca4"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor::create_new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-create_new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-create_new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-create_new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-create_new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $check_presence_in_db_first = (scalar(@_)%2)</div>
+<div class="line"> ? pop @_ # extra <span class="stringliteral">'odd'</span> parameter that would disrupt the hash integrity anyway</div>
+<div class="line"> : 0; # <span class="keywordflow">do</span> not check by <span class="keywordflow">default</span></div>
+<div class="line"></div>
+<div class="line"> my $object = $self->object_class()->new( -adaptor => $self, @_ );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->store( $object, $check_presence_in_db_first );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aee5049447ae13e0e4f41a1843899c4a0"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor::mark_stored </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-mark_stored" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-mark_stored-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-mark_stored-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-mark_stored-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">mark_stored</a> {</div>
+<div class="line"> my ($self, $object, $dbID) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->autoinc_id()) {</div>
+<div class="line"> $object->dbID($dbID);</div>
+<div class="line"> }</div>
+<div class="line"> $object->adaptor($self);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a834186b707376a4ead29771860ab440f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor::object_class </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-object_class" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-object_class-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-object_class-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-object_class-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a834186b707376a4ead29771860ab440f">object_class</a> {</div>
+<div class="line"> die <span class="stringliteral">"Please define object_class() in your specific adaptor class to return the class name of your intended object"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a02d847dd4df770edb4bdbc5ed309a2d5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor::objectify </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-objectify" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-objectify-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-objectify-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-objectify-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a> { # turn the hashref into an object (<span class="keywordflow">if</span> only we could <span class="keyword">inline</span> in Perl!)</div>
+<div class="line"> my ($self, $hashref) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $autoinc_id = $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>();</div>
+<div class="line"></div>
+<div class="line"> return $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a834186b707376a4ead29771860ab440f">object_class</a>()->new( -adaptor => $self, map { (<span class="charliteral">'-'</span>.uc( ($_ eq $autoinc_id) ? <span class="stringliteral">'dbID'</span> : $_ ) => $hashref->{$_}) } keys %$hashref );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af1b4e5cdd9865d10338aafe4c6d047c0"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor::slicer </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-slicer" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-slicer-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-slicer-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-slicer-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">slicer</a> { # take a slice of the object (<span class="keywordflow">if</span> only we could <span class="keyword">inline</span> in Perl!)</div>
+<div class="line"> my ($self, $object, $fields) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $autoinc_id = $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>();</div>
+<div class="line"> my $overflow_limit = $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>();</div>
+<div class="line"></div>
+<div class="line"> return [ map { ($_ eq $autoinc_id)</div>
+<div class="line"> ? $object->dbID()</div>
+<div class="line"> : eval { my $value = $object->$_();</div>
+<div class="line"> my $ol = $overflow_limit->{$_};</div>
+<div class="line"> (defined($ol) and length($value)>$ol)</div>
+<div class="line"> ? $self->db->get_AnalysisDataAdaptor()->store_if_needed( $value )</div>
+<div class="line"> : $value</div>
+<div class="line"> }</div>
+<div class="line"> } @$fields ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_object_adaptor_8pm.html">ObjectAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">ObjectAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
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+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
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+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+<!-- iframe showing the search results (closed by default) -->
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+ name="MSearchResults" id="MSearchResults">
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+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#a66aa80f75c5e69493344e9b8f94142bc">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#ad87ef629a730873721e4486ab5176fd0">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#ae3a6f6b2a9e4e71f62d6f9233c522b06">object_class</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor:</div>
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor:</div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:ad87ef629a730873721e4486ab5176fd0"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#ad87ef629a730873721e4486ab5176fd0">default_table_name</a> ()</td></tr>
+<tr class="separator:ad87ef629a730873721e4486ab5176fd0"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a66aa80f75c5e69493344e9b8f94142bc"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#a66aa80f75c5e69493344e9b8f94142bc">default_insertion_method</a> ()</td></tr>
+<tr class="separator:a66aa80f75c5e69493344e9b8f94142bc"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae3a6f6b2a9e4e71f62d6f9233c522b06"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#ae3a6f6b2a9e4e71f62d6f9233c522b06">object_class</a> ()</td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td></tr>
+<tr class="memitem:a834186b707376a4ead29771860ab440f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a834186b707376a4ead29771860ab440f">object_class</a> ()</td></tr>
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+<tr class="memitem:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a> ()</td></tr>
+<tr class="separator:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
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+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$resource_class_adaptor = $db_adaptor->get_ResourceClassAdaptor;</div>
+<div class="line"></div>
+<div class="line">$resource_class_adaptor = $resource_class_object->adaptor;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Module to encapsulate all db access for persistent class ResourceClass.
+ There should be just one per application and database connection.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a66aa80f75c5e69493344e9b8f94142bc"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor::default_insertion_method </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_insertion_method" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_insertion_method-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_insertion_method-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_insertion_method-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#a66aa80f75c5e69493344e9b8f94142bc">default_insertion_method</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'INSERT_IGNORE'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad87ef629a730873721e4486ab5176fd0"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#ad87ef629a730873721e4486ab5176fd0">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'resource_class'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae3a6f6b2a9e4e71f62d6f9233c522b06"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor::object_class </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-object_class" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-object_class-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-object_class-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-object_class-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#ae3a6f6b2a9e4e71f62d6f9233c522b06">object_class</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'Bio::EnsEMBL::Hive::ResourceClass'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_resource_class_adaptor_8pm.html">ResourceClassAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html">ResourceClassAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor =
+[
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+];
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+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#ac3f259e9b0d6c54b67a3bd027e8e46f9">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#a06ce8d0d67b24247c234a7a9637a3b09">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#aacaba93caa84332eb1713a2218e87b76">object_class</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor_inherit__map" alt="Inheritance graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor_inherit__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor_inherit__map">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor_coll__map">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a06ce8d0d67b24247c234a7a9637a3b09"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#a06ce8d0d67b24247c234a7a9637a3b09">default_table_name</a> ()</td></tr>
+<tr class="separator:a06ce8d0d67b24247c234a7a9637a3b09"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac3f259e9b0d6c54b67a3bd027e8e46f9"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#ac3f259e9b0d6c54b67a3bd027e8e46f9">default_insertion_method</a> ()</td></tr>
+<tr class="separator:ac3f259e9b0d6c54b67a3bd027e8e46f9"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aacaba93caa84332eb1713a2218e87b76"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#aacaba93caa84332eb1713a2218e87b76">object_class</a> ()</td></tr>
+<tr class="separator:aacaba93caa84332eb1713a2218e87b76"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td></tr>
+<tr class="memitem:a834186b707376a4ead29771860ab440f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a834186b707376a4ead29771860ab440f">object_class</a> ()</td></tr>
+<tr class="separator:a834186b707376a4ead29771860ab440f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:af1b4e5cdd9865d10338aafe4c6d047c0 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">slicer</a> ()</td></tr>
+<tr class="separator:af1b4e5cdd9865d10338aafe4c6d047c0 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a02d847dd4df770edb4bdbc5ed309a2d5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a> ()</td></tr>
+<tr class="separator:a02d847dd4df770edb4bdbc5ed309a2d5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aee5049447ae13e0e4f41a1843899c4a0 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">mark_stored</a> ()</td></tr>
+<tr class="separator:aee5049447ae13e0e4f41a1843899c4a0 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a90b0359523ef5040fd0e839edd83cca4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a> ()</td></tr>
+<tr class="separator:a90b0359523ef5040fd0e839edd83cca4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td></tr>
+<tr class="memitem:ae3e95ef6cee275aa2ace188e45da854a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae3e95ef6cee275aa2ace188e45da854a">default_table_name</a> ()</td></tr>
+<tr class="separator:ae3e95ef6cee275aa2ace188e45da854a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a129b813103eead72607723d43d3a6567 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">default_insertion_method</a> ()</td></tr>
+<tr class="separator:a129b813103eead72607723d43d3a6567 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac73267d0e33aad126c188108f7e7c468 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a> ()</td></tr>
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+<tr class="memitem:a2f77cbefb20d4b4e3a40cf75ce420036 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a> ()</td></tr>
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+<tr class="memitem:a1f8bbd7bad6d23b679d4c07ab4121085 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a> ()</td></tr>
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+<tr class="separator:ac7e056384281180e1b314889fc7c317f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9ee7f9cfe42ad4993d0b544acfb4e1f5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a> ()</td></tr>
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+<tr class="memitem:acd1bde351fcbdfddf8fa9896c8716514 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a> ()</td></tr>
+<tr class="separator:acd1bde351fcbdfddf8fa9896c8716514 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a> ()</td></tr>
+<tr class="separator:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a> ()</td></tr>
+<tr class="separator:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a> ()</td></tr>
+<tr class="separator:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a> ()</td></tr>
+<tr class="separator:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a> ()</td></tr>
+<tr class="separator:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a1e7b244d27dcc1244453f725d81d3e54 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a> ()</td></tr>
+<tr class="separator:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> ()</td></tr>
+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a> ()</td></tr>
+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> ()</td></tr>
+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$resource_description_adaptor = $db_adaptor->get_ResourceDescriptionAdaptor;</div>
+<div class="line"></div>
+<div class="line">$resource_description_adaptor = $resource_description_object->adaptor;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Module to encapsulate all db access for persistent class ResourceDescription.
+ There should be just one per application and database connection.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ac3f259e9b0d6c54b67a3bd027e8e46f9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor::default_insertion_method </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_insertion_method" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_insertion_method-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_insertion_method-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_insertion_method-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#ac3f259e9b0d6c54b67a3bd027e8e46f9">default_insertion_method</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'REPLACE'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a06ce8d0d67b24247c234a7a9637a3b09"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#a06ce8d0d67b24247c234a7a9637a3b09">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'resource_description'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aacaba93caa84332eb1713a2218e87b76"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor::object_class </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-object_class" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-object_class-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-object_class-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-object_class-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#aacaba93caa84332eb1713a2218e87b76">object_class</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'Bio::EnsEMBL::Hive::ResourceDescription'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_resource_description_adaptor_8pm.html">ResourceDescriptionAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html">ResourceDescriptionAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor =
+[
+ [ "default_insertion_method", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#ac3f259e9b0d6c54b67a3bd027e8e46f9", null ],
+ [ "default_table_name", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#a06ce8d0d67b24247c234a7a9637a3b09", null ],
+ [ "object_class", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#aacaba93caa84332eb1713a2218e87b76", null ]
+];
\ No newline at end of file
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+<area shape="rect" id="node2" href="$class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html" title="Bio::EnsEMBL::Hive\l::DBSQL::ObjectAdaptor" alt="" coords="25,187,191,229"/>
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+</div><!--header-->
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+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a>, including all inherited members.</p>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a0c2dc02c4e81944f9eb9fa7f670aa753">get_code_sql_schema_version</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#aa6e8545c8a07176e86265ac18f684060">get_sql_schema_patches</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a></td><td class="entry"></td></tr>
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+<title>ensembl-hive: Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor Class Reference</title>
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+ name="MSearchResults" id="MSearchResults">
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+</div>
+
+<div class="header">
+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a4dd0e15f6e51c889ed715aee9275e54d"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a4dd0e15f6e51c889ed715aee9275e54d">find_all_sql_schema_patches</a> ()</td></tr>
+<tr class="separator:a4dd0e15f6e51c889ed715aee9275e54d"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aa6e8545c8a07176e86265ac18f684060"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#aa6e8545c8a07176e86265ac18f684060">get_sql_schema_patches</a> ()</td></tr>
+<tr class="separator:aa6e8545c8a07176e86265ac18f684060"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0c2dc02c4e81944f9eb9fa7f670aa753"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a0c2dc02c4e81944f9eb9fa7f670aa753">get_code_sql_schema_version</a> ()</td></tr>
+<tr class="separator:a0c2dc02c4e81944f9eb9fa7f670aa753"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line"><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a0c2dc02c4e81944f9eb9fa7f670aa753">get_code_sql_schema_version</a>();</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is currently an "objectless" adaptor for finding out the apparent code's SQL schema version
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a4dd0e15f6e51c889ed715aee9275e54d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor::find_all_sql_schema_patches </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-find_all_sql_schema_patches" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-find_all_sql_schema_patches-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-find_all_sql_schema_patches-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-find_all_sql_schema_patches-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a4dd0e15f6e51c889ed715aee9275e54d">find_all_sql_schema_patches</a> {</div>
+<div class="line"></div>
+<div class="line"> my %all_patches = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $hive_root_dir = $ENV{<span class="stringliteral">'EHIVE_ROOT_DIR'</span>} ) {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $patch_path ( split(/\n/, `ls -1 $hive_root_dir/sql/patch_20*.*sql*`) ) {</div>
+<div class="line"> my ($patch_name, $driver) = ($patch_path=~/^(.+)\.(\w+)$/);</div>
+<div class="line"></div>
+<div class="line"> $driver = <span class="stringliteral">'mysql'</span> <span class="keywordflow">if</span> ($driver eq <span class="stringliteral">'sql'</span>); # <span class="keywordflow">for</span> backwards compatibility</div>
+<div class="line"></div>
+<div class="line"> $all_patches{$patch_name}{$driver} = $patch_path;</div>
+<div class="line"> }</div>
+<div class="line"> } # otherwise will sliently <span class="keywordflow">return</span> an empty hash</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> \%all_patches;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0c2dc02c4e81944f9eb9fa7f670aa753"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor::get_code_sql_schema_version </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_code_sql_schema_version" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_code_sql_schema_version-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_code_sql_schema_version-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_code_sql_schema_version-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a0c2dc02c4e81944f9eb9fa7f670aa753">get_code_sql_schema_version</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> scalar( keys %{ $self->find_all_sql_schema_patches() } ); # 0 probably means $ENV{<span class="stringliteral">'EHIVE_ROOT_DIR'</span>} not set correctly</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa6e8545c8a07176e86265ac18f684060"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor::get_sql_schema_patches </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_sql_schema_patches" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_sql_schema_patches-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_sql_schema_patches-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_sql_schema_patches-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#aa6e8545c8a07176e86265ac18f684060">get_sql_schema_patches</a> {</div>
+<div class="line"> my ($self, $after_version, $driver) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $all_patches = $self->find_all_sql_schema_patches();</div>
+<div class="line"> my $code_schema_version = $self->get_code_sql_schema_version();</div>
+<div class="line"></div>
+<div class="line"> my @ordered_patches = ();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $patch_key ( (sort keys %$all_patches)[$after_version..$code_schema_version-1] ) {</div>
+<div class="line"> <span class="keywordflow">if</span>(my $patch_path = $all_patches->{$patch_key}{$driver}) {</div>
+<div class="line"> push @ordered_patches, $patch_path;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> <span class="keywordflow">return</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> \@ordered_patches;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/DBSQL/<a class="el" href="_sql_schema_adaptor_8pm.html">SqlSchemaAdaptor.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">DBSQL</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html">SqlSchemaAdaptor</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.js b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.js
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor =
+[
+ [ "find_all_sql_schema_patches", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a4dd0e15f6e51c889ed715aee9275e54d", null ],
+ [ "get_code_sql_schema_version", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a0c2dc02c4e81944f9eb9fa7f670aa753", null ],
+ [ "get_sql_schema_patches", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#aa6e8545c8a07176e86265ac18f684060", null ]
+];
\ No newline at end of file
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+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
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+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
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+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
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+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+ name="MSearchResults" id="MSearchResults">
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+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DataflowRule Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ad765dadb213174df11b5f31e3248b9db">branch_code</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ad8140faa5aec71033ae2cc3e69571246">from_analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ac13454a4f86e556f82560a7f2967fc53">from_analysis_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#aec851945dd9ebf3652224066b8d271e8">funnel_dataflow_rule_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a7a2ba2f2f0e72775363943785b918b90">input_id_template</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#af8321e0eec4a4057a4d103400e549df3">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ae069a34e628c9f6348c5110a8e9b29b6">to_analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#abe8caedff6ad05cb325d8d7be4ff14ec">to_analysis_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a48471b18b5f0d91bbeb9fee9c468a523">toString</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
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+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Bio::EnsEMBL::Hive::DataflowRule Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
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+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
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+ <div id="navrow2" class="tabs2">
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::DataflowRule Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::DataflowRule:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule_inherit__map" alt="Inheritance graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule_inherit__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule_inherit__map">
+</map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::DataflowRule:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule_coll__map">
+</map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:af8321e0eec4a4057a4d103400e549df3"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#af8321e0eec4a4057a4d103400e549df3">new</a> ()</td></tr>
+<tr class="separator:af8321e0eec4a4057a4d103400e549df3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad765dadb213174df11b5f31e3248b9db"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ad765dadb213174df11b5f31e3248b9db">branch_code</a> ()</td></tr>
+<tr class="separator:ad765dadb213174df11b5f31e3248b9db"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aec851945dd9ebf3652224066b8d271e8"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#aec851945dd9ebf3652224066b8d271e8">funnel_dataflow_rule_id</a> ()</td></tr>
+<tr class="separator:aec851945dd9ebf3652224066b8d271e8"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7a2ba2f2f0e72775363943785b918b90"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a7a2ba2f2f0e72775363943785b918b90">input_id_template</a> ()</td></tr>
+<tr class="separator:a7a2ba2f2f0e72775363943785b918b90"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac13454a4f86e556f82560a7f2967fc53"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ac13454a4f86e556f82560a7f2967fc53">from_analysis_id</a> ()</td></tr>
+<tr class="separator:ac13454a4f86e556f82560a7f2967fc53"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abe8caedff6ad05cb325d8d7be4ff14ec"><td class="memItemLeft" align="right" valign="top">public String </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#abe8caedff6ad05cb325d8d7be4ff14ec">to_analysis_url</a> ()</td></tr>
+<tr class="separator:abe8caedff6ad05cb325d8d7be4ff14ec"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad8140faa5aec71033ae2cc3e69571246"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ad8140faa5aec71033ae2cc3e69571246">from_analysis</a> ()</td></tr>
+<tr class="separator:ad8140faa5aec71033ae2cc3e69571246"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae069a34e628c9f6348c5110a8e9b29b6"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ae069a34e628c9f6348c5110a8e9b29b6">to_analysis</a> ()</td></tr>
+<tr class="separator:ae069a34e628c9f6348c5110a8e9b29b6"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a48471b18b5f0d91bbeb9fee9c468a523"><td class="memItemLeft" align="right" valign="top">public String </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a48471b18b5f0d91bbeb9fee9c468a523">toString</a> ()</td></tr>
+<tr class="separator:a48471b18b5f0d91bbeb9fee9c468a523"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A data container object (methods are intelligent getters/setters) that corresponds to a row stored in 'dataflow_rule' table:
+
+ CREATE TABLE dataflow_rule (
+ dataflow_rule_id int(10) unsigned NOT NULL AUTO_INCREMENT,
+ from_analysis_id int(10) unsigned NOT NULL,
+ branch_code int(10) default 1 NOT NULL,
+ funnel_dataflow_rule_id int(10) unsigned default NULL,
+ to_analysis_url varchar(255) default '' NOT NULL,
+ input_id_template TEXT DEFAULT NULL,
+
+ PRIMARY KEY (dataflow_rule_id),
+ UNIQUE (from_analysis_id, to_analysis_url)
+ );
+
+ A dataflow rule is activated when a Bio::EnsEMBL::Hive::AnalysisJob::dataflow_output_id is called at any moment during a RunnableDB's execution.
+ The current RunnableDB's analysis ($from_analysis) and the requested $branch_code (1 by default) define the entry conditions,
+ and whatever rules match these conditions will generate new jobs with input_ids specified in the dataflow_output_id() call.
+ If input_id_template happens to contain a non-NULL value, it will be used to generate the corresponding intput_id instead.
+
+ Jessica's remark on the structure of to_analysis_url:
+ Extended from design of SimpleRule concept to allow the 'to' analysis to be specified with a network savy URL like
+ mysql://ensadmin:<pass>\@ecs2:3361/compara_hive_test/analysis?logic_name='blast_NCBI34'
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ad765dadb213174df11b5f31e3248b9db"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DataflowRule::branch_code </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Function: getter/setter method for the branch_code of the dataflow rule</pre><pre> </pre><div id="codesection-branch_code" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-branch_code-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-branch_code-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-branch_code-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ad765dadb213174df11b5f31e3248b9db">branch_code</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> my $branch_name_or_code = shift @_;</div>
+<div class="line"> $self->{<span class="stringliteral">'_branch_code'</span>} = $branch_name_or_code && <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a529c8c386c3e60cb1a737231775bf77c">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor::branch_name_2_code</a>( $branch_name_or_code );</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_branch_code'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad8140faa5aec71033ae2cc3e69571246"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> Bio::EnsEMBL::Hive::DataflowRule::from_analysis </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Usage : $self->from_analysis($analysis);
+ Function: Get/set method for the condition analysis object of this rule.
+ Returns : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a>
+ Args : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a></pre><pre> </pre><div id="codesection-from_analysis" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-from_analysis-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-from_analysis-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-from_analysis-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ad8140faa5aec71033ae2cc3e69571246">from_analysis</a> {</div>
+<div class="line"> my ($self,$analysis) = @_;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # setter mode</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>( defined $analysis ) {</div>
+<div class="line"> unless ($analysis->isa(<span class="stringliteral">'Bio::EnsEMBL::Hive::Analysis'</span>)) {</div>
+<div class="line"> <span class="keywordflow">throw</span>(</div>
+<div class="line"> <span class="stringliteral">"from_analysis arg must be a [Bio::EnsEMBL::Hive::Analysis]"</span>.</div>
+<div class="line"> <span class="stringliteral">"not a [$analysis]"</span>);</div>
+<div class="line"> }</div>
+<div class="line"> $self->{<span class="stringliteral">'_from_analysis'</span>} = $analysis;</div>
+<div class="line"> $self->{<span class="stringliteral">'_from_analysis_id'</span>} = $analysis->dbID;</div>
+<div class="line"> }</div>
+<div class="line"> </div>
+<div class="line"><span class="preprocessor"> # lazy load the analysis object if I can</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>(!defined($self->{<span class="stringliteral">'_from_analysis'</span>})</div>
+<div class="line"> and defined($self->from_analysis_id)</div>
+<div class="line"> and defined($self->adaptor))</div>
+<div class="line"> {</div>
+<div class="line"> $self->{<span class="stringliteral">'_from_analysis'</span>} =</div>
+<div class="line"> $self->adaptor->db->get_AnalysisAdaptor->fetch_by_dbID($self->from_analysis_id);</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_from_analysis'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac13454a4f86e556f82560a7f2967fc53"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Int Bio::EnsEMBL::Hive::DataflowRule::from_analysis_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg[1] : (optional) int $dbID
+ Usage : $self->from_analysis_id($dbID);
+ Function: Get/set method for the 'from' analysis objects dbID of this rule.
+ Returns : integer</pre><pre> </pre><div id="codesection-from_analysis_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-from_analysis_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-from_analysis_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-from_analysis_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ac13454a4f86e556f82560a7f2967fc53">from_analysis_id</a> {</div>
+<div class="line"> my ($self,$analysis_id) = @_;</div>
+<div class="line"> <span class="keywordflow">if</span>($analysis_id) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_from_analysis_id'</span>} = $analysis_id;</div>
+<div class="line"> $self->{<span class="stringliteral">'_from_analysis'</span>} = undef;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_from_analysis_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aec851945dd9ebf3652224066b8d271e8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DataflowRule::funnel_dataflow_rule_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Function: getter/setter method for the funnel_dataflow_rule_id of the dataflow rule</pre><pre> </pre><div id="codesection-funnel_dataflow_rule_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-funnel_dataflow_rule_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-funnel_dataflow_rule_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-funnel_dataflow_rule_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#aec851945dd9ebf3652224066b8d271e8">funnel_dataflow_rule_id</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) { # setter mode</div>
+<div class="line"> $self->{<span class="stringliteral">'_funnel_dataflow_rule_id'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_funnel_dataflow_rule_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7a2ba2f2f0e72775363943785b918b90"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DataflowRule::input_id_template </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Function: getter/setter method for the input_id_template of the dataflow rule</pre><pre> </pre><div id="codesection-input_id_template" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-input_id_template-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-input_id_template-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-input_id_template-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a7a2ba2f2f0e72775363943785b918b90">input_id_template</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> my $input_id_template = shift @_;</div>
+<div class="line"> $self->{<span class="stringliteral">'_input_id_template'</span>} = (ref($input_id_template) ? stringify($input_id_template) : $input_id_template),</div>
+<div class="line"> }</div>
+<div class="line"> return $self->{<span class="stringliteral">'_input_id_template'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af8321e0eec4a4057a4d103400e549df3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a> Bio::EnsEMBL::Hive::DataflowRule::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Usage : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a>->new(-from_analysis => $fromAnalysis, -to_analysis => $toAnalysis, -branch_code => $branch_code);
+ Function: Constructor for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">DataflowRule</a> object
+ Returns : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a>
+ Args : a rearrange-compatible hash</pre><pre> </pre><div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = $class->SUPER::new( @_ ); # deal with Storable stuff</div>
+<div class="line"></div>
+<div class="line"> my ($fromAnalysis, $toAnalysis, $from_analysis_id, $branch_code, $funnel_dataflow_rule_id, $to_analysis_url, $input_id_template ) =</div>
+<div class="line"> rearrange( [ qw (FROM_ANALYSIS TO_ANALYSIS FROM_ANALYSIS_ID BRANCH_CODE FUNNEL_DATAFLOW_RULE_ID TO_ANALYSIS_URL INPUT_ID_TEMPLATE) ], @_ );</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # from objects:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->from_analysis( $fromAnalysis ) <span class="keywordflow">if</span>(defined($fromAnalysis));</div>
+<div class="line"> $self->to_analysis( $toAnalysis ) <span class="keywordflow">if</span>(defined($toAnalysis));</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # simple scalars:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->from_analysis_id($from_analysis_id) <span class="keywordflow">if</span>(defined($from_analysis_id));</div>
+<div class="line"> $self->to_analysis_url($to_analysis_url) <span class="keywordflow">if</span>(defined($to_analysis_url));</div>
+<div class="line"> $self->branch_code($branch_code) <span class="keywordflow">if</span>(defined($branch_code));</div>
+<div class="line"> $self->funnel_dataflow_rule_id($funnel_dataflow_rule_id) <span class="keywordflow">if</span>(defined($funnel_dataflow_rule_id));</div>
+<div class="line"> $self->input_id_template($input_id_template) <span class="keywordflow">if</span>(defined($input_id_template));</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae069a34e628c9f6348c5110a8e9b29b6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> Bio::EnsEMBL::Hive::DataflowRule::to_analysis </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Usage : $self->to_analysis($analysis);
+ Function: Get/set method for the goal analysis object of this rule.
+ Returns : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a>
+ Args : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a></pre><pre> </pre><div id="codesection-to_analysis" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-to_analysis-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-to_analysis-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-to_analysis-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ae069a34e628c9f6348c5110a8e9b29b6">to_analysis</a> {</div>
+<div class="line"> my ($self, $analysis_or_nt) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( defined $analysis_or_nt ) {</div>
+<div class="line"> unless ($analysis_or_nt->can(<span class="stringliteral">'url'</span>)) {</div>
+<div class="line"> <span class="keywordflow">throw</span>( <span class="stringliteral">"to_analysis arg must support 'url' method, '$analysis_or_nt' does not know how to do it"</span>);</div>
+<div class="line"> }</div>
+<div class="line"> $self->{<span class="stringliteral">'_to_analysis'</span>} = $analysis_or_nt;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> #if the 'from' and 'to' share the same adaptor, then use a simple logic_name</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #for the URL rather than a full network distributed URL</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my $ref_rule_adaptor = $self->from_analysis && $self->from_analysis->adaptor;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($analysis_or_nt->can(<span class="stringliteral">'logic_name'</span>) and $ref_rule_adaptor and ($ref_rule_adaptor == $analysis_or_nt->adaptor)) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_to_analysis_url'</span>} = $analysis_or_nt-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6528be48120416c630abe32227e70bdb">logic_name</a>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $self->{<span class="stringliteral">'_to_analysis_url'</span>} = $analysis_or_nt->url($ref_rule_adaptor->db);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"><span class="preprocessor"> # lazy load the analysis object if I can</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>(!defined($self->{<span class="stringliteral">'_to_analysis'</span>}) and defined($self->to_analysis_url)) {</div>
+<div class="line"></div>
+<div class="line"> my $url = $self->to_analysis_url;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_to_analysis'</span>} = $self->adaptor</div>
+<div class="line"> ? $self->adaptor->db->get_AnalysisAdaptor->fetch_by_logic_name_or_url($url)</div>
+<div class="line"> : <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#afb5c2b354ab0889fff2d55ef7c87443e">fetch_by_logic_name_or_url</a>($url)</div>
+<div class="line"> or die <span class="stringliteral">"Cannot fetch analysis from logic_name or url '$url' for dataflow rule with id='"</span>.$self->dbID.<span class="stringliteral">"'\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_to_analysis'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="abe8caedff6ad05cb325d8d7be4ff14ec"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public String Bio::EnsEMBL::Hive::DataflowRule::to_analysis_url </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg[1] : (optional) string $url
+ Usage : $self->to_analysis_url($url);
+ Function: Get/set method for the 'to' analysis objects URL for this rule
+ Returns : string</pre><pre> </pre><div id="codesection-to_analysis_url" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-to_analysis_url-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-to_analysis_url-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-to_analysis_url-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#abe8caedff6ad05cb325d8d7be4ff14ec">to_analysis_url</a> {</div>
+<div class="line"> my ($self,$url) = @_;</div>
+<div class="line"> <span class="keywordflow">if</span>($url) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_to_analysis_url'</span>} = $url;</div>
+<div class="line"> $self->{<span class="stringliteral">'_to_analysis'</span>} = undef;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_to_analysis_url'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a48471b18b5f0d91bbeb9fee9c468a523"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public String Bio::EnsEMBL::Hive::DataflowRule::toString </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Args : (none)
+ Example :</pre><div class="fragment"><div class="line">print $df_rule->toString().<span class="stringliteral">"\n"</span>;</div>
+</div><!-- fragment --> <pre> Description: returns a stringified representation of the rule
+ Returntype : string</pre><pre> </pre><div id="codesection-toString" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-toString-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-toString-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-toString-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a48471b18b5f0d91bbeb9fee9c468a523">toString</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> join(<span class="stringliteral">''</span>,</div>
+<div class="line"> <span class="stringliteral">'DataflowRule(dbID='</span>,</div>
+<div class="line"> ($self->dbID || <span class="charliteral">'?'</span>),</div>
+<div class="line"> ($self->funnel_dataflow_rule_id ? <span class="stringliteral">' --|| '</span>.$self->funnel_dataflow_rule_id : <span class="stringliteral">''</span>),</div>
+<div class="line"> <span class="stringliteral">'): [#'</span>,</div>
+<div class="line"> $self->branch_code,</div>
+<div class="line"> <span class="stringliteral">'] '</span>,</div>
+<div class="line"> $self->from_analysis->logic_name,</div>
+<div class="line"> <span class="stringliteral">' -> '</span>,</div>
+<div class="line"> $self->to_analysis_url,</div>
+<div class="line"> ($self->input_id_template ? (<span class="stringliteral">' WITH TEMPLATE: '</span>.$self->input_id_template) : <span class="stringliteral">''</span>),</div>
+<div class="line"> );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_dataflow_rule_8pm.html">DataflowRule.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">DataflowRule</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+ [ "funnel_dataflow_rule_id", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#aec851945dd9ebf3652224066b8d271e8", null ],
+ [ "input_id_template", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a7a2ba2f2f0e72775363943785b918b90", null ],
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+ [ "to_analysis", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ae069a34e628c9f6348c5110a8e9b29b6", null ],
+ [ "to_analysis_url", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#abe8caedff6ad05cb325d8d7be4ff14ec", null ],
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+];
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
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+<script type="text/javascript" src="dynsections.js"></script>
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
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+<tr class="separator:a35e7b3e74c6afda6e8f364b6b84f1348"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaeb1b4b8db00aaa6a80126ff26cb7a0e"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a> ()</td></tr>
+<tr class="separator:aaeb1b4b8db00aaa6a80126ff26cb7a0e"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adca1f94c3e725c8f744517d14ac91853"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> ()</td></tr>
+<tr class="separator:adca1f94c3e725c8f744517d14ac91853"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a58f0a875a481ff975964bbd451773f11"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A parser for PipeConfig files that understands how and when to substitute $self->o() expressions.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="aaeb1b4b8db00aaa6a80126ff26cb7a0e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DependentOptions::hash_leaves </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-hash_leaves" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-hash_leaves-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-hash_leaves-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-hash_leaves-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a> {</div>
+<div class="line"> my ($self, $hash_to, $source, $prefix) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(ref($source) eq <span class="stringliteral">'HASH'</span>) {</div>
+<div class="line"> <span class="keywordflow">while</span>(my ($key, $value) = each %$source) {</div>
+<div class="line"> my $hash_element_prefix = ($prefix ? <span class="stringliteral">"$prefix->"</span> : <span class="stringliteral">''</span>) . <span class="stringliteral">"{'$key'}"</span>;</div>
+<div class="line"></div>
+<div class="line"> $self->hash_leaves($hash_to, $value, $hash_element_prefix);</div>
+<div class="line"> }</div>
+<div class="line"> } elsif(ref($source) eq <span class="stringliteral">'ARRAY'</span>) {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $index (0..scalar(@$source)-1) {</div>
+<div class="line"> my $element = $source->[$index];</div>
+<div class="line"> my $array_element_prefix = ($prefix ? <span class="stringliteral">"$prefix->"</span> : <span class="stringliteral">''</span>) . <span class="stringliteral">"[$index]"</span>;</div>
+<div class="line"></div>
+<div class="line"> $self->hash_leaves($hash_to, $element, $array_element_prefix);</div>
+<div class="line"> }</div>
+<div class="line"> } elsif(!$self->is_fully_substituted_string($source)) {</div>
+<div class="line"> $hash_to->{$prefix} = 1;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $hash_to;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8b28b1e6e1ef24ac3d9143062ddc36d6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DependentOptions::is_fully_substituted_string </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-is_fully_substituted_string" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-is_fully_substituted_string-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-is_fully_substituted_string-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-is_fully_substituted_string-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $input = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> (!defined($input) || $input !~ /#\:.+?\:#/);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a35e7b3e74c6afda6e8f364b6b84f1348"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DependentOptions::is_fully_substituted_structure </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-is_fully_substituted_structure" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-is_fully_substituted_structure-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-is_fully_substituted_structure-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-is_fully_substituted_structure-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $input = shift @_;</div>
+<div class="line"></div>
+<div class="line"> unless(my $ref_type = ref($input)) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->is_fully_substituted_string($input);</div>
+<div class="line"></div>
+<div class="line"> } elsif($ref_type eq <span class="stringliteral">'HASH'</span>) {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $value (values %$input) {</div>
+<div class="line"> unless($self->is_fully_substituted_structure($value)) {</div>
+<div class="line"> <span class="keywordflow">return</span> 0;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> } elsif($ref_type eq <span class="stringliteral">'ARRAY'</span>) {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $element (@$input) {</div>
+<div class="line"> unless($self->is_fully_substituted_structure($element)) {</div>
+<div class="line"> <span class="keywordflow">return</span> 0;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> 1;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac036ce35e64d7310b44481136fad5b18"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DependentOptions::load_cmdline_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-load_cmdline_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-load_cmdline_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-load_cmdline_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-load_cmdline_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $expected = shift @_;</div>
+<div class="line"> my $target = shift @_ || {};</div>
+<div class="line"></div>
+<div class="line"> local @ARGV = @ARGV; # make <span class="keyword">this</span> <span class="keyword">function</span> reenterable by forbidding it to modify the original parameters</div>
+<div class="line"> GetOptions( $target,</div>
+<div class="line"> map { my $ref_type = ref($expected->{$_}); $_=~m{\!$} ? $_ : ($ref_type eq <span class="stringliteral">'HASH'</span>) ? <span class="stringliteral">"$_=s%"</span> : ($ref_type eq <span class="stringliteral">'ARRAY'</span>) ? <span class="stringliteral">"$_=s@"</span> : <span class="stringliteral">"$_=s"</span> } keys %$expected</div>
+<div class="line"> );</div>
+<div class="line"> <span class="keywordflow">return</span> $target;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a33d14b75b2adc800bbcc4451a7ca7819"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DependentOptions::merge_from_rules </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-merge_from_rules" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-merge_from_rules-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-merge_from_rules-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-merge_from_rules-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $from = shift @_;</div>
+<div class="line"> my $top = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $ref_type = ref($$top);</div>
+<div class="line"></div>
+<div class="line"> unless($ref_type) {</div>
+<div class="line"> $$top = $from;</div>
+<div class="line"> } elsif($ref_type eq <span class="stringliteral">'HASH'</span>) {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $key (keys %$from) {</div>
+<div class="line"> $self->merge_from_rules( $from->{$key}, \$$top->{$key} );</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a729f524427ef5292b7e980f134aa456f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DependentOptions::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = bless { @_ }, $class;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="adca1f94c3e725c8f744517d14ac91853"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DependentOptions::o </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-o" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-o-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-o-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-o-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $ptr = $self->root();</div>
+<div class="line"></div>
+<div class="line"> my @syll_seen = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>(defined(my $option_syll = shift @_)) {</div>
+<div class="line"> push @syll_seen, $option_syll;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( exists($ptr->{$option_syll})</div>
+<div class="line"> and ((ref($ptr->{$option_syll}) eq <span class="stringliteral">'HASH'</span>) or $self->is_fully_substituted_string( $ptr->{$option_syll} ))</div>
+<div class="line"> ) {</div>
+<div class="line"> $ptr = $ptr->{$option_syll}; # just descend one level</div>
+<div class="line"> } elsif(@_) {</div>
+<div class="line"> $ptr = $ptr->{$option_syll} = {}; # force intermediate level vivification, even <span class="keywordflow">if</span> it overwrites a fully_substituted_string</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $ptr = $ptr->{$option_syll} = <span class="stringliteral">"#:subst "</span>.join(<span class="stringliteral">'->'</span>,@syll_seen).<span class="stringliteral">":#"</span>; # force leaf level vivification</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $ptr;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1832098d9531567eda925f5e108438a6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DependentOptions::process_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-process_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-process_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-process_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-process_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $definitely_used_options = $self->root();</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # dry-run of these methods allows us to collect definitely_used_options</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">foreach</span> my $method (@{ $self->use_cases() }) {</div>
+<div class="line"> $self->$method();</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $possibly_used_options = { <span class="stringliteral">'ENV'</span> => \%ENV };</div>
+<div class="line"> $self->root( $possibly_used_options );</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # the first run of this method allows us to collect possibly_used_options</span></div>
+<div class="line"><span class="preprocessor"></span> my $rules = $self->default_options();</div>
+<div class="line"></div>
+<div class="line"> $self->load_cmdline_options( { %$definitely_used_options, %$possibly_used_options }, $rules );</div>
+<div class="line"></div>
+<div class="line"> $self->root( $definitely_used_options );</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"> my $rules_to_go;</div>
+<div class="line"> my $attempts = 32;</div>
+<div class="line"> <span class="keywordflow">do</span> {</div>
+<div class="line"> $rules_to_go = 0;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $key (keys %$definitely_used_options) {</div>
+<div class="line"> <span class="keywordflow">if</span>(exists $rules->{$key}) {</div>
+<div class="line"> my $value = $self->substitute( \$rules->{$key} );</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # it has to be intelligently (recursively, on by-element basis) merged back into the tree under $self->o($key):</span></div>
+<div class="line"><span class="preprocessor"></span> $self->merge_from_rules( $value, \$self->root->{$key} );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->is_fully_substituted_structure($value)) {</div>
+<div class="line"><span class="preprocessor"> #warn "Resolved rule: $key -> ".stringify($value)."\n";</span></div>
+<div class="line"><span class="preprocessor"></span> } <span class="keywordflow">else</span> {</div>
+<div class="line"><span class="preprocessor"> #warn "Unresolved rule: $key -> ".stringify($value)."\n";</span></div>
+<div class="line"><span class="preprocessor"></span> $rules_to_go++;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> $attempts--;</div>
+<div class="line"><span class="preprocessor"> #warn "=======================[$rules_to_go rules to go; $attempts attempts to go]=================\n\n";</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #warn " definitely_used_options{} contains: ".stringify($definitely_used_options)."\n";</span></div>
+<div class="line"><span class="preprocessor"></span> } <span class="keywordflow">while</span>($rules_to_go and $attempts);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> #warn "=======================[out of the substitution loop]=================\n\n";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my $missing_options = $self->hash_leaves( {}, $self->root, <span class="stringliteral">''</span> );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(scalar(keys %$missing_options)) {</div>
+<div class="line"> warn <span class="stringliteral">"Missing or incomplete definition of the following options:\n"</span>;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $key (sort keys %$missing_options) {</div>
+<div class="line"> print <span class="stringliteral">"\t$key\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> exit(1);</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"><span class="preprocessor"> #warn "Done parsing options!\n";</span></div>
+<div class="line"><span class="preprocessor"></span> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1191c5f58dd3ebbd26f4024b906ccfcf"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DependentOptions::root </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-root" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-root-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-root-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-root-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a> { # getter/setter <span class="keywordflow">for</span> the <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a></div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{_root} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_root} ||= {};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a58f0a875a481ff975964bbd451773f11"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DependentOptions::substitute </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-substitute" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-substitute-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-substitute-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-substitute-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $ref = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $ref_type = ref($$ref);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($ref_type eq <span class="stringliteral">'HASH'</span>) {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $value (values %$$ref) {</div>
+<div class="line"> $self->substitute( \$value );</div>
+<div class="line"> }</div>
+<div class="line"> } elsif($ref_type eq <span class="stringliteral">'ARRAY'</span>) {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $value (@$$ref) {</div>
+<div class="line"> $self->substitute( \$value );</div>
+<div class="line"> }</div>
+<div class="line"> } elsif( !$ref_type and defined($$ref) ) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($$ref =~ /^#\:subst ([^:]+)\:#$/) { # <span class="keywordflow">if</span> the given <span class="keywordtype">string</span> is one complete substitution, we don<span class="stringliteral">'t want to force the output into a string</span></div>
+<div class="line"><span class="stringliteral"> $$ref = $self->o(split/->/,$1);</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> $$ref =~ s{(?:#\:subst (.+?)\:#)}{$self->o(split(/->/,$1))}eg;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> return $$ref;</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a12fa6e8360e2db6bd40dc318654b9d42"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::DependentOptions::use_cases </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-use_cases" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-use_cases-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-use_cases-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-use_cases-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a> { # getter/setter <span class="keywordflow">for</span> the list of methods from where $self->o() is called</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{_use_cases} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_use_cases} || die <span class="stringliteral">"use_cases() has to be set before using"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_dependent_options_8pm.html">DependentOptions.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">DependentOptions</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
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+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a6e64029524e47016b9db01936324f8d2">available_capacity</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afea6647d740defa4fe2f636cd24b02cd">description</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a968b5a54d803a5e4e291cd9510940309">final_decision</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afb7019e05c935b4eb437ab7aaad54f8c">multiplier</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a89203ff40a85e13c7ef840a46dcf4487">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a344004cad3162eefaa6314cff26fa0b3">preliminary_offer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#ab3f3e0a81d708e08b8c6a0db9d056aac">reached</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
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+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Limiter Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a89203ff40a85e13c7ef840a46dcf4487"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a89203ff40a85e13c7ef840a46dcf4487">new</a> ()</td></tr>
+<tr class="separator:a89203ff40a85e13c7ef840a46dcf4487"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afea6647d740defa4fe2f636cd24b02cd"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afea6647d740defa4fe2f636cd24b02cd">description</a> ()</td></tr>
+<tr class="separator:afea6647d740defa4fe2f636cd24b02cd"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6e64029524e47016b9db01936324f8d2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a6e64029524e47016b9db01936324f8d2">available_capacity</a> ()</td></tr>
+<tr class="separator:a6e64029524e47016b9db01936324f8d2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb7019e05c935b4eb437ab7aaad54f8c"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afb7019e05c935b4eb437ab7aaad54f8c">multiplier</a> ()</td></tr>
+<tr class="separator:afb7019e05c935b4eb437ab7aaad54f8c"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab3f3e0a81d708e08b8c6a0db9d056aac"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#ab3f3e0a81d708e08b8c6a0db9d056aac">reached</a> ()</td></tr>
+<tr class="separator:ab3f3e0a81d708e08b8c6a0db9d056aac"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a344004cad3162eefaa6314cff26fa0b3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a344004cad3162eefaa6314cff26fa0b3">preliminary_offer</a> ()</td></tr>
+<tr class="separator:a344004cad3162eefaa6314cff26fa0b3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a968b5a54d803a5e4e291cd9510940309"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a968b5a54d803a5e4e291cd9510940309">final_decision</a> ()</td></tr>
+<tr class="separator:a968b5a54d803a5e4e291cd9510940309"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A simple data object that has a conditional capper/minimizer built in.
+ Simple but very useful in the context of multi-parameter scheduling.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a6e64029524e47016b9db01936324f8d2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Limiter::available_capacity </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-available_capacity" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-available_capacity-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-available_capacity-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-available_capacity-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a6e64029524e47016b9db01936324f8d2">available_capacity</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{_available_capacity} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_available_capacity};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="afea6647d740defa4fe2f636cd24b02cd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Limiter::description </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-description" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-description-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-description-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-description-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afea6647d740defa4fe2f636cd24b02cd">description</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{_description} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_description};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a968b5a54d803a5e4e291cd9510940309"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Limiter::final_decision </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-final_decision" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-final_decision-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-final_decision-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-final_decision-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a968b5a54d803a5e4e291cd9510940309">final_decision</a> {</div>
+<div class="line"> my ($self, $slots_agreed) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $available_capacity = $self->available_capacity;</div>
+<div class="line"> my $multiplier = $self->multiplier;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( defined($available_capacity) and defined($multiplier) and ($multiplier > 0.0) ) { # <span class="keywordflow">if</span> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afb7019e05c935b4eb437ab7aaad54f8c">multiplier</a> is not positive capacity stays unaffected</div>
+<div class="line"><span class="preprocessor"> # and we should not arrive here if $multiplier==0</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> $self->available_capacity( $available_capacity - $slots_agreed/$multiplier );</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="afb7019e05c935b4eb437ab7aaad54f8c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Limiter::multiplier </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-multiplier" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-multiplier-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-multiplier-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-multiplier-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afb7019e05c935b4eb437ab7aaad54f8c">multiplier</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{_multiplier} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_multiplier};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a89203ff40a85e13c7ef840a46dcf4487"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Limiter::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my ($class, $description, $available_capacity) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = bless {}, $class;</div>
+<div class="line"> $self->description( $description );</div>
+<div class="line"> $self->available_capacity( $available_capacity );</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # we fix the multiplier at 1 for direct limiters, but expect it to be (re)set later by reciprocal limiters:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->multiplier( 1 ); </div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a344004cad3162eefaa6314cff26fa0b3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Limiter::preliminary_offer </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-preliminary_offer" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-preliminary_offer-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-preliminary_offer-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-preliminary_offer-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a344004cad3162eefaa6314cff26fa0b3">preliminary_offer</a> {</div>
+<div class="line"> my ($self, $slots_asked) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $available_capacity = $self->available_capacity;</div>
+<div class="line"> my $multiplier = $self->multiplier;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( defined($available_capacity) and defined($multiplier) and ($multiplier >= 0.0) ) { # <span class="keywordflow">if</span> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afb7019e05c935b4eb437ab7aaad54f8c">multiplier</a> is negative it is not limiting</div>
+<div class="line"></div>
+<div class="line"> my $product = $available_capacity * $multiplier;</div>
+<div class="line"> my $slots_available = int( <span class="stringliteral">"$product"</span> ); # stringification helps to round up things like 0.1*10 (instead of leaving them at 0.99999999)</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ($slots_available<$slots_asked) ? $slots_available : $slots_asked;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $slots_asked;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab3f3e0a81d708e08b8c6a0db9d056aac"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Limiter::reached </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-reached" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-reached-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-reached-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-reached-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#ab3f3e0a81d708e08b8c6a0db9d056aac">reached</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> defined($self->available_capacity) && ($self->available_capacity <= 0.0);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_limiter_8pm.html">Limiter.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Limiter</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.js b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.js
new file mode 100644
index 0000000000000000000000000000000000000000..3351140cfb5f642ddbc4b26125a0ed42105643b6
--- /dev/null
+++ b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.js
@@ -0,0 +1,10 @@
+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter =
+[
+ [ "available_capacity", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a6e64029524e47016b9db01936324f8d2", null ],
+ [ "description", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afea6647d740defa4fe2f636cd24b02cd", null ],
+ [ "final_decision", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a968b5a54d803a5e4e291cd9510940309", null ],
+ [ "multiplier", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afb7019e05c935b4eb437ab7aaad54f8c", null ],
+ [ "new", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a89203ff40a85e13c7ef840a46dcf4487", null ],
+ [ "preliminary_offer", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a344004cad3162eefaa6314cff26fa0b3", null ],
+ [ "reached", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#ab3f3e0a81d708e08b8c6a0db9d056aac", null ]
+];
\ No newline at end of file
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow-members.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow-members.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Meadow Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa5ed36b42e1e9a3eeb2f2474c37cab8f">check_worker_is_alive_and_mine</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">config</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">config_get</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">config_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">context</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#ab8b9ebeacf07bfcb38851edbfdd0ae2f">generate_job_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a8d9888b59ba0e3fe41ac963b6415b894">job_name_prefix</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aad175b19c6c543012f5455740b539ba2">kill_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#abaa21c35b875562cdf4258eee1b717b3">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3685ec781296c30f00d2a8c4f3efeffc">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa65a2353dde2a128123f36543d5aa115">responsible_for_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a0594b46314ad2a8894f055bd58ba923c">signature</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3f921a54a1be9be90a8bb3cd7b7752a3">type</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Bio::EnsEMBL::Hive::Meadow Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
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+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ alt=""/>
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+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Meadow Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::Meadow:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_inherit__map" alt="Inheritance graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_inherit__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_inherit__map">
+<area shape="rect" id="node3" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html" title="Bio::EnsEMBL::Hive\l::Meadow::LOCAL" alt="" coords="5,187,147,229"/><area shape="rect" id="node4" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html" title="Bio::EnsEMBL::Hive\l::Meadow::LSF" alt="" coords="171,187,313,229"/><area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html" title="Bio::EnsEMBL::Hive\l::Configurable" alt="" coords="87,6,229,47"/></map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::Meadow:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_coll__map">
+<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html" title="Bio::EnsEMBL::Hive\l::Configurable" alt="" coords="5,6,147,47"/></map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:abaa21c35b875562cdf4258eee1b717b3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#abaa21c35b875562cdf4258eee1b717b3">new</a> ()</td></tr>
+<tr class="separator:abaa21c35b875562cdf4258eee1b717b3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3f921a54a1be9be90a8bb3cd7b7752a3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3f921a54a1be9be90a8bb3cd7b7752a3">type</a> ()</td></tr>
+<tr class="separator:a3f921a54a1be9be90a8bb3cd7b7752a3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0594b46314ad2a8894f055bd58ba923c"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a0594b46314ad2a8894f055bd58ba923c">signature</a> ()</td></tr>
+<tr class="separator:a0594b46314ad2a8894f055bd58ba923c"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3685ec781296c30f00d2a8c4f3efeffc"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3685ec781296c30f00d2a8c4f3efeffc">pipeline_name</a> ()</td></tr>
+<tr class="separator:a3685ec781296c30f00d2a8c4f3efeffc"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8d9888b59ba0e3fe41ac963b6415b894"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a8d9888b59ba0e3fe41ac963b6415b894">job_name_prefix</a> ()</td></tr>
+<tr class="separator:a8d9888b59ba0e3fe41ac963b6415b894"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab8b9ebeacf07bfcb38851edbfdd0ae2f"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#ab8b9ebeacf07bfcb38851edbfdd0ae2f">generate_job_name</a> ()</td></tr>
+<tr class="separator:ab8b9ebeacf07bfcb38851edbfdd0ae2f"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aa65a2353dde2a128123f36543d5aa115"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa65a2353dde2a128123f36543d5aa115">responsible_for_worker</a> ()</td></tr>
+<tr class="separator:aa65a2353dde2a128123f36543d5aa115"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aa5ed36b42e1e9a3eeb2f2474c37cab8f"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa5ed36b42e1e9a3eeb2f2474c37cab8f">check_worker_is_alive_and_mine</a> ()</td></tr>
+<tr class="separator:aa5ed36b42e1e9a3eeb2f2474c37cab8f"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aad175b19c6c543012f5455740b539ba2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aad175b19c6c543012f5455740b539ba2">kill_worker</a> ()</td></tr>
+<tr class="separator:aad175b19c6c543012f5455740b539ba2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td></tr>
+<tr class="memitem:a38c57142acfd31f32e87a94717620baf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">config</a> ()</td></tr>
+<tr class="separator:a38c57142acfd31f32e87a94717620baf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a419025891535ecd7b2f05183cf2ce8e4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">context</a> ()</td></tr>
+<tr class="separator:a419025891535ecd7b2f05183cf2ce8e4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeed405377caddb6a1aa3cb605ed6304f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">config_get</a> ()</td></tr>
+<tr class="separator:aeed405377caddb6a1aa3cb605ed6304f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3e556c76396430193c3f613c6f3e4079 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">config_set</a> ()</td></tr>
+<tr class="separator:a3e556c76396430193c3f613c6f3e4079 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Meadow is an abstract interface to the queue manager.
+
+ A Meadow knows how to check&change the actual status of Workers on the farm.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="aa5ed36b42e1e9a3eeb2f2474c37cab8f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::check_worker_is_alive_and_mine </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-check_worker_is_alive_and_mine" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-check_worker_is_alive_and_mine-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-check_worker_is_alive_and_mine-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-check_worker_is_alive_and_mine-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa5ed36b42e1e9a3eeb2f2474c37cab8f">check_worker_is_alive_and_mine</a> {</div>
+<div class="line"> my ($self, $worker) = @_;</div>
+<div class="line"></div>
+<div class="line"> die <span class="stringliteral">"Please use a derived method"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab8b9ebeacf07bfcb38851edbfdd0ae2f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::generate_job_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-generate_job_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-generate_job_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-generate_job_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-generate_job_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#ab8b9ebeacf07bfcb38851edbfdd0ae2f">generate_job_name</a> {</div>
+<div class="line"> my ($self, $worker_count, $iteration, $rc_name) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->job_name_prefix()</div>
+<div class="line"> .<span class="stringliteral">"${rc_name}-${iteration}"</span></div>
+<div class="line"> . (($worker_count > 1) ? <span class="stringliteral">"[1-${worker_count}]"</span> : <span class="stringliteral">''</span>);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8d9888b59ba0e3fe41ac963b6415b894"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::job_name_prefix </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-job_name_prefix" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-job_name_prefix-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-job_name_prefix-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-job_name_prefix-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a8d9888b59ba0e3fe41ac963b6415b894">job_name_prefix</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ($self->pipeline_name() ? $self->pipeline_name().<span class="charliteral">'-'</span> : <span class="stringliteral">''</span>) . <span class="stringliteral">'Hive-'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aad175b19c6c543012f5455740b539ba2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::kill_worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-kill_worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-kill_worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-kill_worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-kill_worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aad175b19c6c543012f5455740b539ba2">kill_worker</a> {</div>
+<div class="line"> my ($self, $worker) = @_;</div>
+<div class="line"></div>
+<div class="line"> die <span class="stringliteral">"Please use a derived method"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="abaa21c35b875562cdf4258eee1b717b3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my ($class, $config) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = bless {}, $class;</div>
+<div class="line"></div>
+<div class="line"> $self->config( $config );</div>
+<div class="line"> $self->context( [ <span class="stringliteral">'Meadow'</span>, $self->type, $self->name ] );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3685ec781296c30f00d2a8c4f3efeffc"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::pipeline_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-pipeline_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3685ec781296c30f00d2a8c4f3efeffc">pipeline_name</a> { # <span class="keywordflow">if</span> set, provides a filter <span class="keywordflow">for</span> job-related queries</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) { # <span class="keyword">new</span> value is being set (which can be undef)</div>
+<div class="line"> $self->{<span class="stringliteral">'_pipeline_name'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_pipeline_name'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa65a2353dde2a128123f36543d5aa115"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::responsible_for_worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-responsible_for_worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-responsible_for_worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-responsible_for_worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-responsible_for_worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa65a2353dde2a128123f36543d5aa115">responsible_for_worker</a> {</div>
+<div class="line"> my ($self, $worker) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ($worker->meadow_type eq $self->type) && ($worker->meadow_name eq $self->name);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0594b46314ad2a8894f055bd58ba923c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::signature </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-signature" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-signature-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-signature-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-signature-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a0594b46314ad2a8894f055bd58ba923c">signature</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->type.<span class="charliteral">'/'</span>.$self->name;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3f921a54a1be9be90a8bb3cd7b7752a3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::type </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-type" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-type-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-type-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-type-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3f921a54a1be9be90a8bb3cd7b7752a3">type</a> { # should <span class="keywordflow">return</span> <span class="stringliteral">'LOCAL'</span> or <span class="stringliteral">'LSF'</span></div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $class = ref($class) if(ref($class));</div>
+<div class="line"></div>
+<div class="line"> return (reverse split(/::/, $class ))[0];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_meadow_8pm.html">Meadow.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Meadow</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.js b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.js
new file mode 100644
index 0000000000000000000000000000000000000000..112dbcc6ef84561f9f27db1f67c67438ce4239df
--- /dev/null
+++ b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.js
@@ -0,0 +1,12 @@
+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow =
+[
+ [ "check_worker_is_alive_and_mine", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa5ed36b42e1e9a3eeb2f2474c37cab8f", null ],
+ [ "generate_job_name", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#ab8b9ebeacf07bfcb38851edbfdd0ae2f", null ],
+ [ "job_name_prefix", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a8d9888b59ba0e3fe41ac963b6415b894", null ],
+ [ "kill_worker", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aad175b19c6c543012f5455740b539ba2", null ],
+ [ "new", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#abaa21c35b875562cdf4258eee1b717b3", null ],
+ [ "pipeline_name", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3685ec781296c30f00d2a8c4f3efeffc", null ],
+ [ "responsible_for_worker", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa65a2353dde2a128123f36543d5aa115", null ],
+ [ "signature", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a0594b46314ad2a8894f055bd58ba923c", null ],
+ [ "type", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3f921a54a1be9be90a8bb3cd7b7752a3", null ]
+];
\ No newline at end of file
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l-members.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l-members.html
new file mode 100644
index 0000000000000000000000000000000000000000..0b57a1d879efe93c9e32f5c06552c7280fffb51d
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+++ b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l-members.html
@@ -0,0 +1,145 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Meadow::LOCAL Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a460348aa64020e5d8a747991f831cd05">check_worker_is_alive_and_mine</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html">Bio::EnsEMBL::Hive::Meadow::LOCAL</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">config</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">config_get</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">config_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">context</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#ad61570016524a1d7411c8b3c64354964">count_pending_workers_by_rc_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html">Bio::EnsEMBL::Hive::Meadow::LOCAL</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a414f3e223753f1e7ce0225848ac33379">count_running_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html">Bio::EnsEMBL::Hive::Meadow::LOCAL</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#ab8b9ebeacf07bfcb38851edbfdd0ae2f">generate_job_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a2fec4ae34aa12e9249775e5cc3e5ba1e">get_current_worker_process_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html">Bio::EnsEMBL::Hive::Meadow::LOCAL</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a8d9888b59ba0e3fe41ac963b6415b894">job_name_prefix</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a2b3d6f77f19e0a635a444d551715704e">kill_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html">Bio::EnsEMBL::Hive::Meadow::LOCAL</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a822009e9a5c178598aa5125475b95f18">name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html">Bio::EnsEMBL::Hive::Meadow::LOCAL</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#abaa21c35b875562cdf4258eee1b717b3">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3685ec781296c30f00d2a8c4f3efeffc">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa65a2353dde2a128123f36543d5aa115">responsible_for_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a0594b46314ad2a8894f055bd58ba923c">signature</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#aec32efb161e4f34a44f3d7baf2f3e643">status_of_all_our_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html">Bio::EnsEMBL::Hive::Meadow::LOCAL</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#aebb3d0f07dcab91a3f189c3f150d24ea">submit_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html">Bio::EnsEMBL::Hive::Meadow::LOCAL</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
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+ <div class="headertitle">
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+<tr class="separator:aa5ed36b42e1e9a3eeb2f2474c37cab8f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aad175b19c6c543012f5455740b539ba2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aad175b19c6c543012f5455740b539ba2">kill_worker</a> ()</td></tr>
+<tr class="separator:aad175b19c6c543012f5455740b539ba2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td></tr>
+<tr class="memitem:a38c57142acfd31f32e87a94717620baf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">config</a> ()</td></tr>
+<tr class="separator:a38c57142acfd31f32e87a94717620baf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a419025891535ecd7b2f05183cf2ce8e4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">context</a> ()</td></tr>
+<tr class="separator:a419025891535ecd7b2f05183cf2ce8e4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeed405377caddb6a1aa3cb605ed6304f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">config_get</a> ()</td></tr>
+<tr class="separator:aeed405377caddb6a1aa3cb605ed6304f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3e556c76396430193c3f613c6f3e4079 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">config_set</a> ()</td></tr>
+<tr class="separator:a3e556c76396430193c3f613c6f3e4079 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is the 'Local' implementation of Meadow
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a460348aa64020e5d8a747991f831cd05"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LOCAL::check_worker_is_alive_and_mine </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-check_worker_is_alive_and_mine" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-check_worker_is_alive_and_mine-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-check_worker_is_alive_and_mine-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-check_worker_is_alive_and_mine-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a460348aa64020e5d8a747991f831cd05">check_worker_is_alive_and_mine</a> {</div>
+<div class="line"> my ($self, $worker) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $wpid = $worker->process_id();</div>
+<div class="line"> my $cmd = qq{ps x | grep $wpid | grep -v <span class="stringliteral">'grep $wpid'</span>};</div>
+<div class="line"> my $is_alive_and_mine = qx/$cmd/;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $is_alive_and_mine;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad61570016524a1d7411c8b3c64354964"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LOCAL::count_pending_workers_by_rc_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-count_pending_workers_by_rc_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-count_pending_workers_by_rc_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-count_pending_workers_by_rc_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-count_pending_workers_by_rc_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#ad61570016524a1d7411c8b3c64354964">count_pending_workers_by_rc_name</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ({}, 0); # LOCAL has no concept of pending workers</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a414f3e223753f1e7ce0225848ac33379"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LOCAL::count_running_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-count_running_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-count_running_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-count_running_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-count_running_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a414f3e223753f1e7ce0225848ac33379">count_running_workers</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $cmd = <span class="stringliteral">'ps x | grep runWorker.pl | grep -v "grep runWorker.pl" | wc -l'</span>;</div>
+<div class="line"> my $run_count = qx/$cmd/;</div>
+<div class="line"> chomp($run_count);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $run_count;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2fec4ae34aa12e9249775e5cc3e5ba1e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LOCAL::get_current_worker_process_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_current_worker_process_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_current_worker_process_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_current_worker_process_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_current_worker_process_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a2fec4ae34aa12e9249775e5cc3e5ba1e">get_current_worker_process_id</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $$;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2b3d6f77f19e0a635a444d551715704e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LOCAL::kill_worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-kill_worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-kill_worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-kill_worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-kill_worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a2b3d6f77f19e0a635a444d551715704e">kill_worker</a> {</div>
+<div class="line"> my $worker = pop @_;</div>
+<div class="line"></div>
+<div class="line"> my $cmd = <span class="stringliteral">'kill -9 '</span>.$worker->process_id();</div>
+<div class="line"> system($cmd);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a822009e9a5c178598aa5125475b95f18"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LOCAL::name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a822009e9a5c178598aa5125475b95f18">name</a> { # also called to check <span class="keywordflow">for</span> availability; <span class="keywordflow">for</span> the moment assume LOCAL meadow is always available</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> (split(/\./, hostname))[0]; # only take the first <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a822009e9a5c178598aa5125475b95f18">name</a></div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aec32efb161e4f34a44f3d7baf2f3e643"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LOCAL::status_of_all_our_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-status_of_all_our_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-status_of_all_our_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-status_of_all_our_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-status_of_all_our_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#aec32efb161e4f34a44f3d7baf2f3e643">status_of_all_our_workers</a> { # returns a hashref</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $cmd = <span class="stringliteral">'ps x -o state,pid,command -w -w | grep runWorker.pl | grep -v "grep runWorker.pl" '</span>;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # FIXME: if we want to incorporate Meadow->pipeline_name() filtering here,</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # a dummy parameter to the runWorker.pl should probably be introduced</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # for 'ps' to be able to externally differentiate between local workers</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # working for different hives</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # (but at the moment such a feature is unlikely to be be in demand).</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my %status_hash = ();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $line (`$cmd`) {</div>
+<div class="line"> my ($pre_status, $worker_pid, $job_name) = split(/\s+/, $line);</div>
+<div class="line"></div>
+<div class="line"> my $status = {</div>
+<div class="line"> <span class="charliteral">'R'</span> => <span class="stringliteral">'RUN'</span>, # running</div>
+<div class="line"></div>
+<div class="line"> <span class="charliteral">'S'</span> => <span class="stringliteral">'RUN'</span>, # sleeping (sleeping <span class="keywordflow">for</span> less than 20 sec on a Mac)</div>
+<div class="line"> <span class="charliteral">'I'</span> => <span class="stringliteral">'RUN'</span>, # Mac: idle (sleeping <span class="keywordflow">for</span> more than 20 sec)</div>
+<div class="line"></div>
+<div class="line"> <span class="charliteral">'D'</span> => <span class="stringliteral">'RUN'</span>, # Linux: uninterruptible sleep, usually IO</div>
+<div class="line"> <span class="charliteral">'U'</span> => <span class="stringliteral">'RUN'</span>, # Mac: uninterruptible wait</div>
+<div class="line"></div>
+<div class="line"> <span class="charliteral">'T'</span> => <span class="stringliteral">'SSUSP'</span> # stopped process</div>
+<div class="line"> }->{ substr($pre_status,0,1) }; # only take the first character because of Mac<span class="stringliteral">'s additional modifiers</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # Note: you can locally '</span>kill -19<span class="stringliteral">' a worker to suspend it and '</span>kill -18<span class="stringliteral">' a worker to resume it</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $status_hash{$worker_pid} = $status;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> return \%status_hash;</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aebb3d0f07dcab91a3f189c3f150d24ea"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LOCAL::submit_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-submit_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-submit_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-submit_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-submit_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#aebb3d0f07dcab91a3f189c3f150d24ea">submit_workers</a> {</div>
+<div class="line"> my ($self, $worker_cmd, $required_worker_count, $iteration, $rc_name, $rc_specific_submission_cmd_args, $submit_stdout_file, $submit_stderr_file) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $cmd = <span class="stringliteral">"$worker_cmd &"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> (1..$required_worker_count) {</div>
+<div class="line"> print <span class="stringliteral">"SUBMITTING_CMD:\t\t$rc_specific_submission_cmd_args $cmd\n"</span>;</div>
+<div class="line"> system( $cmd );</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/Meadow/<a class="el" href="_l_o_c_a_l_8pm.html">LOCAL.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Meadow</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html">LOCAL</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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@@ -0,0 +1,11 @@
+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l =
+[
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+ [ "get_current_worker_process_id", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a2fec4ae34aa12e9249775e5cc3e5ba1e", null ],
+ [ "kill_worker", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a2b3d6f77f19e0a635a444d551715704e", null ],
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+ [ "status_of_all_our_workers", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#aec32efb161e4f34a44f3d7baf2f3e643", null ],
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+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
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+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
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+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Meadow::LSF Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html">Bio::EnsEMBL::Hive::Meadow::LSF</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a9a3c0c5e45f0c8d8f39c353f3613366d">check_worker_is_alive_and_mine</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html">Bio::EnsEMBL::Hive::Meadow::LSF</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">config</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">config_get</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">config_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">context</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#aab163089fbc11ff4c488645833e0b89c">count_pending_workers_by_rc_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html">Bio::EnsEMBL::Hive::Meadow::LSF</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a50fe0638cee223af901c6e4fcbb00ce1">count_running_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html">Bio::EnsEMBL::Hive::Meadow::LSF</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#ae6030241c373e061f40881edf6e01878">find_out_causes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html">Bio::EnsEMBL::Hive::Meadow::LSF</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#ab8b9ebeacf07bfcb38851edbfdd0ae2f">generate_job_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a8f756d46474a89b07f63d23ac1b744f9">get_current_worker_process_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html">Bio::EnsEMBL::Hive::Meadow::LSF</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a8d9888b59ba0e3fe41ac963b6415b894">job_name_prefix</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#accdb28c3a317e4ecc45368b83a426a0c">kill_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html">Bio::EnsEMBL::Hive::Meadow::LSF</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a8be5f1cdaa5eb9e07fc29610e678f836">name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html">Bio::EnsEMBL::Hive::Meadow::LSF</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#abaa21c35b875562cdf4258eee1b717b3">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3685ec781296c30f00d2a8c4f3efeffc">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa65a2353dde2a128123f36543d5aa115">responsible_for_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a0594b46314ad2a8894f055bd58ba923c">signature</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Bio::EnsEMBL::Hive::Meadow</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a48885c8ee5f0225f6252b04d82e7b590">status_of_all_our_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html">Bio::EnsEMBL::Hive::Meadow::LSF</a></td><td class="entry"></td></tr>
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+<tr class="memitem:aa5ed36b42e1e9a3eeb2f2474c37cab8f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa5ed36b42e1e9a3eeb2f2474c37cab8f">check_worker_is_alive_and_mine</a> ()</td></tr>
+<tr class="separator:aa5ed36b42e1e9a3eeb2f2474c37cab8f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aad175b19c6c543012f5455740b539ba2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aad175b19c6c543012f5455740b539ba2">kill_worker</a> ()</td></tr>
+<tr class="separator:aad175b19c6c543012f5455740b539ba2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td></tr>
+<tr class="memitem:a38c57142acfd31f32e87a94717620baf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">config</a> ()</td></tr>
+<tr class="separator:a38c57142acfd31f32e87a94717620baf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a419025891535ecd7b2f05183cf2ce8e4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">context</a> ()</td></tr>
+<tr class="separator:a419025891535ecd7b2f05183cf2ce8e4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeed405377caddb6a1aa3cb605ed6304f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">config_get</a> ()</td></tr>
+<tr class="separator:aeed405377caddb6a1aa3cb605ed6304f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3e556c76396430193c3f613c6f3e4079 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">config_set</a> ()</td></tr>
+<tr class="separator:a3e556c76396430193c3f613c6f3e4079 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is the 'LSF' implementation of Meadow
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a9a3c0c5e45f0c8d8f39c353f3613366d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LSF::check_worker_is_alive_and_mine </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-check_worker_is_alive_and_mine" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-check_worker_is_alive_and_mine-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-check_worker_is_alive_and_mine-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-check_worker_is_alive_and_mine-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a9a3c0c5e45f0c8d8f39c353f3613366d">check_worker_is_alive_and_mine</a> {</div>
+<div class="line"> my ($self, $worker) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $wpid = $worker->process_id();</div>
+<div class="line"> my $this_user = $ENV{<span class="stringliteral">'USER'</span>};</div>
+<div class="line"> my $cmd = qq{bjobs $wpid -u $this_user 2>&1 | grep -v <span class="stringliteral">'not found'</span> | grep -v JOBID | grep -v EXIT};</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"># warn "LSF::check_worker_is_alive_and_mine() running cmd:\n\t$cmd\n";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my $is_alive_and_mine = qx/$cmd/;</div>
+<div class="line"> <span class="keywordflow">return</span> $is_alive_and_mine;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aab163089fbc11ff4c488645833e0b89c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LSF::count_pending_workers_by_rc_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-count_pending_workers_by_rc_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-count_pending_workers_by_rc_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-count_pending_workers_by_rc_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-count_pending_workers_by_rc_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#aab163089fbc11ff4c488645833e0b89c">count_pending_workers_by_rc_name</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $jnp = $self->job_name_prefix();</div>
+<div class="line"> my $cmd = <span class="stringliteral">"bjobs -w -J '${jnp}*' 2>/dev/null | grep PEND"</span>; # <span class="stringliteral">"-u all"</span> has been removed to ensure one user<span class="stringliteral">'s PEND processes</span></div>
+<div class="line"><span class="stringliteral"> # do not affect another user helping to run the same pipeline.</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"># warn "LSF::count_pending_workers_by_rc_name() running cmd:\n\t$cmd\n";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my %pending_this_meadow_by_rc_name = ();</span></div>
+<div class="line"><span class="stringliteral"> my $total_pending_this_meadow = 0;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> foreach my $line (qx/$cmd/) {</span></div>
+<div class="line"><span class="stringliteral"> if($line=~/\b\Q$jnp\E(\S+)\-\d+(\[\d+\])?\b/) {</span></div>
+<div class="line"><span class="stringliteral"> $pending_this_meadow_by_rc_name{$1}++;</span></div>
+<div class="line"><span class="stringliteral"> $total_pending_this_meadow++;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> return (\%pending_this_meadow_by_rc_name, $total_pending_this_meadow);</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a50fe0638cee223af901c6e4fcbb00ce1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LSF::count_running_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-count_running_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-count_running_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-count_running_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-count_running_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a50fe0638cee223af901c6e4fcbb00ce1">count_running_workers</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $jnp = $self->job_name_prefix();</div>
+<div class="line"> my $cmd = <span class="stringliteral">"bjobs -w -J '${jnp}*' -u all 2>/dev/null | grep RUN | wc -l"</span>;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"># warn "LSF::count_running_workers() running cmd:\n\t$cmd\n";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my $run_count = qx/$cmd/;</div>
+<div class="line"> chomp($run_count);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $run_count;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae6030241c373e061f40881edf6e01878"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LSF::find_out_causes </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-find_out_causes" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-find_out_causes-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-find_out_causes-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-find_out_causes-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#ae6030241c373e061f40881edf6e01878">find_out_causes</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my %lsf_2_hive = (</div>
+<div class="line"> <span class="stringliteral">'TERM_MEMLIMIT'</span> => <span class="stringliteral">'MEMLIMIT'</span>,</div>
+<div class="line"> <span class="stringliteral">'TERM_RUNLIMIT'</span> => <span class="stringliteral">'RUNLIMIT'</span>,</div>
+<div class="line"> <span class="stringliteral">'TERM_OWNER'</span> => <span class="stringliteral">'KILLED_BY_USER'</span>,</div>
+<div class="line"> );</div>
+<div class="line"></div>
+<div class="line"> my %cod = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span> (my $pid_batch = join(<span class="charliteral">' '</span>, map { <span class="stringliteral">"'$_'"</span> } splice(@_, 0, 20))) { # can<span class="stringliteral">'t fit too many pids on one shell cmdline</span></div>
+<div class="line"><span class="stringliteral"> my $cmd = "bacct -l $pid_batch";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"># warn "LSF::find_out_causes() running cmd:\n\t$cmd\n";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> foreach my $section (split(/\-{10,}\s+/, `$cmd`)) {</span></div>
+<div class="line"><span class="stringliteral"> if($section=~/^Job <(\d+(?:\[\d+\])?)>.+(TERM_MEMLIMIT|TERM_RUNLIMIT|TERM_OWNER): job killed/is) {</span></div>
+<div class="line"><span class="stringliteral"> $cod{$1} = $lsf_2_hive{$2};</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> return \%cod;</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8f756d46474a89b07f63d23ac1b744f9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LSF::get_current_worker_process_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_current_worker_process_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_current_worker_process_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_current_worker_process_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_current_worker_process_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a8f756d46474a89b07f63d23ac1b744f9">get_current_worker_process_id</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $lsb_jobid = $ENV{<span class="stringliteral">'LSB_JOBID'</span>};</div>
+<div class="line"> my $lsb_jobindex = $ENV{<span class="stringliteral">'LSB_JOBINDEX'</span>};</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(defined($lsb_jobid) and defined($lsb_jobindex)) {</div>
+<div class="line"> <span class="keywordflow">if</span>($lsb_jobindex>0) {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">"$lsb_jobid\[$lsb_jobindex\]"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> <span class="keywordflow">return</span> $lsb_jobid;</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> die <span class="stringliteral">"Could not establish the process_id"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="accdb28c3a317e4ecc45368b83a426a0c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LSF::kill_worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-kill_worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-kill_worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-kill_worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-kill_worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#accdb28c3a317e4ecc45368b83a426a0c">kill_worker</a> {</div>
+<div class="line"> my $worker = pop @_;</div>
+<div class="line"></div>
+<div class="line"> my $cmd = <span class="stringliteral">'bkill '</span>.$worker->process_id();</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"># warn "LSF::kill_worker() running cmd:\n\t$cmd\n";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> system($cmd);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8be5f1cdaa5eb9e07fc29610e678f836"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LSF::name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a8be5f1cdaa5eb9e07fc29610e678f836">name</a> { # also called to check <span class="keywordflow">for</span> availability; assume LSF is available <span class="keywordflow">if</span> LSF cluster_name can be established</div>
+<div class="line"> my $mcni = <span class="stringliteral">'My cluster name is'</span>;</div>
+<div class="line"> my $cmd = <span class="stringliteral">"lsid 2>/dev/null | grep '$mcni'"</span>;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"># warn "LSF::name() running cmd:\n\t$cmd\n";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> <span class="keywordflow">if</span>(my $name = `$cmd`) {</div>
+<div class="line"> $name=~/^$mcni\s+(\S+)/;</div>
+<div class="line"> <span class="keywordflow">return</span> $1;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a48885c8ee5f0225f6252b04d82e7b590"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LSF::status_of_all_our_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-status_of_all_our_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-status_of_all_our_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-status_of_all_our_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-status_of_all_our_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a48885c8ee5f0225f6252b04d82e7b590">status_of_all_our_workers</a> { # returns a hashref</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $jnp = $self->job_name_prefix();</div>
+<div class="line"> my $cmd = <span class="stringliteral">"bjobs -w -J '${jnp}*' -u all 2>/dev/null"</span>;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"># warn "LSF::status_of_all_our_workers() running cmd:\n\t$cmd\n";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> my %status_hash = ();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $line (`$cmd`) {</div>
+<div class="line"> my ($group_pid, $user, $status, $queue, $submission_host, $running_host, $job_name) = split(/\s+/, $line);</div>
+<div class="line"></div>
+<div class="line"> next <span class="keywordflow">if</span>(($group_pid eq <span class="stringliteral">'JOBID'</span>) or ($status eq <span class="stringliteral">'DONE'</span>) or ($status eq <span class="stringliteral">'EXIT'</span>));</div>
+<div class="line"></div>
+<div class="line"> my $worker_pid = $group_pid;</div>
+<div class="line"> <span class="keywordflow">if</span>($job_name=~/(\[\d+\])/) {</div>
+<div class="line"> $worker_pid .= $1;</div>
+<div class="line"> }</div>
+<div class="line"> </div>
+<div class="line"> $status_hash{$worker_pid} = $status;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> \%status_hash;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a653c9100f50d013f0b761a20536cc67f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Meadow::LSF::submit_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-submit_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-submit_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-submit_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-submit_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a653c9100f50d013f0b761a20536cc67f">submit_workers</a> {</div>
+<div class="line"> my ($self, $worker_cmd, $required_worker_count, $iteration, $rc_name, $rc_specific_submission_cmd_args, $submit_stdout_file, $submit_stderr_file) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $job_name = $self->generate_job_name($required_worker_count, $iteration, $rc_name);</div>
+<div class="line"> my $meadow_specific_submission_cmd_args = $self->config_get(<span class="stringliteral">'SubmissionOptions'</span>);</div>
+<div class="line"></div>
+<div class="line"> $submit_stdout_file ||= <span class="stringliteral">'/dev/null'</span>; # a value is required</div>
+<div class="line"> $submit_stderr_file ||= <span class="stringliteral">'/dev/null'</span>; # a value is required</div>
+<div class="line"></div>
+<div class="line"> $ENV{<span class="stringliteral">'LSB_STDOUT_DIRECT'</span>} = <span class="charliteral">'y'</span>; # unbuffer the output of the bsub command</div>
+<div class="line"></div>
+<div class="line"> my $cmd = qq{bsub -o $submit_stdout_file -e $submit_stderr_file -J <span class="stringliteral">"${job_name}"</span> $rc_specific_submission_cmd_args $meadow_specific_submission_cmd_args $worker_cmd};</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"LSF::submit_workers() running cmd:\n\t$cmd\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> system($cmd) && die <span class="stringliteral">"Could not submit job(s): $!, $?"</span>; # let<span class="stringliteral">'s abort the beekeeper and let the user check the syntax</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/Meadow/<a class="el" href="_l_s_f_8pm.html">LSF.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Meadow</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html">LSF</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
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+];
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+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html">Bio::EnsEMBL::Hive::NakedTable</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#ae26cea149a37ce38a76340febf821ea3">adaptor</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html">Bio::EnsEMBL::Hive::NakedTable</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a34c62ade6f73ec76a1b2e46eefdc3f41">dataflow</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html">Bio::EnsEMBL::Hive::NakedTable</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a386c4340b8343abd91aaf33ad66d61a1">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html">Bio::EnsEMBL::Hive::NakedTable</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a86e40bedaa4255b62bb61b92e1b663c8">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html">Bio::EnsEMBL::Hive::NakedTable</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a6442b5f290356a70eec3d0f15e5004ca">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html">Bio::EnsEMBL::Hive::NakedTable</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a2a7e0b5d326bdfbcbb8135bda2d2b842">url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html">Bio::EnsEMBL::Hive::NakedTable</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
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+ <li class="footer">Generated by
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diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html
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+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+ <li><a href="annotated.html"><span>Class List</span></a></li>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+<div class="header">
+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::NakedTable Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a86e40bedaa4255b62bb61b92e1b663c8"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a86e40bedaa4255b62bb61b92e1b663c8">new</a> ()</td></tr>
+<tr class="separator:a86e40bedaa4255b62bb61b92e1b663c8"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae26cea149a37ce38a76340febf821ea3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#ae26cea149a37ce38a76340febf821ea3">adaptor</a> ()</td></tr>
+<tr class="separator:ae26cea149a37ce38a76340febf821ea3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6442b5f290356a70eec3d0f15e5004ca"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a6442b5f290356a70eec3d0f15e5004ca">table_name</a> ()</td></tr>
+<tr class="separator:a6442b5f290356a70eec3d0f15e5004ca"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a386c4340b8343abd91aaf33ad66d61a1"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a386c4340b8343abd91aaf33ad66d61a1">insertion_method</a> ()</td></tr>
+<tr class="separator:a386c4340b8343abd91aaf33ad66d61a1"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2a7e0b5d326bdfbcbb8135bda2d2b842"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a2a7e0b5d326bdfbcbb8135bda2d2b842">url</a> ()</td></tr>
+<tr class="separator:a2a7e0b5d326bdfbcbb8135bda2d2b842"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a34c62ade6f73ec76a1b2e46eefdc3f41"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a34c62ade6f73ec76a1b2e46eefdc3f41">dataflow</a> ()</td></tr>
+<tr class="separator:a34c62ade6f73ec76a1b2e46eefdc3f41"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A data container object that links together an adaptor, a table and a preferred insertion method (insert/insert-ignore/replace).
+ This object is generated from specially designed datalow URLs.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ae26cea149a37ce38a76340febf821ea3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::NakedTable::adaptor </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-adaptor" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-adaptor-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-adaptor-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-adaptor-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#ae26cea149a37ce38a76340febf821ea3">adaptor</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_adaptor'</span>} = shift @_;</div>
+<div class="line"> weaken $self->{<span class="stringliteral">'_adaptor'</span>};</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_adaptor'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a34c62ade6f73ec76a1b2e46eefdc3f41"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::NakedTable::dataflow </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-dataflow" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dataflow-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dataflow-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dataflow-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a34c62ade6f73ec76a1b2e46eefdc3f41">dataflow</a> {</div>
+<div class="line"> my ( $self, $output_ids, $emitting_job ) = @_;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # we have to do this the ugly way</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # because Registry code currently prevents us from passing arguments to adaptors' new() methods</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # (and by caching guarantees there is only one instance of each adaptor per DBAdaptor)</span></div>
+<div class="line"><span class="preprocessor"></span> my $adaptor = $self->adaptor();</div>
+<div class="line"> $adaptor->table_name( $self->table_name() );</div>
+<div class="line"> $adaptor->insertion_method( $self->insertion_method() );</div>
+<div class="line"></div>
+<div class="line"> my @column_names = keys %{$self->adaptor->column_set};</div>
+<div class="line"> my @rows = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $output_id (@$output_ids) {</div>
+<div class="line"> my %row_hash = ();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $column (@column_names) {</div>
+<div class="line"> $row_hash{ $column } = $emitting_job->_param_possibly_overridden($column, $output_id);</div>
+<div class="line"> }</div>
+<div class="line"> push @rows, \%row_hash;</div>
+<div class="line"> }</div>
+<div class="line"> $adaptor->store( \@rows );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a386c4340b8343abd91aaf33ad66d61a1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::NakedTable::insertion_method </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-insertion_method" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-insertion_method-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-insertion_method-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-insertion_method-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a386c4340b8343abd91aaf33ad66d61a1">insertion_method</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_insertion_method'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_insertion_method'</span>} || <span class="stringliteral">'INSERT_IGNORE'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a86e40bedaa4255b62bb61b92e1b663c8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::NakedTable::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = bless {}, $class;</div>
+<div class="line"></div>
+<div class="line"> my ($adaptor, $table_name, $insertion_method) = </div>
+<div class="line"> rearrange([qw(<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#ae26cea149a37ce38a76340febf821ea3">adaptor</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a6442b5f290356a70eec3d0f15e5004ca">table_name</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a386c4340b8343abd91aaf33ad66d61a1">insertion_method</a>) ], @_);</div>
+<div class="line"></div>
+<div class="line"> $self->adaptor($adaptor) <span class="keywordflow">if</span>(defined($adaptor));</div>
+<div class="line"> $self->table_name($table_name) <span class="keywordflow">if</span>(defined($table_name));</div>
+<div class="line"> $self->insertion_method($insertion_method) <span class="keywordflow">if</span>(defined($insertion_method));</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a6442b5f290356a70eec3d0f15e5004ca"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::NakedTable::table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a6442b5f290356a70eec3d0f15e5004ca">table_name</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_table_name'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_table_name'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2a7e0b5d326bdfbcbb8135bda2d2b842"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::NakedTable::url </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-url" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-url-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-url-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-url-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a2a7e0b5d326bdfbcbb8135bda2d2b842">url</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $ref_dba = shift @_; # <span class="keywordflow">if</span> reference dba is the same as <span class="stringliteral">'our'</span> dba, a shorter <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a2a7e0b5d326bdfbcbb8135bda2d2b842">url</a> can be generated</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $adaptor = $self->adaptor) {</div>
+<div class="line"> my $conn_prefix = ($adaptor->db == $ref_dba) ? <span class="stringliteral">':///'</span> : $adaptor->db->dbc->url();</div>
+<div class="line"> <span class="keywordflow">return</span> $conn_prefix .<span class="charliteral">'/'</span>. $self->table_name() . <span class="stringliteral">'?insertion_method='</span> . $self->insertion_method();</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> <span class="keywordflow">return</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_naked_table_8pm.html">NakedTable.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html">NakedTable</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+[
+ [ "adaptor", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#ae26cea149a37ce38a76340febf821ea3", null ],
+ [ "dataflow", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a34c62ade6f73ec76a1b2e46eefdc3f41", null ],
+ [ "insertion_method", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a386c4340b8343abd91aaf33ad66d61a1", null ],
+ [ "new", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a86e40bedaa4255b62bb61b92e1b663c8", null ],
+ [ "table_name", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a6442b5f290356a70eec3d0f15e5004ca", null ],
+ [ "url", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a2a7e0b5d326bdfbcbb8135bda2d2b842", null ]
+];
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
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+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
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+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
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+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Params Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a0536cad5480d931d7982fe0f049ebfaf">_param_possibly_overridden</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a416e12ae4a4511ba13ba427cfc2361d5">_param_silent</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a960052271c6be58027f13c1cadbe5ad8">_subst_one_hashpair</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a77d324a4242b0c01f6f1288846db43d6">csvq</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7c9b7527f3745f962277b5022d1d09ca">mysql_conn</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7660586a322000f6f797927a3a216676">mysql_dbname</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a5be508c964ea50f555fbd9692a226f67">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#aacc3d8e3ec1b0f940cc274c95c93e834">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a46b02fdd5e620c96f4f8abe8e1bc017b">param_exists</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a03f67c01a12beaa839338be4da9bf9cb">param_init</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#ad6dba01319677081085a59310e235c51">param_is_defined</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a82a8b3a737120fdf27b3152bc1c63bab">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a261b12abc17c65fac5fd4ccffbb73d6d">param_substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Bio::EnsEMBL::Hive::Params</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html
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+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Bio::EnsEMBL::Hive::Params Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+var searchBox = new SearchBox("searchBox", "search",false,'Search');
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+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Params Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::Params:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params_inherit__map" alt="Inheritance graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params_inherit__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params_inherit__map">
+<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html" title="Bio::EnsEMBL::Hive\l::AnalysisJob" alt="" coords="5,97,147,138"/></map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a5be508c964ea50f555fbd9692a226f67"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a5be508c964ea50f555fbd9692a226f67">new</a> ()</td></tr>
+<tr class="separator:a5be508c964ea50f555fbd9692a226f67"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a03f67c01a12beaa839338be4da9bf9cb"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a03f67c01a12beaa839338be4da9bf9cb">param_init</a> ()</td></tr>
+<tr class="separator:a03f67c01a12beaa839338be4da9bf9cb"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0536cad5480d931d7982fe0f049ebfaf"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a0536cad5480d931d7982fe0f049ebfaf">_param_possibly_overridden</a> ()</td></tr>
+<tr class="separator:a0536cad5480d931d7982fe0f049ebfaf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a416e12ae4a4511ba13ba427cfc2361d5"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a416e12ae4a4511ba13ba427cfc2361d5">_param_silent</a> ()</td></tr>
+<tr class="separator:a416e12ae4a4511ba13ba427cfc2361d5"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a82a8b3a737120fdf27b3152bc1c63bab"><td class="memItemLeft" align="right" valign="top">public Any </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a82a8b3a737120fdf27b3152bc1c63bab">param_required</a> ()</td></tr>
+<tr class="separator:a82a8b3a737120fdf27b3152bc1c63bab"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a46b02fdd5e620c96f4f8abe8e1bc017b"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a46b02fdd5e620c96f4f8abe8e1bc017b">param_exists</a> ()</td></tr>
+<tr class="separator:a46b02fdd5e620c96f4f8abe8e1bc017b"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad6dba01319677081085a59310e235c51"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#ad6dba01319677081085a59310e235c51">param_is_defined</a> ()</td></tr>
+<tr class="separator:ad6dba01319677081085a59310e235c51"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aacc3d8e3ec1b0f940cc274c95c93e834"><td class="memItemLeft" align="right" valign="top">public Any </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#aacc3d8e3ec1b0f940cc274c95c93e834">param</a> ()</td></tr>
+<tr class="separator:aacc3d8e3ec1b0f940cc274c95c93e834"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a261b12abc17c65fac5fd4ccffbb73d6d"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a261b12abc17c65fac5fd4ccffbb73d6d">param_substitute</a> ()</td></tr>
+<tr class="separator:a261b12abc17c65fac5fd4ccffbb73d6d"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7c9b7527f3745f962277b5022d1d09ca"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7c9b7527f3745f962277b5022d1d09ca">mysql_conn</a> ()</td></tr>
+<tr class="separator:a7c9b7527f3745f962277b5022d1d09ca"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7660586a322000f6f797927a3a216676"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7660586a322000f6f797927a3a216676">mysql_dbname</a> ()</td></tr>
+<tr class="separator:a7660586a322000f6f797927a3a216676"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a77d324a4242b0c01f6f1288846db43d6"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a77d324a4242b0c01f6f1288846db43d6">csvq</a> ()</td></tr>
+<tr class="separator:a77d324a4242b0c01f6f1288846db43d6"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a960052271c6be58027f13c1cadbe5ad8"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a960052271c6be58027f13c1cadbe5ad8">_subst_one_hashpair</a> ()</td></tr>
+<tr class="separator:a960052271c6be58027f13c1cadbe5ad8"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">By inheriting from <span class="keyword">this</span> module you make your module able to deal with parameters:</div>
+<div class="line"></div>
+<div class="line"> 1) parsing of parameters in the order of precedence, starting with the lowest:</div>
+<div class="line"> #</div>
+<div class="line"> ## general usage:</div>
+<div class="line"> # $self->param_init( $lowest_precedence_hashref, $middle_precedence_hashref, $highest_precedence_hashref );</div>
+<div class="line"><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> ## typical usage:</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # $job->param_init( </span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # $runObj->param_defaults(), # module-wide built-in defaults have the lowest precedence (will always be the same for this module)</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # $self->db->get_MetaContainer->get_param_hash(), # then come the pipeline-wide parameters from the 'meta' table (define things common to all modules in this pipeline)</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # $self->analysis->parameters(), # analysis-wide 'parameters' are even more specific (can be defined differently for several occurence of the same module)</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # $job->input_id(), # job-specific 'input_id' parameters have the highest precedence</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # );</span></div>
+<div class="line"><span class="preprocessor"></span> </div>
+<div class="line"></div>
+<div class="line"> 2) reading a parameter<span class="stringliteral">'s value</span></div>
+<div class="line"><span class="stringliteral"> #</span></div>
+<div class="line"><span class="stringliteral"> # my $source = $self->param('</span>source<span class="stringliteral">'); )</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> 3) dynamically setting a parameter'</span>s value</div>
+<div class="line"> #</div>
+<div class="line"> # $self->param(<span class="stringliteral">'binpath'</span>, <span class="stringliteral">'/software/ensembl/compara'</span>);</div>
+<div class="line"><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span> Note: It proved to be a convenient mechanism to exchange params</div>
+<div class="line"> between fetch_input(), run(), write_output() and other methods.</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Most of Compara RunnableDB methods work under assumption
+ that both analysis.parameters and job.input_id fields contain a Perl-style parameter hashref as a string.
+
+ This module implements a generic param() method that allows to set parameters according to the following parameter precedence rules:
+
+ (1) Job-Specific parameters defined in job.input_id hash, they have the highest priority and override everything else.
+
+ (2) Analysis-Wide parameters defined in analysis.parameters hash. Can be overridden by (1).
+
+ (3) Pipeline-Wide parameters defined in the 'meta' table. Can be overridden by (1) and (2).
+
+ (4) Module_Defaults that are hard-coded into modules have the lowest precedence. Can be overridden by (1), (2) and (3).
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a0536cad5480d931d7982fe0f049ebfaf"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Params::_param_possibly_overridden </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_param_possibly_overridden" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_param_possibly_overridden-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_param_possibly_overridden-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_param_possibly_overridden-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a0536cad5480d931d7982fe0f049ebfaf">_param_possibly_overridden</a> {</div>
+<div class="line"> my ($self, $param_name, $overriding_hash) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ( ( (ref($overriding_hash) eq <span class="stringliteral">'HASH'</span>) && exists($overriding_hash->{ $param_name }) )</div>
+<div class="line"> ? $overriding_hash->{ $param_name }</div>
+<div class="line"> : $self->_param_silent($param_name)</div>
+<div class="line"> );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a416e12ae4a4511ba13ba427cfc2361d5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Params::_param_silent </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_param_silent" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_param_silent-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_param_silent-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_param_silent-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a416e12ae4a4511ba13ba427cfc2361d5">_param_silent</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $param_name = shift @_</div>
+<div class="line"> or die <span class="stringliteral">"ParamError: calling param() without arguments\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) { # If there is a value (even <span class="keywordflow">if</span> undef), then set it!</div>
+<div class="line"> $self->{<span class="stringliteral">'_param_hash'</span>}{$param_name} = shift @_;</div>
+<div class="line"> } elsif( !exists( $self->{<span class="stringliteral">'_param_hash'</span>}{$param_name} )</div>
+<div class="line"> and exists( $self->{<span class="stringliteral">'_unsubstituted_param_hash'</span>}{$param_name} ) ) {</div>
+<div class="line"> my $unsubstituted = $self->{<span class="stringliteral">'_unsubstituted_param_hash'</span>}{$param_name};</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_param_hash'</span>}{$param_name} = $self->param_substitute( $unsubstituted );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> exists( $self->{<span class="stringliteral">'_param_hash'</span>}{$param_name} )</div>
+<div class="line"> ? $self->{<span class="stringliteral">'_param_hash'</span>}{$param_name}</div>
+<div class="line"> : undef;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a960052271c6be58027f13c1cadbe5ad8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Params::_subst_one_hashpair </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: this is a private method that performs one substitution. Called by <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a261b12abc17c65fac5fd4ccffbb73d6d">param_substitute()</a>.</pre><pre> </pre><div id="codesection-_subst_one_hashpair" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_subst_one_hashpair-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_subst_one_hashpair-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_subst_one_hashpair-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a960052271c6be58027f13c1cadbe5ad8">_subst_one_hashpair</a> {</div>
+<div class="line"> my ($self, $inside_hashes, $overriding_hash) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->{<span class="stringliteral">'_substitution_in_progress'</span>}{$inside_hashes}++) {</div>
+<div class="line"> die <span class="stringliteral">"ParamError: substitution loop among {"</span>.join(<span class="stringliteral">', '</span>, map {<span class="stringliteral">"'$_'"</span>} keys %{$self->{<span class="stringliteral">'_substitution_in_progress'</span>}}).<span class="stringliteral">"} has been detected\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $value;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($inside_hashes=~/^\w+$/) {</div>
+<div class="line"></div>
+<div class="line"> $value = $self->_param_possibly_overridden($inside_hashes, $overriding_hash);</div>
+<div class="line"></div>
+<div class="line"> } elsif($inside_hashes=~/^(\w+):(\w+)$/) {</div>
+<div class="line"></div>
+<div class="line"> $value = $self->$1($self->_param_possibly_overridden($2, $overriding_hash));</div>
+<div class="line"></div>
+<div class="line"> } elsif($inside_hashes=~/^expr\((.*)\)expr$/) {</div>
+<div class="line"></div>
+<div class="line"> my $expression = $1;</div>
+<div class="line"><span class="preprocessor"> # FIXME: the following two lines will have to be switched to drop support for $old_substitution_syntax and stay with #new_substitution_syntax#</span></div>
+<div class="line"><span class="preprocessor"></span> $expression=~s{(?:\$(\w+)|#(\w+)#)}{stringify($self->_param_possibly_overridden($1 <span class="comment">// $2, $overriding_hash))}eg; # substitute-by-value (bulky, but supports old syntax)</span></div>
+<div class="line"># $expression=~s{(?:#(\w+)#)}{\$self->_param_possibly_overridden(<span class="stringliteral">'$1'</span>, \$overriding_hash)}g; # substitute-by-call (no longer supports old syntax)</div>
+<div class="line"></div>
+<div class="line"> $value = eval <span class="stringliteral">"return $expression"</span>; # NB: <span class="stringliteral">'return'</span> is needed to protect the hashrefs from being interpreted as scoping blocks</div>
+<div class="line"><span class="preprocessor"># warn "SOH: #$inside_hashes# becomes $expression and is then evaluated into ".stringify($value)."\n";</span></div>
+<div class="line"><span class="preprocessor"></span> }</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"ParamWarning: substituting an undefined value of #$inside_hashes#\n"</span> unless(defined($value));</div>
+<div class="line"></div>
+<div class="line"> <span class="keyword">delete</span> $self->{<span class="stringliteral">'_substitution_in_progress'</span>}{$inside_hashes};</div>
+<div class="line"> <span class="keywordflow">return</span> $value;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a77d324a4242b0c01f6f1288846db43d6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Params::csvq </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-csvq" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-csvq-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-csvq-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-csvq-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a77d324a4242b0c01f6f1288846db43d6">csvq</a> { # another example stringification formatter</div>
+<div class="line"> my ($self, $list) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> join(<span class="charliteral">','</span>, map { <span class="stringliteral">"'$_'"</span> } @$list);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7c9b7527f3745f962277b5022d1d09ca"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Params::mysql_conn </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-mysql_conn" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-mysql_conn-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-mysql_conn-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-mysql_conn-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7c9b7527f3745f962277b5022d1d09ca">mysql_conn</a> { # an example stringification formatter (others can be defined here or in a descendent of Params)</div>
+<div class="line"> my ($self, $db_conn) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(ref($db_conn) eq <span class="stringliteral">'HASH'</span>) {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">"--host=$db_conn->{-host} --port=$db_conn->{-port} --user='$db_conn->{-user}' --password='$db_conn->{-pass}' $db_conn->{-dbname}"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> my $dbc = go_figure_dbc( $db_conn );</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'--host='</span>.$dbc->host.<span class="stringliteral">' --port='</span>.$dbc->port.<span class="stringliteral">" --user='"</span>.$dbc->username.<span class="stringliteral">"' --password='"</span>.$dbc->password.<span class="stringliteral">"' "</span>.$dbc->dbname;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7660586a322000f6f797927a3a216676"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Params::mysql_dbname </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-mysql_dbname" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-mysql_dbname-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-mysql_dbname-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-mysql_dbname-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7660586a322000f6f797927a3a216676">mysql_dbname</a> { # another example stringification formatter</div>
+<div class="line"> my ($self, $db_conn) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(ref($db_conn) eq <span class="stringliteral">'HASH'</span>) {</div>
+<div class="line"> <span class="keywordflow">return</span> $db_conn->{-dbname};</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> my $dbc = go_figure_dbc( $db_conn );</div>
+<div class="line"> <span class="keywordflow">return</span> $dbc->dbname;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a5be508c964ea50f555fbd9692a226f67"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Params::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: a trivial constructor, mostly for testing a <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Params</a> object</pre><pre> </pre><div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> bless {}, $class;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aacc3d8e3ec1b0f940cc274c95c93e834"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Any Bio::EnsEMBL::Hive::Params::param </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : string $param_name</pre><pre> Arg [2] : (optional) $param_value</pre><pre> Description: A getter/setter method for a job's parameters that are initialized through 4 levels of precedence (see <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a03f67c01a12beaa839338be4da9bf9cb">param_init()</a> )</pre><pre> Example 1 : my $source = $self->param('source'); # acting as a getter</pre><pre> Example 2 : $self->param('binpath', '/software/ensembl/compara'); # acting as a setter</pre><pre> Returntype : any Perl structure or object that you dared to store</pre><pre> </pre><div id="codesection-param" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#aacc3d8e3ec1b0f940cc274c95c93e834">param</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $param_name = shift @_</div>
+<div class="line"> or die <span class="stringliteral">"ParamError: calling param() without arguments\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $value = $self->_param_silent( $param_name, @_ );</div>
+<div class="line"> </div>
+<div class="line"> unless( $self->param_exists( $param_name ) ) {</div>
+<div class="line"> warn <span class="stringliteral">"ParamWarning: value for param('$param_name') is used before having been initialized!\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $value;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a46b02fdd5e620c96f4f8abe8e1bc017b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Boolean Bio::EnsEMBL::Hive::Params::param_exists </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : string $param_name</pre><pre> Description: A predicate tester for whether the parameter has been initialized (even to undef)</pre><pre> Example :</pre><div class="fragment"><div class="line"><span class="keywordflow">if</span>( $self->param_exists(<span class="stringliteral">'source'</span>) ) { print <span class="stringliteral">"'source' exists\n"</span>; } <span class="keywordflow">else</span> { print <span class="stringliteral">"never heard of 'source'\n"</span>; }</div>
+</div><!-- fragment --> <pre> Returntype : boolean</pre><pre> </pre><div id="codesection-param_exists" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_exists-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_exists-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_exists-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a46b02fdd5e620c96f4f8abe8e1bc017b">param_exists</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $param_name = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> exists( $self->{<span class="stringliteral">'_param_hash'</span>}{$param_name} )</div>
+<div class="line"> ? 1</div>
+<div class="line"> : 0;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a03f67c01a12beaa839338be4da9bf9cb"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Params::param_init </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: First parses the parameters from all sources in the reverse precedence order (supply the lowest precedence hash first),
+ then preforms "total" parameter substitution.
+ Will fail on detecting a substitution loop.</pre><pre> </pre><div id="codesection-param_init" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_init-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_init-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_init-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a03f67c01a12beaa839338be4da9bf9cb">param_init</a> {</div>
+<div class="line"> </div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $strict_hash_format = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my %unsubstituted_param_hash = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $source (@_) {</div>
+<div class="line"> <span class="keywordflow">if</span>(ref($source) ne <span class="stringliteral">'HASH'</span>) {</div>
+<div class="line"> <span class="keywordflow">if</span>($strict_hash_format or $source=~/^\{.*\}$/) {</div>
+<div class="line"> my $param_hash = eval($source) || {};</div>
+<div class="line"> <span class="keywordflow">if</span>($@ or (ref($param_hash) ne <span class="stringliteral">'HASH'</span>)) {</div>
+<div class="line"> <span class="keywordflow">if</span>($self->can(<span class="stringliteral">'transient_error'</span>)) {</div>
+<div class="line"> $self->transient_error(0);</div>
+<div class="line"> }</div>
+<div class="line"> die <span class="stringliteral">"Expected a {'param'=>'value'} hashref, but got the following string instead: '$source'\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> $source = $param_hash;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $source = {};</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">while</span>(my ($k,$v) = each %$source ) {</div>
+<div class="line"> $unsubstituted_param_hash{$k} = $v;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_unsubstituted_param_hash'</span>} = \%unsubstituted_param_hash;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad6dba01319677081085a59310e235c51"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Boolean Bio::EnsEMBL::Hive::Params::param_is_defined </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : string $param_name</pre><pre> Description: A predicate tester for definedness of a parameter</pre><pre> Example :</pre><div class="fragment"><div class="line"><span class="keywordflow">if</span>( $self->param_is_defined(<span class="stringliteral">'source'</span>) ) { print <span class="stringliteral">"defined, possibly zero"</span>; } <span class="keywordflow">else</span> { print <span class="stringliteral">"undefined"</span>; }</div>
+</div><!-- fragment --> <pre> Returntype : boolean</pre><pre> </pre><div id="codesection-param_is_defined" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_is_defined-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_is_defined-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_is_defined-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#ad6dba01319677081085a59310e235c51">param_is_defined</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $param_name = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> defined( $self->_param_silent($param_name) )</div>
+<div class="line"> ? 1</div>
+<div class="line"> : 0;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a82a8b3a737120fdf27b3152bc1c63bab"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Any Bio::EnsEMBL::Hive::Params::param_required </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : string $param_name</pre><pre> Description: A strict getter method for a job's parameter; will die if the parameter was not set or is undefined</pre><pre> Example :</pre><div class="fragment"><div class="line">my $source = $self->param_required(<span class="stringliteral">'source'</span>);</div>
+</div><!-- fragment --> <pre> Returntype : any Perl structure or object that you dared to store</pre><pre> </pre><div id="codesection-param_required" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_required-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_required-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_required-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a82a8b3a737120fdf27b3152bc1c63bab">param_required</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $param_name = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $value = $self->_param_silent($param_name);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> defined( $value )</div>
+<div class="line"> ? $value</div>
+<div class="line"> : die <span class="stringliteral">"ParamError: value for param_required('$param_name') is required and has to be defined\n"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a261b12abc17c65fac5fd4ccffbb73d6d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Params::param_substitute </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : Perl structure $string_with_templates</pre><pre> Description: Performs parameter substitution on strings that contain templates like " #param_name# followed by #another_param_name# " .</pre><pre> Returntype : *another* Perl structure with matching topology (may be more complex as a result of substituting a substructure for a term)</pre><pre> </pre><div id="codesection-param_substitute" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_substitute-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_substitute-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_substitute-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a261b12abc17c65fac5fd4ccffbb73d6d">param_substitute</a> {</div>
+<div class="line"> my ($self, $structure, $overriding_hash) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $ref_type = ref($structure);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(!$ref_type) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(!$structure) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $structure;</div>
+<div class="line"></div>
+<div class="line"> } elsif($structure=~/^(?:#(expr\(.+?\)expr|[\w:]+)#)$/) { # <span class="keywordflow">if</span> the given <span class="keywordtype">string</span> is one complete substitution, we don<span class="stringliteral">'t want to force the output into a string</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> return $self->_subst_one_hashpair($1, $overriding_hash);</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> my $scalar_defined = 1;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $structure=~s/(?:#(expr\(.+?\)expr|[\w:]+)#)/my $value = $self->_subst_one_hashpair($1, $overriding_hash); $scalar_defined &&= defined($value); $value/eg;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> return $scalar_defined ? $structure : undef;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> } elsif($ref_type eq '</span>ARRAY<span class="stringliteral">') {</span></div>
+<div class="line"><span class="stringliteral"> my @substituted_array = ();</span></div>
+<div class="line"><span class="stringliteral"> foreach my $element (@$structure) {</span></div>
+<div class="line"><span class="stringliteral"> push @substituted_array, $self->param_substitute($element, $overriding_hash);</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
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+<div class="title">Bio::EnsEMBL::Hive::PipeConfig::AnyCommands_conf Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_any_commands__conf.html">Bio::EnsEMBL::Hive::PipeConfig::AnyCommands_conf</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a28568127780ecee07cde885f1ec1a1f3">default_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_any_commands__conf.html#a44f48f0a63c2c7b84a029e2f77f99786">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_any_commands__conf.html">Bio::EnsEMBL::Hive::PipeConfig::AnyCommands_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
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+<tr class="separator:a639062a270bf3af88f896c9231f38133 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:af4d7bd7b523fc76a3c58aa15141c5f2c inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ab46a140ff5e2b90989979ea6cba6bf06 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a16457254eff693383b5e2a9dcc5b19b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:adb95548d620d772327085f7bb96b8b3a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td></tr>
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+<tr class="separator:a729f524427ef5292b7e980f134aa456f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a12fa6e8360e2db6bd40dc318654b9d42 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a> ()</td></tr>
+<tr class="separator:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a> ()</td></tr>
+<tr class="separator:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="memitem:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> ()</td></tr>
+<tr class="separator:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_any_commands__conf.html">Bio::EnsEMBL::Hive::PipeConfig::AnyCommands_conf</a> -password <your_password></div>
+<div class="line"></div>
+<div class="line">seed_pipeline.pl -url $HIVE_URL -logic_name perform_cmd -input_id <span class="stringliteral">"{'cmd' => 'gzip pdfs/RondoAllaTurca_Mozart_Am.pdf; sleep 5'}"</span></div>
+<div class="line"></div>
+<div class="line">runWorker.pl -url $HIVE_URL</div>
+<div class="line"></div>
+<div class="line">seed_pipeline.pl -url $HIVE_URL -logic_name perform_cmd -input_id <span class="stringliteral">"{'cmd' => 'gzip -d pdfs/RondoAllaTurca_Mozart_Am.pdf.gz ; sleep 4'}"</span></div>
+<div class="line"></div>
+<div class="line">runWorker.pl -url $HIVE_URL</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is the smallest Hive pipeline example possible.
+ The pipeline has only one analysis, which can run any shell command defined in each job by setting its 'cmd' parameter.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a44f48f0a63c2c7b84a029e2f77f99786"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::AnyCommands_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_any_commands__conf.html#a44f48f0a63c2c7b84a029e2f77f99786">pipeline_analyses</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> { -logic_name => <span class="stringliteral">'perform_cmd'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/PipeConfig/<a class="el" href="_any_commands__conf_8pm.html">AnyCommands_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_any_commands__conf.html">AnyCommands_conf</a></li>
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+<div class="title">Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf Member List</div> </div>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
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+<tr class="separator:a96f20328299d6747be0b641087c012ee inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:af4d7bd7b523fc76a3c58aa15141c5f2c inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a> ()</td></tr>
+<tr class="separator:af4d7bd7b523fc76a3c58aa15141c5f2c inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab46a140ff5e2b90989979ea6cba6bf06 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a> ()</td></tr>
+<tr class="separator:ab46a140ff5e2b90989979ea6cba6bf06 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a766a75f28b07ea491d7e8fdc97ee2ad6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a> ()</td></tr>
+<tr class="separator:a766a75f28b07ea491d7e8fdc97ee2ad6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a194b948521dcdf1e6a8f83a4fc3b1c11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a> ()</td></tr>
+<tr class="separator:a194b948521dcdf1e6a8f83a4fc3b1c11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a16457254eff693383b5e2a9dcc5b19b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a> ()</td></tr>
+<tr class="separator:a16457254eff693383b5e2a9dcc5b19b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adb95548d620d772327085f7bb96b8b3a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a> ()</td></tr>
+<tr class="separator:adb95548d620d772327085f7bb96b8b3a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td></tr>
+<tr class="memitem:a729f524427ef5292b7e980f134aa456f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a> ()</td></tr>
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+<tr class="memitem:a12fa6e8360e2db6bd40dc318654b9d42 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a> ()</td></tr>
+<tr class="separator:a12fa6e8360e2db6bd40dc318654b9d42 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a> ()</td></tr>
+<tr class="separator:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a> ()</td></tr>
+<tr class="separator:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8b28b1e6e1ef24ac3d9143062ddc36d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a> ()</td></tr>
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+<tr class="memitem:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a> ()</td></tr>
+<tr class="separator:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a> ()</td></tr>
+<tr class="separator:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> ()</td></tr>
+<tr class="separator:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_apply_to_databases__conf.html">Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf</a> -password <your_password></div>
+<div class="line"></div>
+<div class="line">init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_apply_to_databases__conf.html">Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf</a> -password <your_password> -only_databases <span class="charliteral">'%'</span></div>
+</div><!-- fragment --> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a9e6433a752ae91242daaed87123f7ad3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf::default_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_apply_to_databases__conf.html#a9e6433a752ae91242daaed87123f7ad3">default_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{ $self->SUPER::default_options() }, # inherit other stuff from the base <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'pipeline_name'</span> => <span class="stringliteral">'apply_to_databases'</span>, # name used by the beekeeper to prefix job names on the farm</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'source_server1'</span> => <span class="stringliteral">'mysql://ensadmin:'</span>.$self->o(<span class="stringliteral">'password'</span>).<span class="stringliteral">'@127.0.0.1:3306/'</span>,</div>
+<div class="line"> <span class="stringliteral">'source_server2'</span> => <span class="stringliteral">'mysql://ensadmin:'</span>.$self->o(<span class="stringliteral">'password'</span>).<span class="stringliteral">'@127.0.0.1:2914/'</span>,</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'only_databases'</span> => <span class="stringliteral">'%\_core\_%'</span>, # use <span class="charliteral">'%'</span> to <span class="keyword">get</span> a list of all available databases</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad1acd6cf7955d0a0ed331020d25dbca8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_apply_to_databases__conf.html#ad1acd6cf7955d0a0ed331020d25dbca8">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> { -logic_name => <span class="stringliteral">'get_databases'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::JobFactory'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'inputquery'</span> => q{SHOW DATABASES LIKE <span class="stringliteral">"}.$self->o('only_databases').q{"</span>},</div>
+<div class="line"> <span class="stringliteral">'column_names'</span> => [ <span class="stringliteral">'dbname'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> -input_ids => [</div>
+<div class="line"> { <span class="stringliteral">'db_conn'</span> => $self->o(<span class="stringliteral">'source_server1'</span>) },</div>
+<div class="line"> { <span class="stringliteral">'db_conn'</span> => $self->o(<span class="stringliteral">'source_server2'</span>) },</div>
+<div class="line"> ],</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"> 2 => { <span class="stringliteral">'run_sql'</span> => { <span class="stringliteral">'db_conn'</span> => <span class="stringliteral">'#db_conn##dbname#'</span> },</div>
+<div class="line"> }</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> { -logic_name => <span class="stringliteral">'run_sql'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::Dummy'</span>, # use SqlCmd.pm to <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a> your query or another JobFactory.pm to make another fan on table names</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> },</div>
+<div class="line"> -analysis_capacity => 10, # allow several workers to perform identical tasks in parallel</div>
+<div class="line"> -input_ids => [</div>
+<div class="line"><span class="preprocessor"> # (jobs for this analysis will be flown_into via branch-2 from 'get_databases' jobs above)</span></div>
+<div class="line"><span class="preprocessor"></span> ],</div>
+<div class="line"> },</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/PipeConfig/<a class="el" href="_apply_to_databases__conf_8pm.html">ApplyToDatabases_conf.pm</a></li>
+</ul>
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+</div><!-- doc-content -->
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+ <ul>
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+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="dynsections.js"></script>
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ <li><a href="pages.html"><span>Related Pages</span></a></li>
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+ <li><a href="files.html"><span>Files</span></a></li>
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+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
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+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
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+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html','');});
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+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+<div class="title">Bio::EnsEMBL::Hive::PipeConfig::CompressFiles_conf Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html">Bio::EnsEMBL::Hive::PipeConfig::CompressFiles_conf</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a28568127780ecee07cde885f1ec1a1f3">default_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html#a8420a6236b02bab63cb9cd160728ce72">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html">Bio::EnsEMBL::Hive::PipeConfig::CompressFiles_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
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+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::PipeConfig::CompressFiles_conf:</div>
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+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html">Bio::EnsEMBL::Hive::PipeConfig::CompressFiles_conf</a> -password <your_password></div>
+<div class="line"></div>
+<div class="line">seed_pipeline.pl -url <url> -logic_name find_files -input_id <span class="stringliteral">"{ 'directory' => 'dumps' }"</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is an example pipeline put together from two basic building blocks:
+
+ Analysis_1: JobFactory.pm is used to turn the list of files in a given directory into jobs
+
+ these jobs are sent down the branch #2 into the second analysis
+
+ Analysis_2: SystemCmd.pm is used to run these compression/decompression jobs in parallel.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a8420a6236b02bab63cb9cd160728ce72"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::CompressFiles_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html#a8420a6236b02bab63cb9cd160728ce72">pipeline_analyses()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that defines the structure of the pipeline: analyses, jobs, rules, etc.
+ Here it defines two analyses:</pre><pre> 'find_files' generates a list of files whose names match the pattern #only_files#
+ Each job of this analysis will dataflow (create jobs) via branch #2 into 'compress_a_file' analysis.</pre><pre> 'compress_a_file' actually performs the (un)gzipping of the files in parallel</pre><pre> </pre><div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html#a8420a6236b02bab63cb9cd160728ce72">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> { -logic_name => <span class="stringliteral">'find_files'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::JobFactory'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'inputcmd'</span> => <span class="stringliteral">'find #directory# -type f'</span>,</div>
+<div class="line"> <span class="stringliteral">'column_names'</span> => [ <span class="stringliteral">'filename'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"> 2 => [ <span class="stringliteral">'compress_a_file'</span> ], # will create a fan of jobs</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> { -logic_name => <span class="stringliteral">'compress_a_file'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'gzip #filename#'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> -analysis_capacity => 4, # limit the number of workers that will be performing jobs in parallel</div>
+<div class="line"> },</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/PipeConfig/<a class="el" href="_compress_files__conf_8pm.html">CompressFiles_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html">CompressFiles_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
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+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
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+ </tr>
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+<div class="title">Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html">Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html#a1763292c10a5df1d25ec8ffbbaeefd75">default_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html">Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html#a3c0d2ac018f87a5adb6f78764154228f">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html">Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html">Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf</a> -password <your_password></div>
+<div class="line"></div>
+<div class="line">init_pipeline.pl FailureTest_conf.pm -host=localhost -password <your_password> -job_count 100 -failure_rate 3</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is an example pipeline built around FailureTest.pm RunnableDB. It consists of two analyses:
+
+ Analysis_1: JobFactory.pm is used to create an array of jobs -
+
+ these jobs are sent down the branch #2 into the second analysis
+
+ Analysis_2: FailureTest.pm either succeeds or dies, depending on the parameters.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a1763292c10a5df1d25ec8ffbbaeefd75"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf::default_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html#a1763292c10a5df1d25ec8ffbbaeefd75">default_options()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that is used to initialize default options.
+ In addition to the standard things it defines three options:
+ o('job_count') controls the total number of FailureTest jobs
+ o('failure_rate') controls the rate of jobs that are programmed to fail
+ o('state') controls the state in which the jobs will be failing
+ o('lethal_after') when job_number is above this (nonzero) threshold, job's death becomes lethal to the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Worker</a></pre><pre> There is a rule dependent on one option that does not have a default (this makes it mandatory):
+ o('password') your read-write password for creation and maintenance of the hive database</pre><pre> </pre><div id="codesection-default_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html#a1763292c10a5df1d25ec8ffbbaeefd75">default_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{ $self->SUPER::default_options() }, # inherit other stuff from the base <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'pipeline_name'</span> => <span class="stringliteral">'failure_test'</span>, # name used by the beekeeper to prefix job names on the farm</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'job_count'</span> => 20, # controls the total number of FailureTest jobs</div>
+<div class="line"> <span class="stringliteral">'failure_rate'</span> => 3, # controls the rate of jobs that are programmed to fail</div>
+<div class="line"> <span class="stringliteral">'state'</span> => <span class="stringliteral">'RUN'</span>, # controls in which state the jobs are programmed to fail</div>
+<div class="line"> <span class="stringliteral">'lethal_after'</span> => 0,</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3c0d2ac018f87a5adb6f78764154228f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html#a3c0d2ac018f87a5adb6f78764154228f">pipeline_analyses()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that defines the structure of the pipeline: analyses, jobs, rules, etc.
+ Here it defines two analyses:</pre><pre> 'generate_jobs' generates a list of jobs</pre><pre> 'failure_test' either succeeds or fails, depending on parameters</pre><pre> </pre><div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html#a3c0d2ac018f87a5adb6f78764154228f">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> { -logic_name => <span class="stringliteral">'generate_jobs'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::JobFactory'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'inputlist'</span> => <span class="stringliteral">'#expr([0..$job_count-1])expr#'</span>, # <span class="keyword">this</span> expression will evaluate into a listref</div>
+<div class="line"> <span class="stringliteral">'column_names'</span> => [ <span class="stringliteral">'value'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> -input_ids => [</div>
+<div class="line"> { <span class="stringliteral">'job_count'</span> => $self->o(<span class="stringliteral">'job_count'</span>) },</div>
+<div class="line"> ],</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"> 2 => [ <span class="stringliteral">'failure_test'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> { -logic_name => <span class="stringliteral">'failure_test'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::FailureTest'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'divisor'</span> => $self->o(<span class="stringliteral">'failure_rate'</span>),</div>
+<div class="line"> <span class="stringliteral">'state'</span> => $self->o(<span class="stringliteral">'state'</span>),</div>
+<div class="line"> <span class="stringliteral">'lethal_after'</span> => $self->o(<span class="stringliteral">'lethal_after'</span>),</div>
+<div class="line"> }</div>
+<div class="line"> },</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/PipeConfig/<a class="el" href="_failure_test__conf_8pm.html">FailureTest_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html">FailureTest_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
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+  <span id="projectnumber">1.9</span>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#a77596009fcf0b4b84e07090667b28e2f">default_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html">Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#aaee0e442c23012ab2f414b85adb6a719">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html">Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#ad8d93256c230c0134de507b0fc067dee">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html">Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+<tr class="separator:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a8b28b1e6e1ef24ac3d9143062ddc36d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html">Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf</a> -inputfile reference.fasta -chunks_dir reference_chunks</div>
+</div><!-- fragment --> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a77596009fcf0b4b84e07090667b28e2f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf::default_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#a77596009fcf0b4b84e07090667b28e2f">default_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{ $self->SUPER::default_options() }, # inherit other stuff from the base <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'pipeline_name'</span> => <span class="stringliteral">'split_fasta'</span>, # name used by the beekeeper to prefix job names on the farm</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # runnable-specific parameters' defaults:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'max_chunk_length'</span> => 500000,</div>
+<div class="line"> <span class="stringliteral">'output_prefix'</span> => <span class="stringliteral">'chunk_number_'</span>,</div>
+<div class="line"> <span class="stringliteral">'output_suffix'</span> => <span class="stringliteral">'.fasta'</span>,</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'chunks_dir'</span> => <span class="stringliteral">'fasta_split_chunks'</span>,</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aaee0e442c23012ab2f414b85adb6a719"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#aaee0e442c23012ab2f414b85adb6a719">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> { -logic_name => <span class="stringliteral">'split_fasta'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::FastaFactory'</span>,</div>
+<div class="line"> -input_ids => [ {</div>
+<div class="line"> <span class="stringliteral">'inputfile'</span> => $self->o(<span class="stringliteral">'inputfile'</span>),</div>
+<div class="line"> <span class="stringliteral">'max_chunk_length'</span> => $self->o(<span class="stringliteral">'max_chunk_length'</span>),</div>
+<div class="line"> <span class="stringliteral">'output_prefix'</span> => $self->o(<span class="stringliteral">'chunks_dir'</span>).<span class="charliteral">'/'</span>.$self->o(<span class="stringliteral">'output_prefix'</span>),</div>
+<div class="line"> <span class="stringliteral">'output_suffix'</span> => $self->o(<span class="stringliteral">'output_suffix'</span>),</div>
+<div class="line"> } ],</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"> 2 => [ <span class="stringliteral">'align'</span> ], # will create a fan of jobs</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> { -logic_name => <span class="stringliteral">'align'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::Dummy'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad8d93256c230c0134de507b0fc067dee"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf::pipeline_create_commands </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-pipeline_create_commands" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_create_commands-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_create_commands-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_create_commands-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#ad8d93256c230c0134de507b0fc067dee">pipeline_create_commands</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> @{$self->SUPER::pipeline_create_commands}, # inheriting database and hive tables<span class="stringliteral">' creation</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> '</span>mkdir -p <span class="stringliteral">'.$self->o('</span>chunks_dir<span class="stringliteral">'),</span></div>
+<div class="line"><span class="stringliteral"> ];</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/PipeConfig/<a class="el" href="_fasta_splitter__conf_8pm.html">FastaSplitter_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html">FastaSplitter_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>, including all inherited members.</p>
+<table class="directory">
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a28568127780ecee07cde885f1ec1a1f3">default_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7072b951f3d57b690c0d2a2465d75d9b">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf:</div>
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+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
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+<tr class="memitem:af4d7bd7b523fc76a3c58aa15141c5f2c"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a> ()</td></tr>
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+<tr class="memitem:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a> ()</td></tr>
+<tr class="separator:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a> ()</td></tr>
+<tr class="separator:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8b28b1e6e1ef24ac3d9143062ddc36d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a> ()</td></tr>
+<tr class="separator:a8b28b1e6e1ef24ac3d9143062ddc36d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a> ()</td></tr>
+<tr class="separator:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a> ()</td></tr>
+<tr class="separator:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> ()</td></tr>
+<tr class="separator:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line"><span class="preprocessor"> # Example 1: specifying only the mandatory option:</span></div>
+<div class="line"><span class="preprocessor"></span>init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> -password <mypass></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Example 2: specifying the mandatory options as well as overriding some defaults:</span></div>
+<div class="line"><span class="preprocessor">init_pipeline.pl Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf -host <myhost> -dbname <mydbname> -password <mypass></span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Generic configuration module for all Hive pipelines with loader functionality.
+ All other Hive PipeConfig modules should inherit from this module and will probably need to redefine some or all of the following interface methods:
+
+ default_options: returns a hash of (possibly multilevel) defaults for the options on which depend the rest of the configuration
+
+ pipeline_create_commands: returns a list of strings that will be executed as system commands needed to create and set up the pipeline database
+
+ pipeline_wide_parameters: returns a hash of pipeline-wide parameter names and their values
+
+ resource_classes: returns a hash of resource class definitions
+
+ pipeline_analyses: returns a list of hash structures that define analysis objects bundled with definitions of corresponding jobs, rules and resources
+
+ beekeeper_extra_cmdline_options returns a string with command line options that you want to be passed to the beekeeper.pl
+
+ When defining anything except the keys of default_options() a call to $self->o('myoption') can be used.
+ This call means "substitute this call for the value of 'myoption' at the time of configuring the pipeline".
+ All option names mentioned in $self->o() calls within the five interface methods above can be given non-default values from the command line.
+
+ Please make sure you have studied the pipeline configuraton examples in Bio::EnsEMBL::Hive::PipeConfig before creating your own PipeConfig modules.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a7a8b253910f9f1bd288b4c1526353cd8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::beekeeper_extra_cmdline_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Interface method that should return a string with extra parameters that you want to be passed to <a class="el" href="beekeeper_8pl.html">beekeeper.pl</a></pre><pre> </pre><div id="codesection-beekeeper_extra_cmdline_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-beekeeper_extra_cmdline_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-beekeeper_extra_cmdline_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-beekeeper_extra_cmdline_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">''</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a766a75f28b07ea491d7e8fdc97ee2ad6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::db_cmd </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Returns a <a class="el" href="db__cmd_8pl.html">db_cmd.pl</a>-based command line that should execute by any supported driver (mysql/pgsql/sqlite)</pre><pre> </pre><div id="codesection-db_cmd" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-db_cmd-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-db_cmd-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-db_cmd-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a> {</div>
+<div class="line"> my ($self, $sql_command, $db_url) = @_;</div>
+<div class="line"></div>
+<div class="line"> $db_url <span class="comment">//= $self->pipeline_url();</span></div>
+<div class="line"> my $db_cmd_path = $self->o(<span class="stringliteral">'hive_root_dir'</span>).<span class="stringliteral">'/scripts/db_cmd.pl'</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">"$db_cmd_path -url $db_url"</span>.($sql_command ? <span class="stringliteral">" -sql '$sql_command'"</span> : <span class="stringliteral">''</span>);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="afa08fa64e8dc50604507f72fece0b9e2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::db_connect_command </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description :</p>
+<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000004">Deprecated:</a></b></dt><dd>method. Please use $self-><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd()</a> instead.</dd></dl>
+</pre><pre> </pre><div id="codesection-db_connect_command" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-db_connect_command-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-db_connect_command-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-db_connect_command-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a> {</div>
+<div class="line"> my ($self, $db_conn) = @_;</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"\nDEPRECATED: db_connect_command() method is no longer supported, please call db_cmd(\$sql_command) instead, it will be more portable\n\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $driver = $self->o($db_conn, <span class="stringliteral">'-driver'</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'sqlite'</span> => <span class="stringliteral">'sqlite3 '</span>.$self->o($db_conn, <span class="stringliteral">'-dbname'</span>),</div>
+<div class="line"> <span class="stringliteral">'mysql'</span> => <span class="stringliteral">'mysql '</span>.$self->dbconn_2_mysql($db_conn, 1),</div>
+<div class="line"> <span class="stringliteral">'pgsql'</span> => <span class="stringliteral">"env PGPASSWORD='"</span>.$self->o($db_conn,<span class="stringliteral">'-pass'</span>).<span class="stringliteral">"' psql "</span>.$self->dbconn_2_pgsql($db_conn, 1),</div>
+<div class="line"> }->{ $driver };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a96f20328299d6747be0b641087c012ee"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::db_execute_command </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description :</p>
+<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000005">Deprecated:</a></b></dt><dd>method. Please use $self-><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd()</a> instead.</dd></dl>
+</pre><pre> </pre><div id="codesection-db_execute_command" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-db_execute_command-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-db_execute_command-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-db_execute_command-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a> {</div>
+<div class="line"> my ($self, $db_conn, $sql_command, $with_db) = @_;</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"\nDEPRECATED: db_execute_command() method is no longer supported, please call db_cmd(\$sql_command) instead, it will be more portable\n\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> $with_db = 1 unless(defined($with_db));</div>
+<div class="line"></div>
+<div class="line"> my $driver = $self->o($db_conn, <span class="stringliteral">'-driver'</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(($driver eq <span class="stringliteral">'sqlite'</span>) && !$with_db) { # in these special cases we pretend sqlite can understand these commands</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">"rm -f $1"</span> <span class="keywordflow">if</span>($sql_command=~/DROP\s+DATABASE\s+(?:IF\s+EXISTS\s+)?(\w+)/);</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">"touch $1"</span> <span class="keywordflow">if</span>($sql_command=~/CREATE\s+DATABASE\s+(\w+)/);</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'sqlite'</span> => <span class="stringliteral">'sqlite3 '</span>.$self->o($db_conn, <span class="stringliteral">'-dbname'</span>).<span class="stringliteral">" '$sql_command'"</span>,</div>
+<div class="line"> <span class="stringliteral">'mysql'</span> => <span class="stringliteral">'mysql '</span>.$self->dbconn_2_mysql($db_conn, $with_db).<span class="stringliteral">" -e '$sql_command'"</span>,</div>
+<div class="line"> <span class="stringliteral">'pgsql'</span> => <span class="stringliteral">"env PGPASSWORD='"</span>.$self->o($db_conn,<span class="stringliteral">'-pass'</span>).<span class="stringliteral">"' psql --command='$sql_command' "</span>.$self->dbconn_2_pgsql($db_conn, $with_db),</div>
+<div class="line"> }->{ $driver };</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a08af9a5dfe9c8a40757a6b3140d4a569"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::dbconn_2_mysql </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description :</p>
+<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000002">Deprecated:</a></b></dt><dd>method. Please use $self-><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd()</a> instead.</dd></dl>
+</pre><pre> </pre><div id="codesection-dbconn_2_mysql" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dbconn_2_mysql-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dbconn_2_mysql-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dbconn_2_mysql-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a> { # will save you a lot of typing</div>
+<div class="line"> my ($self, $db_conn, $with_db) = @_;</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"\nDEPRECATED: dbconn_2_mysql() method is no longer supported, please call db_cmd(\$sql_command) instead, it will be more portable\n\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $port = $self->o($db_conn,<span class="stringliteral">'-port'</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'--host='</span>.$self->o($db_conn,<span class="stringliteral">'-host'</span>).<span class="charliteral">' '</span></div>
+<div class="line"> .($port ? <span class="stringliteral">'--port='</span>.$self->o($db_conn,<span class="stringliteral">'-port'</span>).<span class="charliteral">' '</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> .<span class="stringliteral">'--user="'</span>.$self->o($db_conn,<span class="stringliteral">'-user'</span>).<span class="stringliteral">'" '</span></div>
+<div class="line"> .<span class="stringliteral">'--password="'</span>.$self->o($db_conn,<span class="stringliteral">'-pass'</span>).<span class="stringliteral">'" '</span></div>
+<div class="line"> .($with_db ? ($self->o($db_conn,<span class="stringliteral">'-dbname'</span>).<span class="charliteral">' '</span>) : <span class="stringliteral">''</span>);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a116f65a759b66589980b5c84b0cfe1c4"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::dbconn_2_pgsql </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description :</p>
+<dl class="deprecated"><dt><b><a class="el" href="deprecated.html#_deprecated000003">Deprecated:</a></b></dt><dd>method. Please use $self-><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd()</a> instead.</dd></dl>
+</pre><pre> </pre><div id="codesection-dbconn_2_pgsql" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dbconn_2_pgsql-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dbconn_2_pgsql-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dbconn_2_pgsql-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a> { # will save you a lot of typing</div>
+<div class="line"> my ($self, $db_conn, $with_db) = @_;</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"\nDEPRECATED: dbconn_2_pgsql() method is no longer supported, please call db_cmd(\$sql_command) instead, it will be more portable\n\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $port = $self->o($db_conn,<span class="stringliteral">'-port'</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'--host='</span>.$self->o($db_conn,<span class="stringliteral">'-host'</span>).<span class="charliteral">' '</span></div>
+<div class="line"> .($port ? <span class="stringliteral">'--port='</span>.$self->o($db_conn,<span class="stringliteral">'-port'</span>).<span class="charliteral">' '</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> .<span class="stringliteral">'--username="'</span>.$self->o($db_conn,<span class="stringliteral">'-user'</span>).<span class="stringliteral">'" '</span></div>
+<div class="line"> .($with_db ? ($self->o($db_conn,<span class="stringliteral">'-dbname'</span>).<span class="charliteral">' '</span>) : <span class="stringliteral">''</span>);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af4d7bd7b523fc76a3c58aa15141c5f2c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::dbconn_2_url </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : A convenience method used to stringify a connection-parameters hash into a 'pipeline_url' that <a class="el" href="beekeeper_8pl.html">beekeeper.pl</a> will undestand</pre><pre> </pre><div id="codesection-dbconn_2_url" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dbconn_2_url-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dbconn_2_url-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dbconn_2_url-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a> {</div>
+<div class="line"> my ($self, $db_conn, $with_db) = @_;</div>
+<div class="line"></div>
+<div class="line"> $with_db = 1 unless(defined($with_db));</div>
+<div class="line"></div>
+<div class="line"> my $driver = $self->o($db_conn, <span class="stringliteral">'-driver'</span>);</div>
+<div class="line"> my $port = $self->o($db_conn,<span class="stringliteral">'-port'</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ( ($driver eq <span class="stringliteral">'sqlite'</span>)</div>
+<div class="line"> ? $driver.<span class="stringliteral">':///'</span></div>
+<div class="line"> : $driver.<span class="stringliteral">'://'</span>.$self->o($db_conn,<span class="stringliteral">'-user'</span>).<span class="charliteral">':'</span>.$self->o($db_conn,<span class="stringliteral">'-pass'</span>).<span class="charliteral">'@'</span>.$self->o($db_conn,<span class="stringliteral">'-host'</span>).($port ? <span class="charliteral">':'</span>.$port : <span class="stringliteral">''</span>).<span class="charliteral">'/'</span></div>
+<div class="line"> ) . ($with_db ? $self->o($db_conn,<span class="stringliteral">'-dbname'</span>) : <span class="stringliteral">''</span>);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a28568127780ecee07cde885f1ec1a1f3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::default_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Interface method that should return a hash of option_name->default_option_value pairs.
+ Please see existing <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a> modules for examples.</pre><pre> </pre><div id="codesection-default_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a28568127780ecee07cde885f1ec1a1f3">default_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"><span class="preprocessor"> # Please note: ENVironment variables may be "exported" to inherit from enclosing shell,</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # but if you want to *prevent* that you need to specifically say so</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # (setting a password to empty string does exactly that - sets it to an empty string)</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # [bash] export -n ENSEMBL_CVS_ROOT_DIR # will stop exporting, but the value in current shell stays as it was</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # [tcsh] unsetenv ENSEMBL_CVS_ROOT_DIR # will destroy the variable even in current shell, and stop exporting</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> <span class="stringliteral">'ensembl_cvs_root_dir'</span> => $ENV{<span class="stringliteral">'ENSEMBL_CVS_ROOT_DIR'</span>} || $self->o(<span class="stringliteral">'ensembl_cvs_root_dir'</span>), # it will make sense to set <span class="keyword">this</span> variable <span class="keywordflow">if</span> you are going to use ehive with ensembl</div>
+<div class="line"> <span class="stringliteral">'ensembl_release'</span> => Bio::EnsEMBL::ApiVersion::software_version(), # snapshot of EnsEMBL Core API version. Please <span class="keywordflow">do</span> not change <span class="keywordflow">if</span> not sure.</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'hive_root_dir'</span> => $ENV{<span class="stringliteral">'EHIVE_ROOT_DIR'</span>} # <span class="keyword">this</span> value is set up automatically <span class="keywordflow">if</span> <span class="keyword">this</span> code is <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a> by init_pipeline.pl</div>
+<div class="line"> || $self->o(<span class="stringliteral">'ensembl_cvs_root_dir'</span>).<span class="stringliteral">'/ensembl-hive'</span>, # otherwise we have to rely on other means</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'hive_driver'</span> => <span class="stringliteral">'mysql'</span>,</div>
+<div class="line"> <span class="stringliteral">'host'</span> => $ENV{<span class="stringliteral">'EHIVE_HOST'</span>} || <span class="stringliteral">'localhost'</span>, # BEWARE that <span class="stringliteral">'localhost'</span> <span class="keywordflow">for</span> mysql driver usually means a UNIX socket, not a TCPIP socket!</div>
+<div class="line"><span class="preprocessor"> # If you need to connect to TCPIP socket, set -host => '127.0.0.1' instead.</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> <span class="stringliteral">'port'</span> => $ENV{<span class="stringliteral">'EHIVE_PORT'</span>}, # or remain undef, which means <span class="keywordflow">default</span> <span class="keywordflow">for</span> the driver</div>
+<div class="line"> <span class="stringliteral">'user'</span> => $ENV{<span class="stringliteral">'EHIVE_USER'</span>} || <span class="stringliteral">'ensadmin'</span>,</div>
+<div class="line"> <span class="stringliteral">'password'</span> => $ENV{<span class="stringliteral">'EHIVE_PASS'</span>} <span class="comment">// $ENV{'ENSADMIN_PSW'} // $self->o('password'), # people will have to make an effort NOT to insert it into config files like .bashrc etc</span></div>
+<div class="line"> <span class="stringliteral">'dbowner'</span> => $ENV{<span class="stringliteral">'EHIVE_USER'</span>} || $ENV{<span class="stringliteral">'USER'</span>} || $self->o(<span class="stringliteral">'dbowner'</span>), # although it is very unlikely $ENV{USER} is not set</div>
+<div class="line"> <span class="stringliteral">'pipeline_name'</span> => $self->pipeline_name(),</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'hive_use_triggers'</span> => 0, # there have been a few cases of big pipelines misbehaving with triggers on, let<span class="stringliteral">'s keep the default off.</span></div>
+<div class="line"><span class="stringliteral"> '</span>hive_use_param_stack<span class="stringliteral">' => 0, # do not reconstruct the calling stack of parameters by default (yet)</span></div>
+<div class="line"><span class="stringliteral"> '</span>hive_force_init<span class="stringliteral">' => 0, # setting it to 1 will drop the database prior to creation (use with care!)</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> '</span>pipeline_db<span class="stringliteral">' => {</span></div>
+<div class="line"><span class="stringliteral"> -driver => $self->o('</span>hive_driver<span class="stringliteral">'),</span></div>
+<div class="line"><span class="stringliteral"> -host => $self->o('</span>host<span class="stringliteral">'),</span></div>
+<div class="line"><span class="stringliteral"> -port => $self->o('</span>port<span class="stringliteral">'),</span></div>
+<div class="line"><span class="stringliteral"> -user => $self->o('</span>user<span class="stringliteral">'),</span></div>
+<div class="line"><span class="stringliteral"> -pass => $self->o('</span>password<span class="stringliteral">'),</span></div>
+<div class="line"><span class="stringliteral"> -dbname => $self->o('</span>dbowner<span class="stringliteral">').'</span>_<span class="stringliteral">'.$self->o('</span><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a><span class="stringliteral">'), # example of a linked definition (resolved via saturation)</span></div>
+<div class="line"><span class="stringliteral"> },</span></div>
+<div class="line"><span class="stringliteral"> };</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a35edd8ed45d8aea1de4f5c5124455a21"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::hive_meta_table </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-hive_meta_table" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-hive_meta_table-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-hive_meta_table-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-hive_meta_table-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'hive_sql_schema_version'</span> => <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a0c2dc02c4e81944f9eb9fa7f670aa753">get_code_sql_schema_version</a>(),</div>
+<div class="line"> <span class="stringliteral">'hive_pipeline_name'</span> => $self->o(<span class="stringliteral">'pipeline_name'</span>),</div>
+<div class="line"> <span class="stringliteral">'hive_use_param_stack'</span> => $self->o(<span class="stringliteral">'hive_use_param_stack'</span>),</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7072b951f3d57b690c0d2a2465d75d9b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Interface method that should return a list of hashes that define analysis bundled with corresponding jobs, dataflow and analysis_ctrl rules and resource_id.
+ Please see existing <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a> modules for examples.</pre><pre> </pre><div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7072b951f3d57b690c0d2a2465d75d9b">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a24011bab6821ed4f89114444eb997215"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::pipeline_create_commands </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Interface method that should return a list of command lines to be run in order to create and set up the pipeline database.
+ Please see existing <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a> modules for examples.</pre><pre> </pre><div id="codesection-pipeline_create_commands" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_create_commands-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_create_commands-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_create_commands-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $pipeline_url = $self->pipeline_url();</div>
+<div class="line"> my $parsed_url = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l.html#ac80cc911eba215fb0ed17104861fe5f7">Bio::EnsEMBL::Hive::Utils::URL::parse</a>( $pipeline_url );</div>
+<div class="line"> my $driver = $parsed_url ? $parsed_url->{<span class="stringliteral">'driver'</span>} : <span class="stringliteral">''</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> $self->o(<span class="stringliteral">'hive_force_init'</span>) ? $self->db_cmd(<span class="stringliteral">'DROP DATABASE IF EXISTS'</span>) : (),</div>
+<div class="line"> $self->db_cmd(<span class="stringliteral">'CREATE DATABASE'</span>),</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # we got table definitions for all drivers:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->db_cmd().<span class="stringliteral">' <'</span>.$self->o(<span class="stringliteral">'hive_root_dir'</span>).<span class="stringliteral">'/sql/tables.'</span>.$driver,</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # auto-sync'ing triggers are off by default and not yet available in pgsql:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->o(<span class="stringliteral">'hive_use_triggers'</span>) && ($driver ne <span class="stringliteral">'pgsql'</span>) ? ( $self->db_cmd().<span class="stringliteral">' <'</span>.$self->o(<span class="stringliteral">'hive_root_dir'</span>).<span class="stringliteral">'/sql/triggers.'</span>.$driver ) : (),</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # FOREIGN KEY constraints cannot be defined in sqlite separately from table definitions, so they are off there:</span></div>
+<div class="line"><span class="preprocessor"></span> ($driver ne <span class="stringliteral">'sqlite'</span>) ? ( $self->db_cmd().<span class="stringliteral">' <'</span>.$self->o(<span class="stringliteral">'hive_root_dir'</span>).<span class="stringliteral">'/sql/foreign_keys.sql'</span> ) : (),</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # we got procedure definitions for all drivers:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->db_cmd().<span class="stringliteral">' <'</span>.$self->o(<span class="stringliteral">'hive_root_dir'</span>).<span class="stringliteral">'/sql/procedures.'</span>.$driver,</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a194b948521dcdf1e6a8f83a4fc3b1c11"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::pipeline_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-pipeline_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $pipeline_name = shift @_;</div>
+<div class="line"></div>
+<div class="line"> unless($pipeline_name) { # or turn the ClassName into <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>:</div>
+<div class="line"> $pipeline_name = ref($self); # <span class="keyword">get</span> the original <span class="keyword">class </span>name</div>
+<div class="line"> $pipeline_name=~s/^.*::<span class="comment">//; # trim the leading classpath prefix</span></div>
+<div class="line"> $pipeline_name=~s/_conf$<span class="comment">//; # trim the optional _conf from the end</span></div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $pipeline_name=~s/([[:lower:]])([[:upper:]])/${1}_${2}/g; # CamelCase into Camel_Case</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> lc($pipeline_name);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab46a140ff5e2b90989979ea6cba6bf06"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::pipeline_url </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-pipeline_url" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_url-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_url-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_url-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->root()->{<span class="stringliteral">'pipeline_url'</span>} || $self->dbconn_2_url(<span class="stringliteral">'pipeline_db'</span>, 1); # used to force vivification of the whole <span class="stringliteral">'pipeline_db'</span> structure (used in <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>() )</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0c6ccdb318ca662f0ead725ab661273e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::pipeline_wide_parameters </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Interface method that should return a hash of pipeline_wide_parameter_name->pipeline_wide_parameter_value pairs.
+ The value doesn't have to be a scalar, can be any Perl structure now (will be stringified and de-stringified automagically).
+ Please see existing <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a> modules for examples.</pre><pre> </pre><div id="codesection-pipeline_wide_parameters" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_wide_parameters-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_wide_parameters-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_wide_parameters-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'schema_version'</span> => $self->o(<span class="stringliteral">'ensembl_release'</span>), # keep compatibility with core API</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a639062a270bf3af88f896c9231f38133"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::pre_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-pre_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pre_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pre_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pre_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'help!'</span> => <span class="stringliteral">''</span>,</div>
+<div class="line"> <span class="stringliteral">'job_topup!'</span> => <span class="stringliteral">''</span>,</div>
+<div class="line"> <span class="stringliteral">'analysis_topup!'</span> => <span class="stringliteral">''</span>,</div>
+<div class="line"> <span class="stringliteral">'pipeline_url'</span> => <span class="stringliteral">''</span>,</div>
+<div class="line"><span class="preprocessor"># 'hive_use_triggers' => '',</span></div>
+<div class="line"><span class="preprocessor"></span> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a16457254eff693383b5e2a9dcc5b19b2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::process_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : The method that does all the parameter parsing magic.
+ It is two-pass through the interface methods: first pass collects the options, second is intelligent substitution.</pre><pre> Caller : <a class="el" href="init__pipeline_8pl.html">init_pipeline.pl</a> or any other script that will drive this module.</pre><pre> Note : You can override parsing the command line bit by providing a hash as the argument to this method.
+ This hash should contain definitions of all the parameters you would otherwise be providing from the command line.
+ Useful if you are creating batches of hive pipelines using a script.</pre><pre> </pre><div id="codesection-process_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-process_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-process_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-process_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # pre-patch definitely_used_options:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->{<span class="stringliteral">'_extra_options'</span>} = $self->load_cmdline_options( $self->pre_options() );</div>
+<div class="line"> $self->root()->{<span class="stringliteral">'pipeline_url'</span>} = $self->{<span class="stringliteral">'_extra_options'</span>}{<span class="stringliteral">'pipeline_url'</span>};</div>
+<div class="line"></div>
+<div class="line"> $self->use_cases( [ <span class="stringliteral">'pipeline_create_commands'</span>, <span class="stringliteral">'pipeline_wide_parameters'</span>, <span class="stringliteral">'resource_classes'</span>, <span class="stringliteral">'pipeline_analyses'</span>, <span class="stringliteral">'beekeeper_extra_cmdline_options'</span>, <span class="stringliteral">'pipeline_url'</span>, <span class="stringliteral">'hive_meta_table'</span> ] );</div>
+<div class="line"> <span class="keywordflow">return</span> $self->SUPER::process_options();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a6d9612ad9a85971bc0734cbfb26854d7"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::resource_classes </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Interface method that should return a hash of resource_description_id->resource_description_hash.
+ Please see existing <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a> modules for examples.</pre><pre> </pre><div id="codesection-resource_classes" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-resource_classes-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-resource_classes-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-resource_classes-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"><span class="preprocessor">## Old style:</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"># 1 => { -desc => 'default', 'LSF' => '' },</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"># 2 => { -desc => 'urgent', 'LSF' => '-q yesterday' },</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor">## New style:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'default'</span> => { <span class="stringliteral">'LSF'</span> => <span class="stringliteral">''</span> },</div>
+<div class="line"> <span class="stringliteral">'urgent'</span> => { <span class="stringliteral">'LSF'</span> => <span class="stringliteral">'-q yesterday'</span> },</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="adb95548d620d772327085f7bb96b8b3a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : The method that uses the Hive/EnsEMBL API to actually create all the analyses, jobs, dataflow and control rules and resource descriptions.</pre><pre> Caller : <a class="el" href="init__pipeline_8pl.html">init_pipeline.pl</a> or any other script that will drive this module.</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $analysis_topup = $self->{<span class="stringliteral">'_extra_options'</span>}{<span class="stringliteral">'analysis_topup'</span>};</div>
+<div class="line"> my $job_topup = $self->{<span class="stringliteral">'_extra_options'</span>}{<span class="stringliteral">'job_topup'</span>};</div>
+<div class="line"> my $pipeline_url = $self->pipeline_url();</div>
+<div class="line"> my $pipeline_name = $self->o(<span class="stringliteral">'pipeline_name'</span>);</div>
+<div class="line"></div>
+<div class="line"> unless($analysis_topup || $job_topup) {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $cmd (@{$self->pipeline_create_commands}) {</div>
+<div class="line"> warn <span class="stringliteral">"Running the command:\n\t$cmd\n"</span>;</div>
+<div class="line"> <span class="keywordflow">if</span>(my $retval = system($cmd)) {</div>
+<div class="line"> die <span class="stringliteral">"Return value = $retval, possibly an error\n"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"Done.\n\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> Bio::EnsEMBL::Registry->no_version_check(1);</div>
+<div class="line"> my $hive_dba = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#abf2b541c5d7e3b124323a34356e3ace6">new</a>( -url => $pipeline_url, -no_sql_schema_version_check => 1 );</div>
+<div class="line"> my $resource_class_adaptor = $hive_dba->get_ResourceClassAdaptor;</div>
+<div class="line"></div>
+<div class="line"> unless($job_topup) {</div>
+<div class="line"> my $meta_adaptor = $hive_dba->get_MetaAdaptor; # the <span class="keyword">new</span> adaptor <span class="keywordflow">for</span> <span class="stringliteral">'hive_meta'</span> table</div>
+<div class="line"> warn <span class="stringliteral">"Loading hive_meta table ...\n"</span>;</div>
+<div class="line"> my $hive_meta_table = $self->hive_meta_table;</div>
+<div class="line"> <span class="keywordflow">while</span>( my($meta_key, $meta_value) = each %$hive_meta_table ) {</div>
+<div class="line"> $meta_adaptor->store_pair( $meta_key, $meta_value );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $meta_container = $hive_dba->get_MetaContainer; # adaptor over core<span class="stringliteral">'s '</span>meta<span class="stringliteral">' table for compatibility with core API</span></div>
+<div class="line"><span class="stringliteral"> warn "Loading pipeline-wide parameters ...\n";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $pipeline_wide_parameters = $self->pipeline_wide_parameters;</span></div>
+<div class="line"><span class="stringliteral"> while( my($meta_key, $meta_value) = each %$pipeline_wide_parameters ) {</span></div>
+<div class="line"><span class="stringliteral"> if($analysis_topup) {</span></div>
+<div class="line"><span class="stringliteral"> $meta_container->remove_all_by_meta_key($meta_key);</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> $meta_container->store_pair($meta_key, $meta_value);</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> warn "Done.\n\n";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # pre-load resource_class and resource_description tables:</span></div>
+<div class="line"><span class="stringliteral"> my $resource_description_adaptor = $hive_dba->get_ResourceDescriptionAdaptor;</span></div>
+<div class="line"><span class="stringliteral"> warn "Loading the Resources ...\n";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $resource_classes_hash = $self->resource_classes;</span></div>
+<div class="line"><span class="stringliteral"> my @resource_classes_order = sort { ($b eq '</span><span class="keywordflow">default</span><span class="stringliteral">') or -($a eq '</span><span class="keywordflow">default</span><span class="stringliteral">') or ($a cmp $b) } keys %$resource_classes_hash; # put '</span><span class="keywordflow">default</span><span class="stringliteral">' to the front</span></div>
+<div class="line"><span class="stringliteral"> my %seen_resource_name = ();</span></div>
+<div class="line"><span class="stringliteral"> foreach my $rc_id (@resource_classes_order) {</span></div>
+<div class="line"><span class="stringliteral"> my $mt2param = $resource_classes_hash->{$rc_id};</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $rc_name = delete $mt2param->{-desc};</span></div>
+<div class="line"><span class="stringliteral"> if($rc_id!~/^\d+$/) {</span></div>
+<div class="line"><span class="stringliteral"> $rc_name = $rc_id;</span></div>
+<div class="line"><span class="stringliteral"> $rc_id = undef;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if(!$rc_name or $seen_resource_name{lc($rc_name)}++) {</span></div>
+<div class="line"><span class="stringliteral"> die "Every resource has to have a unique description, please fix the PipeConfig file";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my ($rc, $rc_newly_created) = $resource_class_adaptor->create_new(</span></div>
+<div class="line"><span class="stringliteral"> defined($rc_id) ? (-DBID => $rc_id) : (),</span></div>
+<div class="line"><span class="stringliteral"> -NAME => $rc_name,</span></div>
+<div class="line"><span class="stringliteral"> 1 # check whether this ResourceClass was already present in the database</span></div>
+<div class="line"><span class="stringliteral"> );</span></div>
+<div class="line"><span class="stringliteral"> $rc_id = $rc->dbID();</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($rc_newly_created) {</span></div>
+<div class="line"><span class="stringliteral"> warn "Creating resource_class $rc_name($rc_id).\n";</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> warn "Attempt to re-create and potentially redefine resource_class $rc_name($rc_id). NB: This may affect already created analyses!\n";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> while( my($meadow_type, $resource_param_list) = each %$mt2param ) {</span></div>
+<div class="line"><span class="stringliteral"> $resource_param_list = [ $resource_param_list ] unless(ref($resource_param_list)); # expecting either a scalar or a 2-element array</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $resource_description_adaptor->create_new(</span></div>
+<div class="line"><span class="stringliteral"> -resource_class_id => $rc_id,</span></div>
+<div class="line"><span class="stringliteral"> -meadow_type => $meadow_type,</span></div>
+<div class="line"><span class="stringliteral"> -submission_cmd_args => $resource_param_list->[0],</span></div>
+<div class="line"><span class="stringliteral"> -worker_cmd_args => $resource_param_list->[1],</span></div>
+<div class="line"><span class="stringliteral"> );</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> unless(my $default_rc = $resource_class_adaptor->fetch_by_name('</span><span class="keywordflow">default</span><span class="stringliteral">')) {</span></div>
+<div class="line"><span class="stringliteral"> warn "\tNB:'</span><span class="keywordflow">default</span><span class="stringliteral">' resource class is not in the database (did you forget to inherit from SUPER::resource_classes ?) - creating it for you\n";</span></div>
+<div class="line"><span class="stringliteral"> $resource_class_adaptor->create_new(-NAME => '</span><span class="keywordflow">default</span><span class="stringliteral">');</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> warn "Done.\n\n";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $analysis_adaptor = $hive_dba->get_AnalysisAdaptor;</span></div>
+<div class="line"><span class="stringliteral"> my $analysis_stats_adaptor = $hive_dba->get_AnalysisStatsAdaptor;</span></div>
+<div class="line"><span class="stringliteral"> my $job_adaptor = $hive_dba->get_AnalysisJobAdaptor;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $valley = Bio::EnsEMBL::Hive::Valley->new( {}, '</span>LOCAL<span class="stringliteral">' );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my %seen_logic_name = ();</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> foreach my $aha (@{$self->pipeline_analyses}) {</span></div>
+<div class="line"><span class="stringliteral"> my ($logic_name, $module, $parameters_hash, $input_ids, $blocked, $batch_size, $hive_capacity, $failed_job_tolerance,</span></div>
+<div class="line"><span class="stringliteral"> $max_retry_count, $can_be_empty, $rc_id, $rc_name, $priority, $meadow_type, $analysis_capacity)</span></div>
+<div class="line"><span class="stringliteral"> = @{$aha}{qw(-logic_name -module -parameters -input_ids -blocked -batch_size -hive_capacity -failed_job_tolerance</span></div>
+<div class="line"><span class="stringliteral"> -max_retry_count -can_be_empty -rc_id -rc_name -priority -meadow_type -analysis_capacity)}; # slicing a hash reference</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> unless($logic_name) {</span></div>
+<div class="line"><span class="stringliteral"> die "logic_name'</span> must be defined in every analysis<span class="stringliteral">";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($seen_logic_name{$logic_name}++) {</span></div>
+<div class="line"><span class="stringliteral"> die "</span>an entry with logic_name <span class="stringliteral">'$logic_name'</span> appears at least twice in the configuration file, can<span class="stringliteral">'t continue";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $analysis = $analysis_adaptor->fetch_by_logic_name($logic_name);</span></div>
+<div class="line"><span class="stringliteral"> if( $analysis ) {</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($analysis_topup) {</span></div>
+<div class="line"><span class="stringliteral"> warn "Skipping creation of already existing analysis '</span>$logic_name<span class="stringliteral">'.\n";</span></div>
+<div class="line"><span class="stringliteral"> next;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($job_topup) {</span></div>
+<div class="line"><span class="stringliteral"> die "Could not fetch analysis '</span>$logic_name<span class="stringliteral">'";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> warn "Creating analysis '</span>$logic_name<span class="stringliteral">'.\n";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($rc_id) {</span></div>
+<div class="line"><span class="stringliteral"> warn "(-rc_id => $rc_id) syntax is deprecated, please start using (-rc_name => '</span>your_resource_class_name<span class="stringliteral">')";</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> $rc_name ||= '</span><span class="keywordflow">default</span><span class="stringliteral">';</span></div>
+<div class="line"><span class="stringliteral"> my $rc = $resource_class_adaptor->fetch_by_name($rc_name ) or die "Could not fetch resource with name '</span>$rc_name<span class="stringliteral">', please check that resource_classes() method of your PipeConfig either contain it or inherit from the parent class";</span></div>
+<div class="line"><span class="stringliteral"> $rc_id = $rc->dbID();</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if ($meadow_type and not exists $valley->available_meadow_hash()->{$meadow_type}) {</span></div>
+<div class="line"><span class="stringliteral"> die "The meadow '</span>$meadow_type<span class="stringliteral">' is currently not registered (analysis '</span>$logic_name<span class="stringliteral">')\n";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $parameters_hash ||= {}; # in case nothing was given</span></div>
+<div class="line"><span class="stringliteral"> die "'</span>-parameters<span class="stringliteral">' has to be a hash" unless(ref($parameters_hash) eq '</span>HASH<span class="stringliteral">');</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $analysis = Bio::EnsEMBL::Hive::Analysis->new(</span></div>
+<div class="line"><span class="stringliteral"> -logic_name => $logic_name,</span></div>
+<div class="line"><span class="stringliteral"> -module => $module,</span></div>
+<div class="line"><span class="stringliteral"> -parameters => $parameters_hash,</span></div>
+<div class="line"><span class="stringliteral"> -resource_class_id => $rc_id,</span></div>
+<div class="line"><span class="stringliteral"> -failed_job_tolerance => $failed_job_tolerance,</span></div>
+<div class="line"><span class="stringliteral"> -max_retry_count => $max_retry_count,</span></div>
+<div class="line"><span class="stringliteral"> -can_be_empty => $can_be_empty,</span></div>
+<div class="line"><span class="stringliteral"> -priority => $priority,</span></div>
+<div class="line"><span class="stringliteral"> -meadow_type => $meadow_type,</span></div>
+<div class="line"><span class="stringliteral"> -analysis_capacity => $analysis_capacity,</span></div>
+<div class="line"><span class="stringliteral"> );</span></div>
+<div class="line"><span class="stringliteral"> $analysis->get_compiled_module_name(); # check if it compiles and is named correctly</span></div>
+<div class="line"><span class="stringliteral"> $analysis_adaptor->store($analysis);</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $stats = Bio::EnsEMBL::Hive::AnalysisStats->new(</span></div>
+<div class="line"><span class="stringliteral"> -analysis_id => $analysis->dbID,</span></div>
+<div class="line"><span class="stringliteral"> -batch_size => $batch_size,</span></div>
+<div class="line"><span class="stringliteral"> -hive_capacity => $hive_capacity,</span></div>
+<div class="line"><span class="stringliteral"> -status => $blocked ? '</span>BLOCKED<span class="stringliteral">' : '</span>EMPTY<span class="stringliteral">', # be careful, as this "soft" way of blocking may be accidentally unblocked by deep sync</span></div>
+<div class="line"><span class="stringliteral"> -total_job_count => 0,</span></div>
+<div class="line"><span class="stringliteral"> -semaphored_job_count => 0,</span></div>
+<div class="line"><span class="stringliteral"> -ready_job_count => 0,</span></div>
+<div class="line"><span class="stringliteral"> -done_job_count => 0,</span></div>
+<div class="line"><span class="stringliteral"> -failed_job_count => 0,</span></div>
+<div class="line"><span class="stringliteral"> -num_running_workers => 0,</span></div>
+<div class="line"><span class="stringliteral"> -num_required_workers => 0,</span></div>
+<div class="line"><span class="stringliteral"> -behaviour => '</span>STATIC<span class="stringliteral">',</span></div>
+<div class="line"><span class="stringliteral"> -input_capacity => 4,</span></div>
+<div class="line"><span class="stringliteral"> -output_capacity => 4,</span></div>
+<div class="line"><span class="stringliteral"> -sync_lock => 0,</span></div>
+<div class="line"><span class="stringliteral"> );</span></div>
+<div class="line"><span class="stringliteral"> $analysis_stats_adaptor->store($stats);</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # now create the corresponding jobs (if there are any):</span></div>
+<div class="line"><span class="stringliteral"> if($input_ids) {</span></div>
+<div class="line"><span class="stringliteral"> my @jobs = map { Bio::EnsEMBL::Hive::AnalysisJob->new(</span></div>
+<div class="line"><span class="stringliteral"> -prev_job_id => undef, # these jobs are created by the initialization script, not by another job</span></div>
+<div class="line"><span class="stringliteral"> -analysis_id => $analysis->dbID,</span></div>
+<div class="line"><span class="stringliteral"> -input_id => $_, # input_ids are now centrally stringified in the AnalysisJob itself</span></div>
+<div class="line"><span class="stringliteral"> ) } @$input_ids;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $job_adaptor->store_jobs_and_adjust_counters( \@jobs );</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> unless($job_topup) {</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # Now, run separately through the already created analyses and link them together:</span></div>
+<div class="line"><span class="stringliteral"> #</span></div>
+<div class="line"><span class="stringliteral"> my $ctrl_rule_adaptor = $hive_dba->get_AnalysisCtrlRuleAdaptor;</span></div>
+<div class="line"><span class="stringliteral"> my $dataflow_rule_adaptor = $hive_dba->get_DataflowRuleAdaptor;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> foreach my $aha (@{$self->pipeline_analyses}) {</span></div>
+<div class="line"><span class="stringliteral"> my ($logic_name, $wait_for, $flow_into)</span></div>
+<div class="line"><span class="stringliteral"> = @{$aha}{qw(-logic_name -wait_for -flow_into)}; # slicing a hash reference</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $analysis = $analysis_adaptor->fetch_by_logic_name($logic_name);</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $wait_for ||= [];</span></div>
+<div class="line"><span class="stringliteral"> $wait_for = [ $wait_for ] unless(ref($wait_for) eq '</span>ARRAY<span class="stringliteral">'); # force scalar into an arrayref</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # create control rules:</span></div>
+<div class="line"><span class="stringliteral"> foreach my $condition_url (@$wait_for) {</span></div>
+<div class="line"><span class="stringliteral"> unless ($condition_url =~ m{^\w*://}) {</span></div>
+<div class="line"><span class="stringliteral"> my $condition_analysis = $analysis_adaptor->fetch_by_logic_name($condition_url);</span></div>
+<div class="line"><span class="stringliteral"> die "Could not fetch analysis '</span>$condition_url<span class="stringliteral">' to create a control rule (in '</span><span class="stringliteral">".($analysis->logic_name)."</span><span class="stringliteral">')\n" unless defined $condition_analysis;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> my $c_rule = Bio::EnsEMBL::Hive::AnalysisCtrlRule->new(</span></div>
+<div class="line"><span class="stringliteral"> -condition_analysis_url => $condition_url,</span></div>
+<div class="line"><span class="stringliteral"> -ctrled_analysis_id => $analysis->dbID,</span></div>
+<div class="line"><span class="stringliteral"> );</span></div>
+<div class="line"><span class="stringliteral"> $ctrl_rule_adaptor->store( $c_rule, 1 );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> warn $c_rule->toString."\n";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $flow_into ||= {};</span></div>
+<div class="line"><span class="stringliteral"> $flow_into = { 1 => $flow_into } unless(ref($flow_into) eq '</span>HASH<span class="stringliteral">'); # force non-hash into a hash</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my %group_tag_to_funnel_dataflow_rule_id = ();</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $semaphore_sign = '</span>-><span class="stringliteral">';</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my @all_branch_tags = keys %$flow_into;</span></div>
+<div class="line"><span class="stringliteral"> foreach my $branch_tag ((grep {/^[A-Z]$semaphore_sign/} @all_branch_tags), (grep {/$semaphore_sign[A-Z]$/} @all_branch_tags), (grep {!/$semaphore_sign/} @all_branch_tags)) {</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my ($branch_name_or_code, $group_role, $group_tag);</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($branch_tag=~/^([A-Z])$semaphore_sign(-?\w+)$/) {</span></div>
+<div class="line"><span class="stringliteral"> ($branch_name_or_code, $group_role, $group_tag) = ($2, '</span>funnel<span class="stringliteral">', $1);</span></div>
+<div class="line"><span class="stringliteral"> } elsif($branch_tag=~/^(-?\w+)$semaphore_sign([A-Z])$/) {</span></div>
+<div class="line"><span class="stringliteral"> ($branch_name_or_code, $group_role, $group_tag) = ($1, '</span>fan<span class="stringliteral">', $2);</span></div>
+<div class="line"><span class="stringliteral"> } elsif($branch_tag=~/^(-?\w+)$/) {</span></div>
+<div class="line"><span class="stringliteral"> ($branch_name_or_code, $group_role, $group_tag) = ($1, '</span><span class="stringliteral">');</span></div>
+<div class="line"><span class="stringliteral"> } elsif($branch_tag=~/:/) {</span></div>
+<div class="line"><span class="stringliteral"> die "Please use newer '</span>2${semaphore_sign}A<span class="stringliteral">' and '</span>A${semaphore_sign}1<span class="stringliteral">' notation instead of '</span>2:1<span class="stringliteral">' and '</span>1<span class="stringliteral">'\n";</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> die "Error parsing the group tag '</span>$branch_tag<span class="stringliteral">'\n";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $funnel_dataflow_rule_id = undef; # NULL by default</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($group_role eq '</span>fan<span class="stringliteral">') {</span></div>
+<div class="line"><span class="stringliteral"> unless($funnel_dataflow_rule_id = $group_tag_to_funnel_dataflow_rule_id{$group_tag}) {</span></div>
+<div class="line"><span class="stringliteral"> die "No funnel dataflow_rule defined for group '</span>$group_tag<span class="stringliteral">'\n";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $heirs = $flow_into->{$branch_tag};</span></div>
+<div class="line"><span class="stringliteral"> $heirs = [ $heirs ] unless(ref($heirs)); # force scalar into an arrayref first</span></div>
+<div class="line"><span class="stringliteral"> $heirs = { map { ($_ => undef) } @$heirs } if(ref($heirs) eq '</span>ARRAY<span class="stringliteral">'); # now force it into a hash if it wasn'</span>t</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>(my ($heir_url, $input_id_template_list) = each %$heirs) {</div>
+<div class="line"></div>
+<div class="line"> unless ($heir_url =~ m{^\w*:<span class="comment">//}) {</span></div>
+<div class="line"> my $heir_analysis = $analysis_adaptor->fetch_by_logic_name($heir_url);</div>
+<div class="line"> die <span class="stringliteral">"No analysis named '$heir_url' (dataflow from analysis '"</span>.($analysis->logic_name).<span class="stringliteral">"')\n"</span> unless defined $heir_analysis;</div>
+<div class="line"> }</div>
+<div class="line"> </div>
+<div class="line"> $input_id_template_list = [ $input_id_template_list ] unless(ref($input_id_template_list) eq <span class="stringliteral">'ARRAY'</span>); # allow <span class="keywordflow">for</span> more than one <span class="keyword">template</span> per analysis</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $input_id_template (@$input_id_template_list) {</div>
+<div class="line"></div>
+<div class="line"> my $df_rule = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">Bio::EnsEMBL::Hive::DataflowRule</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#af8321e0eec4a4057a4d103400e549df3">new</a>(</div>
+<div class="line"> -from_analysis => $analysis,</div>
+<div class="line"> -to_analysis_url => $heir_url,</div>
+<div class="line"> -branch_code => $branch_name_or_code,</div>
+<div class="line"> -input_id_template => $input_id_template,</div>
+<div class="line"> -funnel_dataflow_rule_id => $funnel_dataflow_rule_id,</div>
+<div class="line"> );</div>
+<div class="line"> $dataflow_rule_adaptor->store( $df_rule, 1 );</div>
+<div class="line"></div>
+<div class="line"> warn $df_rule-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a48471b18b5f0d91bbeb9fee9c468a523">toString</a>.<span class="stringliteral">"\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($group_role eq <span class="stringliteral">'funnel'</span>) {</div>
+<div class="line"> <span class="keywordflow">if</span>($group_tag_to_funnel_dataflow_rule_id{$group_tag}) {</div>
+<div class="line"> die <span class="stringliteral">"More than one funnel dataflow_rule defined for group '$group_tag'\n"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $group_tag_to_funnel_dataflow_rule_id{$group_tag} = $df_rule->dbID();</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> } # /<span class="keywordflow">for</span> all templates</div>
+<div class="line"> } # /<span class="keywordflow">for</span> all heirs</div>
+<div class="line"> } # /<span class="keywordflow">for</span> all branch_tags</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> print <span class="stringliteral">"\n\n# --------------------[Useful commands]--------------------------\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">" # It is convenient to store the pipeline url in a variable:\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\texport EHIVE_URL=$pipeline_url\t\t\t# bash version\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"(OR)\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\tsetenv EHIVE_URL $pipeline_url\t\t\t# [t]csh version\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">" # Add a new job to the pipeline (usually done once before running, but pipeline can be \"topped-up\" at any time) :\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\tseed_pipeline.pl -url $pipeline_url -logic_name <analysis_name> -input_id <param_hash>\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">" # Synchronize the Hive (should be done before [re]starting a pipeline) :\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\tbeekeeper.pl -url $pipeline_url -sync\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">" # Run the pipeline (can be interrupted and restarted) :\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\tbeekeeper.pl -url $pipeline_url "</span>.$self->beekeeper_extra_cmdline_options().<span class="stringliteral">" -loop\t\t# run in looped automatic mode (a scheduling step performed every minute)\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"(OR)\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\tbeekeeper.pl -url $pipeline_url "</span>.$self->beekeeper_extra_cmdline_options().<span class="stringliteral">" -run \t\t# run one scheduling step of the pipeline and exit (useful for debugging/learning)\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"(OR)\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\trunWorker.pl -url $pipeline_url "</span>.$self->beekeeper_extra_cmdline_options().<span class="stringliteral">" \t\t# run exactly one Worker locally (useful for debugging/learning)\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">" # At any moment during or after execution you can request a pipeline diagram in an image file (desired format is set via extension) :\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\tgenerate_graph.pl -url $pipeline_url -out $pipeline_name.png\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">" # If you are running the pipeline on LSF, you can collect actual resource usage statistics :\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\tlsf_report.pl -url $pipeline_url\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">" # After having run lsf_report.pl, you can request a resource usage timeline in an image file (desired format is set via extension) :\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\tgenerate_timeline.pl -url $pipeline_url -out timeline_$pipeline_name.png\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">" # Peek into your pipeline database with a database client (useful to have open while the pipeline is running) :\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\tdb_cmd.pl -url $pipeline_url\n\n"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/PipeConfig/<a class="el" href="_hive_generic__conf_8pm.html">HiveGeneric_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a28568127780ecee07cde885f1ec1a1f3">default_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a0046c9bd300412bda32547458e60064d">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a031b9cfa37aaf95c3c83fba5c243cad2">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a5b977e0be30a4f60ec9429a399db0fc8">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf:</div>
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf:</div>
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+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a031b9cfa37aaf95c3c83fba5c243cad2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a031b9cfa37aaf95c3c83fba5c243cad2">pipeline_create_commands</a> ()</td></tr>
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+<tr class="memitem:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> ()</td></tr>
+<tr class="separator:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line"><span class="preprocessor"> # initialize the database and build the graph in it (it will also print the value of EHIVE_URL) :</span></div>
+<div class="line"><span class="preprocessor"></span>init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a> -password <mypass></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # optionally also seed it with your specific values:</span></div>
+<div class="line"><span class="preprocessor"></span>seed_pipeline.pl -url $EHIVE_URL -logic_name take_b_apart -input_id <span class="stringliteral">'{ "a_multiplier" => "12345678", "b_multiplier" => "3359559666" }'</span></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # run the pipeline:</span></div>
+<div class="line"><span class="preprocessor">beekeeper.pl -url $EHIVE_URL -loop</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is the PipeConfig file for the long multiplication pipeline example.
+ The main point of this pipeline is to provide an example of how to write Hive Runnables and link them together into a pipeline.
+
+ Please refer to Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf module to understand the interface implemented here.
+
+ The setting. let's assume we are given two loooooong numbers to multiply. reeeeally long.
+ soooo long that they do not fit into registers of the cpu and should be multiplied digit-by-digit.
+ For the purposes of this example we also assume this task is very computationally intensive and has to be done in parallel.
+
+ The long multiplication pipeline consists of three "analyses" (types of tasks):
+ 'take_b_apart', 'part_multiply' and 'add_together' that we use to examplify various features of the Hive.
+
+ A 'take_b_apart' job takes in two string parameters, 'a_multiplier' and 'b_multiplier',
+ takes the second one apart into digits, finds what _different_ digits are there,
+ creates several jobs of the 'part_multiply' analysis and one job of 'add_together' analysis.
+
+ A 'part_multiply' job takes in 'a_multiplier' and 'digit', multiplies them and accumulates the result in 'partial_product' accumulator.
+
+ An 'add_together' job waits for the first two analyses to complete,
+ takes in 'a_multiplier', 'b_multiplier' and 'partial_product' hash and produces the final result in 'final_result' table.
+
+ Please see the implementation details in Runnable modules themselves.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a0046c9bd300412bda32547458e60064d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a0046c9bd300412bda32547458e60064d">pipeline_analyses()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that defines the structure of the pipeline: analyses, jobs, rules, etc.
+ Here it defines three analyses:
+ 'take_b_apart' that is auto-seeded with a pair of jobs (to check the commutativity of multiplication).
+ Each job will dataflow (create more jobs) via branch #2 into 'part_multiply' and via branch #1 into 'add_together'.</pre><pre> 'part_multiply' with jobs fed from take_b_apart#2.
+ It multiplies input parameters 'a_multiplier' and 'digit' and dataflows 'partial_product' parameter into branch #1.</pre><pre> 'add_together' with jobs fed from take_b_apart#1.
+ It adds together results of partial multiplication computed by 'part_multiply'.
+ These results are accumulated in 'partial_product' hash.
+ Until the hash is complete the corresponding 'add_together' job is blocked by a semaphore.</pre><pre> </pre><div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a0046c9bd300412bda32547458e60064d">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> { -logic_name => <span class="stringliteral">'take_b_apart'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory'</span>,</div>
+<div class="line"> -meadow_type=> <span class="stringliteral">'LOCAL'</span>, # <span class="keywordflow">do</span> not bother the farm with such a simple task (and <span class="keyword">get</span> it done faster)</div>
+<div class="line"> -analysis_capacity => 2, # use per-analysis limiter</div>
+<div class="line"> -input_ids => [</div>
+<div class="line"> { <span class="stringliteral">'a_multiplier'</span> => <span class="stringliteral">'9650156169'</span>, <span class="stringliteral">'b_multiplier'</span> => <span class="stringliteral">'327358788'</span> },</div>
+<div class="line"> { <span class="stringliteral">'a_multiplier'</span> => <span class="stringliteral">'327358788'</span>, <span class="stringliteral">'b_multiplier'</span> => <span class="stringliteral">'9650156169'</span> },</div>
+<div class="line"> ],</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"><span class="preprocessor"> # will create a semaphored fan of jobs; will use a template to top-up the hashes:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'2->A'</span> => { <span class="stringliteral">'part_multiply'</span> => { <span class="stringliteral">'a_multiplier'</span> => <span class="stringliteral">'#a_multiplier#'</span>, <span class="stringliteral">'digit'</span> => <span class="stringliteral">'#digit#'</span>, <span class="stringliteral">'take_time'</span> => <span class="stringliteral">'#take_time#'</span> } },</div>
+<div class="line"><span class="preprocessor"> # will create a semaphored funnel job to wait for the fan to complete and add the results:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'A->1'</span> => [ <span class="stringliteral">'add_together'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> { -logic_name => <span class="stringliteral">'part_multiply'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply'</span>,</div>
+<div class="line"> -analysis_capacity => 4, # use per-analysis limiter</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"> 1 => [ <span class="stringliteral">':////accu?partial_product={digit}'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"> </div>
+<div class="line"> { -logic_name => <span class="stringliteral">'add_together'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether'</span>,</div>
+<div class="line"><span class="preprocessor"># -analysis_capacity => 0, # this is a way to temporarily block a given analysis</span></div>
+<div class="line"><span class="preprocessor"></span> -flow_into => {</div>
+<div class="line"> 1 => [ <span class="stringliteral">':////final_result'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a031b9cfa37aaf95c3c83fba5c243cad2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf::pipeline_create_commands </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a031b9cfa37aaf95c3c83fba5c243cad2">pipeline_create_commands()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that lists the commands that will create and set up the <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a> database.
+ In addition to the standard creation of the database and populating it with <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a> tables and procedures it also creates two pipeline-specific tables used by Runnables to communicate.</pre><pre> </pre><div id="codesection-pipeline_create_commands" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_create_commands-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_create_commands-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_create_commands-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a031b9cfa37aaf95c3c83fba5c243cad2">pipeline_create_commands</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> @{$self->SUPER::pipeline_create_commands}, # inheriting database and hive tables<span class="stringliteral">' creation</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # additional tables needed for long multiplication pipeline'</span>s operation:</div>
+<div class="line"> $self->db_cmd(<span class="stringliteral">'CREATE TABLE final_result (a_multiplier char(40) NOT NULL, b_multiplier char(40) NOT NULL, result char(80) NOT NULL, PRIMARY KEY (a_multiplier, b_multiplier))'</span>),</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a5b977e0be30a4f60ec9429a399db0fc8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf::pipeline_wide_parameters </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Interface method that should return a hash of pipeline_wide_parameter_name->pipeline_wide_parameter_value pairs.
+ The value doesn't have to be a scalar, can be any Perl structure now (will be stringified and de-stringified automagically).
+ Please see existing <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a> modules for examples.</pre><pre> </pre><div id="codesection-pipeline_wide_parameters" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_wide_parameters-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_wide_parameters-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_wide_parameters-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a5b977e0be30a4f60ec9429a399db0fc8">pipeline_wide_parameters</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{$self->SUPER::pipeline_wide_parameters}, # here we inherit anything from the base <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'take_time'</span> => 1,</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/PipeConfig/<a class="el" href="_long_mult__conf_8pm.html">LongMult_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html">LongMult_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<div class="title">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf Member List</div> </div>
+</div><!--header-->
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+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a28568127780ecee07cde885f1ec1a1f3">default_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a354e9305c82d67b99b5d0b159f2382db">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a3c2b04c792006bd1a20941e65aea45ef">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a4e1bcdc9dbc1cdcef52e15361d1ebd09">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a3fa7a29fdd8d17ceae1d20c828c85e9e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+<tr class="separator:af4d7bd7b523fc76a3c58aa15141c5f2c inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ab46a140ff5e2b90989979ea6cba6bf06 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a766a75f28b07ea491d7e8fdc97ee2ad6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a> ()</td></tr>
+<tr class="separator:a766a75f28b07ea491d7e8fdc97ee2ad6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a194b948521dcdf1e6a8f83a4fc3b1c11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a16457254eff693383b5e2a9dcc5b19b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adb95548d620d772327085f7bb96b8b3a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a> ()</td></tr>
+<tr class="separator:adb95548d620d772327085f7bb96b8b3a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td></tr>
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+<tr class="separator:a729f524427ef5292b7e980f134aa456f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a12fa6e8360e2db6bd40dc318654b9d42 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a> ()</td></tr>
+<tr class="separator:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a8b28b1e6e1ef24ac3d9143062ddc36d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> ()</td></tr>
+<tr class="separator:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line"><span class="preprocessor"> # initialize the database and build the graph in it (it will also print the value of EHIVE_URL) :</span></div>
+<div class="line"><span class="preprocessor"></span>init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a> -password <mypass></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # optionally also seed it with your specific values:</span></div>
+<div class="line"><span class="preprocessor"></span>seed_pipeline.pl -url $EHIVE_URL -logic_name take_b_apart -input_id <span class="stringliteral">'{ "a_multiplier" => "12345678", "b_multiplier" => "3359559666" }'</span></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # run the pipeline:</span></div>
+<div class="line"><span class="preprocessor">beekeeper.pl -url $EHIVE_URL -loop</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is a special version of LongMult_conf with hive_use_param_stack mode switched on.
+
+ This is the PipeConfig file for the long multiplication pipeline example.
+ The main point of this pipeline is to provide an example of how to write Hive Runnables and link them together into a pipeline.
+
+ Please refer to Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf module to understand the interface implemented here.
+
+ The setting. Let's assume we are given two loooooong numbers to multiply. Reeeeally long.
+ Soooo long that they do not fit into registers of the CPU and should be multiplied digit-by-digit.
+ For the purposes of this example we also assume this task is very computationally intensive and has to be done in parallel.
+
+ The long multiplication pipeline consists of three "analyses" (types of tasks):
+ 'take_b_apart', 'part_multiply' and 'add_together' that we use to examplify various features of the Hive.
+
+ A 'take_b_apart' job takes in two string parameters, 'a_multiplier' and 'b_multiplier',
+ takes the second one apart into digits, finds what _different_ digits are there,
+ creates several jobs of the 'part_multiply' analysis and one job of 'add_together' analysis.
+
+ A 'part_multiply' job takes in 'a_multiplier' and 'digit', multiplies them and accumulates the result in 'partial_product' accumulator.
+
+ An 'add_together' job waits for the first two analyses to complete,
+ takes in 'a_multiplier', 'b_multiplier' and 'partial_product' hash and produces the final result in 'final_result' table.
+
+ Please see the implementation details in Runnable modules themselves.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a354e9305c82d67b99b5d0b159f2382db"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf::hive_meta_table </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-hive_meta_table" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-hive_meta_table-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-hive_meta_table-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-hive_meta_table-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a354e9305c82d67b99b5d0b159f2382db">hive_meta_table</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{$self->SUPER::hive_meta_table}, # here we inherit anything from the base <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'hive_use_param_stack'</span> => 1, # <span class="keywordflow">switch</span> on the <span class="keyword">new</span> param_stack mechanism</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3c2b04c792006bd1a20941e65aea45ef"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a3c2b04c792006bd1a20941e65aea45ef">pipeline_analyses()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that defines the structure of the pipeline: analyses, jobs, rules, etc.
+ Here it defines three analyses:
+ 'take_b_apart' that is auto-seeded with a pair of jobs (to check the commutativity of multiplication).
+ Each job will dataflow (create more jobs) via branch #2 into 'part_multiply' and via branch #1 into 'add_together'.</pre><pre> 'part_multiply' with jobs fed from take_b_apart#2.
+ It multiplies input parameters 'a_multiplier' and 'digit' and dataflows 'partial_product' parameter into branch #1.</pre><pre> 'add_together' with jobs fed from take_b_apart#1.
+ It adds together results of partial multiplication computed by 'part_multiply'.
+ These results are accumulated in 'partial_product' hash.
+ Until the hash is complete the corresponding 'add_together' job is blocked by a semaphore.</pre><pre> </pre><div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a3c2b04c792006bd1a20941e65aea45ef">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> { -logic_name => <span class="stringliteral">'take_b_apart'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory'</span>,</div>
+<div class="line"> -meadow_type=> <span class="stringliteral">'LOCAL'</span>, # <span class="keywordflow">do</span> not bother the farm with such a simple task (and <span class="keyword">get</span> it done faster)</div>
+<div class="line"> -analysis_capacity => 2, # use per-analysis limiter</div>
+<div class="line"> -input_ids => [</div>
+<div class="line"> { <span class="stringliteral">'a_multiplier'</span> => <span class="stringliteral">'9650156169'</span>, <span class="stringliteral">'b_multiplier'</span> => <span class="stringliteral">'327358788'</span> },</div>
+<div class="line"> { <span class="stringliteral">'a_multiplier'</span> => <span class="stringliteral">'327358788'</span>, <span class="stringliteral">'b_multiplier'</span> => <span class="stringliteral">'9650156169'</span> },</div>
+<div class="line"> ],</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"> <span class="stringliteral">'2->A'</span> => [ <span class="stringliteral">'part_multiply'</span> ], # will create a semaphored fan of jobs; will use param_stack mechanism to pass parameters around</div>
+<div class="line"> <span class="stringliteral">'A->1'</span> => [ <span class="stringliteral">'add_together'</span> ], # will create a semaphored funnel job to wait <span class="keywordflow">for</span> the fan to complete and add the results</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> { -logic_name => <span class="stringliteral">'part_multiply'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply'</span>,</div>
+<div class="line"> -analysis_capacity => 4, # use per-analysis limiter</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"> 1 => [ <span class="stringliteral">':////accu?partial_product={digit}'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"> </div>
+<div class="line"> { -logic_name => <span class="stringliteral">'add_together'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether'</span>,</div>
+<div class="line"><span class="preprocessor"># -analysis_capacity => 0, # this is a way to temporarily block a given analysis</span></div>
+<div class="line"><span class="preprocessor"></span> -flow_into => {</div>
+<div class="line"> 1 => [ <span class="stringliteral">':////final_result'</span>, <span class="stringliteral">'last'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> { -logic_name => <span class="stringliteral">'last'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::Dummy'</span>,</div>
+<div class="line"> }</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4e1bcdc9dbc1cdcef52e15361d1ebd09"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf::pipeline_create_commands </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a4e1bcdc9dbc1cdcef52e15361d1ebd09">pipeline_create_commands()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that lists the commands that will create and set up the <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a> database.
+ In addition to the standard creation of the database and populating it with <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a> tables and procedures it also creates two pipeline-specific tables used by Runnables to communicate.</pre><pre> </pre><div id="codesection-pipeline_create_commands" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_create_commands-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_create_commands-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_create_commands-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a4e1bcdc9dbc1cdcef52e15361d1ebd09">pipeline_create_commands</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> @{$self->SUPER::pipeline_create_commands}, # inheriting database and hive tables<span class="stringliteral">' creation</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # additional tables needed for long multiplication pipeline'</span>s operation:</div>
+<div class="line"> $self->db_cmd(<span class="stringliteral">'CREATE TABLE final_result (a_multiplier char(40) NOT NULL, b_multiplier char(40) NOT NULL, result char(80) NOT NULL, PRIMARY KEY (a_multiplier, b_multiplier))'</span>),</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3fa7a29fdd8d17ceae1d20c828c85e9e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf::pipeline_wide_parameters </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Interface method that should return a hash of pipeline_wide_parameter_name->pipeline_wide_parameter_value pairs.
+ The value doesn't have to be a scalar, can be any Perl structure now (will be stringified and de-stringified automagically).
+ Please see existing <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a> modules for examples.</pre><pre> </pre><div id="codesection-pipeline_wide_parameters" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_wide_parameters-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_wide_parameters-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_wide_parameters-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a3fa7a29fdd8d17ceae1d20c828c85e9e">pipeline_wide_parameters</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{$self->SUPER::pipeline_wide_parameters}, # here we inherit anything from the base <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'take_time'</span> => 1,</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/PipeConfig/<a class="el" href="_long_mult_st__conf_8pm.html">LongMultSt_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html">LongMultSt_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+<div class="title">Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html">Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a28568127780ecee07cde885f1ec1a1f3">default_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html#a828e67804c29620ff20f5774983a734a">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html">Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html#af4f9a637c96b4abb18b8139fff3e885b">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html">Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+<tr class="memitem:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a> ()</td></tr>
+<tr class="separator:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> ()</td></tr>
+<tr class="separator:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html">Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf</a> -password <your_password></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is another example pipeline built around FailureTest.pm RunnableDB. It consists of two analyses:
+
+ Analysis_1: JobFactory.pm is used to create an array of jobs -
+
+ these jobs are sent down the branch #2 into the second analysis
+
+ Analysis_2: FailureTest.pm in "memory grab" mode may overrun the current resource's memory limit and be killed by the LSF
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a828e67804c29620ff20f5774983a734a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html#a828e67804c29620ff20f5774983a734a">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> { -logic_name => <span class="stringliteral">'generate_jobs'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::JobFactory'</span>,</div>
+<div class="line"> -meadow_type => <span class="stringliteral">'LOCAL'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'column_names'</span> => [ <span class="stringliteral">'grab_mln'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> -input_ids => [</div>
+<div class="line"> { <span class="stringliteral">'inputlist'</span> => [ 0.6 , 0.8 , 1.0 , 1.2 , 1.4 , 1.6 , 1.8 , 2.0, 2.5, 3.0, 5.0, 7.0, 10 ], },</div>
+<div class="line"> ],</div>
+<div class="line"></div>
+<div class="line"> -flow_into => {</div>
+<div class="line"> 2 => [ <span class="stringliteral">'failure_test'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> { -logic_name => <span class="stringliteral">'failure_test'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::FailureTest'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'time_RUN'</span> => 30,</div>
+<div class="line"> },</div>
+<div class="line"> -rc_name => <span class="stringliteral">'default'</span>, # pick a valid value from <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html#af4f9a637c96b4abb18b8139fff3e885b">resource_classes</a>() section</div>
+<div class="line"> },</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af4f9a637c96b4abb18b8139fff3e885b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf::resource_classes </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-resource_classes" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-resource_classes-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-resource_classes-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-resource_classes-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html#af4f9a637c96b4abb18b8139fff3e885b">resource_classes</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{$self->SUPER::resource_classes}, # inherit <span class="stringliteral">'default'</span> from the parent <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'default'</span> => {<span class="stringliteral">'LSF'</span> => <span class="stringliteral">'-C0 -M100 -R"select[mem>100] rusage[mem=100]"'</span> }, # to make sure it fails similarly on both farms</div>
+<div class="line"> <span class="stringliteral">'200Mb_job'</span> => {<span class="stringliteral">'LSF'</span> => <span class="stringliteral">'-C0 -M200 -R"select[mem>200] rusage[mem=200]"'</span> },</div>
+<div class="line"> <span class="stringliteral">'400Mb_job'</span> => {<span class="stringliteral">'LSF'</span> => <span class="stringliteral">'-C0 -M400 -R"select[mem>400] rusage[mem=400]"'</span> },</div>
+<div class="line"> <span class="stringliteral">'1Gb_job'</span> => {<span class="stringliteral">'LSF'</span> => <span class="stringliteral">'-C0 -M1000 -R"select[mem>1000] rusage[mem=1000]"'</span> },</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/PipeConfig/<a class="el" href="_memlimit_test__conf_8pm.html">MemlimitTest_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html">MemlimitTest_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
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+  <span id="projectnumber">1.9</span>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html#a2a5f21f07b20e9a7a2e188771f7e5400">default_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html">Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html#a4cbb91c590ae6014d587728430df6d11">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html">Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+<div class="title">Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf Class Reference</div> </div>
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf:</div>
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+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf:</div>
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+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf_coll__map">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
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+<tr class="separator:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html">Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf</a> -password <your_password> -inputfile file_with_cmds.txt</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is an example pipeline put together from basic building blocks:
+
+ Analysis_1: JobFactory.pm is used to turn the list of commands in a file into jobs
+
+ these jobs are sent down the branch #2 into the second analysis
+
+ Analysis_2: SystemCmd.pm is used to run these jobs in parallel.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a2a5f21f07b20e9a7a2e188771f7e5400"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf::default_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html#a2a5f21f07b20e9a7a2e188771f7e5400">default_options()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that is used to initialize default options.
+ In addition to the standard things it defines three options:
+ o('capacity') defines how many files can be run in parallel</pre><pre> There are rules dependent on two options that do not have defaults (this makes them mandatory):
+ o('password') your read-write password for creation and maintenance of the hive database
+ o('inputfile') name of the inputfile where the commands are</pre><pre> </pre><div id="codesection-default_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html#a2a5f21f07b20e9a7a2e188771f7e5400">default_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{ $self->SUPER::default_options() }, # inherit other stuff from the base <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'pipeline_name'</span> => <span class="stringliteral">'ifile_syscmd'</span>, # name used by the beekeeper to prefix job names on the farm</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'capacity'</span> => 100, # how many commands can be <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a> in parallel</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4cbb91c590ae6014d587728430df6d11"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html#a4cbb91c590ae6014d587728430df6d11">pipeline_analyses()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that defines the structure of the pipeline: analyses, jobs, rules, etc.
+ Here it defines two analyses:</pre><pre> 'create_jobs' reads commands line-by-line from inputfile
+ Each job of this analysis will dataflow (create jobs) via branch #2 into 'run_cmd' analysis.</pre><pre> 'run_cmd' actually runs the commands in parallel</pre><pre> </pre><div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html#a4cbb91c590ae6014d587728430df6d11">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> { -logic_name => <span class="stringliteral">'create_jobs'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::JobFactory'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'column_names'</span> => [ <span class="stringliteral">'cmd'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> -input_ids => [</div>
+<div class="line"> { <span class="stringliteral">'inputfile'</span> => $self->o(<span class="stringliteral">'inputfile'</span>) }, # A <span class="keyword">new</span> file-with-commands could be loaded at each -topup_jobs execution of init_pipeline</div>
+<div class="line"> ],</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"> 2 => [ <span class="stringliteral">'run_cmd'</span> ], # will create a fan of jobs</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> { -logic_name => <span class="stringliteral">'run_cmd'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => { },</div>
+<div class="line"> -analysis_capacity => $self->o(<span class="stringliteral">'capacity'</span>), # allow several workers to perform identical tasks in parallel</div>
+<div class="line"> },</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/PipeConfig/<a class="el" href="_run_list_of_commands_on_farm__conf_8pm.html">RunListOfCommandsOnFarm_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html">RunListOfCommandsOnFarm_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html">Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a28568127780ecee07cde885f1ec1a1f3">default_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html#a34f0292081b57df3025252e36ba2afa2">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html">Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html#a722ee2d7f0974ab6865a73290f55adf9">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html">Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf:</div>
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+<tr class="memitem:a194b948521dcdf1e6a8f83a4fc3b1c11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a> ()</td></tr>
+<tr class="separator:a194b948521dcdf1e6a8f83a4fc3b1c11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a16457254eff693383b5e2a9dcc5b19b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a> ()</td></tr>
+<tr class="separator:a16457254eff693383b5e2a9dcc5b19b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adb95548d620d772327085f7bb96b8b3a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a> ()</td></tr>
+<tr class="separator:adb95548d620d772327085f7bb96b8b3a inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td></tr>
+<tr class="memitem:a729f524427ef5292b7e980f134aa456f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a> ()</td></tr>
+<tr class="separator:a729f524427ef5292b7e980f134aa456f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a12fa6e8360e2db6bd40dc318654b9d42 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a> ()</td></tr>
+<tr class="separator:a12fa6e8360e2db6bd40dc318654b9d42 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a> ()</td></tr>
+<tr class="separator:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a> ()</td></tr>
+<tr class="separator:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8b28b1e6e1ef24ac3d9143062ddc36d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a> ()</td></tr>
+<tr class="separator:a8b28b1e6e1ef24ac3d9143062ddc36d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a> ()</td></tr>
+<tr class="separator:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a> ()</td></tr>
+<tr class="separator:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> ()</td></tr>
+<tr class="separator:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html">Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf</a> -password $ENSADMIN_PSW -db_conn <span class="stringliteral">"mysql://ensadmin:${ENSADMIN_PSW}@localhost/lg4_long_mult"</span></div>
+<div class="line"></div>
+<div class="line">seed_pipeline.pl -url <span class="stringliteral">"mysql://ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_zip_tables"</span> -logic_name find_tables -input_id <span class="stringliteral">"{'only_tables' => '%_result'}"</span></div>
+<div class="line"></div>
+<div class="line">runWorker.pl -url mysql:<span class="comment">//ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_zip_tables</span></div>
+<div class="line">runWorker.pl -url mysql:<span class="comment">//ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_zip_tables</span></div>
+<div class="line">runWorker.pl -url mysql:<span class="comment">//ensadmin:${ENSADMIN_PSW}@localhost:3306/lg4_zip_tables</span></div>
+</div><!-- fragment --> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a34f0292081b57df3025252e36ba2afa2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html#a34f0292081b57df3025252e36ba2afa2">pipeline_analyses()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that defines the structure of the pipeline: analyses, jobs, rules, etc.
+ Here it defines two analyses:</pre><pre> 'find_tables' generates a list of tables whose names match the pattern #only_tables#
+ Each job of this analysis will dataflow (create jobs) via branch #2 into 'table_dumper' analysis.</pre><pre> 'table_dumper' dumps table contents (possibly with table definition) and flows via branch #1 into 'file_compressor' analysis.</pre><pre> 'file_compressor' compresses the dump file</pre><pre> </pre><div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html#a34f0292081b57df3025252e36ba2afa2">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"> { -logic_name => <span class="stringliteral">'find_tables'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::JobFactory'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'inputquery'</span> => <span class="stringliteral">'SELECT table_name FROM information_schema.tables WHERE table_schema = "#mysql_dbname:db_conn#" AND table_name #matching_op# "#only_tables#"'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"><span class="preprocessor"># 2 => { 'table_dumper' => { 'table_name' => '#table_name#', 'db_conn' => '#db_conn#' }, },</span></div>
+<div class="line"><span class="preprocessor"></span> 2 => [ <span class="stringliteral">'table_dumper'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> { -logic_name => <span class="stringliteral">'table_dumper'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'filename'</span> => <span class="stringliteral">'#directory#/#table_name#.sql'</span>,</div>
+<div class="line"> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'mysqldump #mysql_conn:db_conn# #dumping_flags# #table_name# >#filename#'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> -analysis_capacity => 2,</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"><span class="preprocessor"># 1 => { 'file_compressor' => { 'filename' => '#filename#' }, },</span></div>
+<div class="line"><span class="preprocessor"></span> 1 => [ <span class="stringliteral">'file_compressor'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> { -logic_name => <span class="stringliteral">'file_compressor'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'filename'</span> => <span class="stringliteral">'#directory#/#table_name#.sql'</span>,</div>
+<div class="line"> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'gzip #filename#'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> -analysis_capacity => 8,</div>
+<div class="line"> },</div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a722ee2d7f0974ab6865a73290f55adf9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf::pipeline_wide_parameters </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Interface method that should return a hash of pipeline_wide_parameter_name->pipeline_wide_parameter_value pairs.
+ The value doesn't have to be a scalar, can be any Perl structure (will be stringified and de-stringified automagically).</pre><pre> </pre><div id="codesection-pipeline_wide_parameters" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_wide_parameters-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_wide_parameters-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_wide_parameters-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html#a722ee2d7f0974ab6865a73290f55adf9">pipeline_wide_parameters</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{$self->SUPER::pipeline_wide_parameters}, # here we inherit anything from the base <span class="keyword">class</span>, then add our own stuff</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'db_conn'</span> => $self->o(<span class="stringliteral">'db_conn'</span>),</div>
+<div class="line"> <span class="stringliteral">'dumping_flags'</span> => <span class="stringliteral">'-t'</span>, # <span class="stringliteral">'-t'</span> <span class="keywordflow">for</span> <span class="stringliteral">"dump without table definition"</span> or <span class="stringliteral">''</span> <span class="keywordflow">for</span> <span class="stringliteral">"dump with table definition"</span></div>
+<div class="line"> <span class="stringliteral">'directory'</span> => <span class="charliteral">'.'</span>, # directory where both source and target files are located</div>
+<div class="line"> <span class="stringliteral">'matching_op'</span> => <span class="stringliteral">'LIKE'</span>, # <span class="stringliteral">'LIKE'</span> or <span class="stringliteral">'NOT LIKE'</span></div>
+<div class="line"> <span class="stringliteral">'only_tables'</span> => <span class="charliteral">'%'</span>, # any wildcard understood by MySQL</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/PipeConfig/<a class="el" href="_table_dumper_zipper__conf_8pm.html">TableDumperZipper_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">PipeConfig</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html">TableDumperZipper_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
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+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
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+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
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+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
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+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
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+ <div id="nav-sync" class="sync"></div>
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+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+ name="MSearchResults" id="MSearchResults">
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+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Process Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
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+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Abstract superclass. Each Process makes up the individual building blocks
+ of the system. Instances of these processes are created in a hive workflow
+ graph of Analysis entries that are linked together with dataflow and
+ AnalysisCtrl rules.
+
+ Instances of these Processes are created by the system as work is done.
+ The newly created Process will have preset $self->db, $self->dbc,
+ $self->input_id, $self->analysis and several other variables.
+ From this input and configuration data, each Process can then proceed to
+ do something. The flow of execution within a Process is:
+ pre_cleanup() if($retry_count>0); # clean up databases/filesystem before subsequent attempts
+ fetch_input(); # fetch the data from databases/filesystems
+ run(); # perform the main computation
+ write_output(); # record the results in databases/filesystems
+ post_cleanup(); # destroy all non-trivial data structures after the job is done
+ The developer can implement their own versions of
+ pre_cleanup, fetch_input, run, write_output, and post_cleanup to do what they need.
+
+ The entire system is based around the concept of a workflow graph which
+ can split and loop back on itself. This is accomplished by dataflow
+ rules (similar to Unix pipes) that connect one Process (or analysis) to others.
+ Where a Unix command line program can send output on STDOUT STDERR pipes,
+ a hive Process has access to unlimited pipes referenced by numerical
+ branch_codes. This is accomplished within the Process via
+ $self->dataflow_output_id(...);
+
+ The design philosophy is that each Process does its work and creates output,
+ but it doesn't worry about where the input came from, or where its output
+ goes. If the system has dataflow pipes connected, then the output jobs
+ have purpose, if not - the output work is thrown away. The workflow graph
+ 'controls' the behaviour of the system, not the processes. The processes just
+ need to do their job. The design of the workflow graph is based on the knowledge
+ of what each Process does so that the graph can be correctly constructed.
+ The workflow graph can be constructed a priori or can be constructed and
+ modified by intelligent Processes as the system runs.
+
+
+ The Hive is based on AI concepts and modeled on the social structure and
+ behaviour of a honey bee hive. So where a worker honey bee's purpose is
+ (go find pollen, bring back to hive, drop off pollen, repeat), an ensembl-hive
+ worker's purpose is (find a job, create a Process for that job, run it,
+ drop off output job(s), repeat). While most workflow systems are based
+ on 'smart' central controllers and external control of 'dumb' processes,
+ the Hive is based on 'dumb' workflow graphs and job kiosk, and 'smart' workers
+ (autonomous agents) who are self configuring and figure out for themselves what
+ needs to be done, and then do it. The workers are based around a set of
+ emergent behaviour rules which allow a predictible system behaviour to emerge
+ from what otherwise might appear at first glance to be a chaotic system. There
+ is an inherent asynchronous disconnect between one worker and the next.
+ Work (or jobs) are simply 'posted' on a blackboard or kiosk within the hive
+ database where other workers can find them.
+ The emergent behaviour rules of a worker are:
+ 1) If a job is posted, someone needs to do it.
+ 2) Don't grab something that someone else is working on
+ 3) Don't grab more than you can handle
+ 4) If you grab a job, it needs to be finished correctly
+ 5) Keep busy doing work
+ 6) If you fail, do the best you can to report back
+
+ For further reading on the AI principles employed in this design see:
+ http://en.wikipedia.org/wiki/Autonomous_Agent
+ http://en.wikipedia.org/wiki/Emergence
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a21e51ec58fe708d8875617da6912ca46"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> Bio::EnsEMBL::Hive::Process::analysis </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : analysis
+ Usage : $self->analysis;
+ Function: Returns the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Analysis</a> object associated with this
+ instance of the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Process</a>.
+ Returns : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> object</pre><pre> </pre><div id="codesection-analysis" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-analysis-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-analysis-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-analysis-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> {</div>
+<div class="line"> my ($self, $analysis) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($analysis) {</div>
+<div class="line"> <span class="keywordflow">throw</span>(<span class="stringliteral">"Not a Bio::EnsEMBL::Hive::Analysis object"</span>)</div>
+<div class="line"> unless ($analysis->isa(<span class="stringliteral">"Bio::EnsEMBL::Hive::Analysis"</span>));</div>
+<div class="line"> $self->{<span class="stringliteral">'_analysis'</span>} = $analysis;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_analysis'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a35dbbcb04656e835a31cbc927b2c8584"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::cleanup_worker_temp_directory </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : cleanup_worker_temp_directory
+ Function: Cleans up the directory on the local /tmp disk that is used for the
+ worker. It can be used to remove files left there by previous jobs.
+ Usage : $self->cleanup_worker_temp_directory;</pre><pre> </pre><div id="codesection-cleanup_worker_temp_directory" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-cleanup_worker_temp_directory-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-cleanup_worker_temp_directory-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-cleanup_worker_temp_directory-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $tmp_dir = $self->worker_temp_directory_name();</div>
+<div class="line"> <span class="keywordflow">if</span>(-e $tmp_dir) {</div>
+<div class="line"> my $cmd = <span class="stringliteral">"rm -r $tmp_dir"</span>;</div>
+<div class="line"> system($cmd);</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="afe4af3210589a3123a939ceaf83c0462"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::DBSQL::DBConnection Bio::EnsEMBL::Hive::Process::data_dbc </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : data_dbc
+ Usage : my $data_dbc = $self->data_dbc;
+ Function: returns a <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> object (the "current" one by default, but can be set up otherwise)
+ Returns : Bio::EnsEMBL::DBSQL::DBConnection</pre><pre> </pre><div id="codesection-data_dbc" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-data_dbc-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-data_dbc-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-data_dbc-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $given_db_conn = shift @_ || ($self->param_is_defined(<span class="stringliteral">'db_conn'</span>) ? $self->param(<span class="stringliteral">'db_conn'</span>) : $self);</div>
+<div class="line"> my $given_ref = ref( $given_db_conn );</div>
+<div class="line"> my $given_signature = ($given_ref eq <span class="stringliteral">'ARRAY'</span> or $given_ref eq <span class="stringliteral">'HASH'</span>) ? stringify ( $given_db_conn ) : <span class="stringliteral">"$given_db_conn"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( !$self->{<span class="stringliteral">'_cached_db_signature'</span>} or ($self->{<span class="stringliteral">'_cached_db_signature'</span>} ne $given_signature) ) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_cached_db_signature'</span>} = $given_signature;</div>
+<div class="line"> $self->{<span class="stringliteral">'_cached_data_dbc'</span>} = go_figure_dbc( $given_db_conn );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_cached_data_dbc'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3fd5b992716a3aa9a5810da1f007aa5b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::dataflow_output_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-dataflow_output_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dataflow_output_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dataflow_output_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dataflow_output_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->input_job->dataflow_output_id(@_);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8ca200c10405c13d535353f2646b49a1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> Bio::EnsEMBL::Hive::Process::db </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : db
+ Usage : my $hiveDBA = $self->db;
+ Function: returns DBAdaptor to <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a> database
+ Returns : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a></pre><pre> </pre><div id="codesection-db" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-db-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-db-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-db-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_db'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_db'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="afb5ddec979f7e2ed1f2dc375e26c4456"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> Bio::EnsEMBL::Hive::Process::dbc </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : dbc
+ Usage : my $hiveDBConnection = $self->dbc;
+ Function: returns DBConnection to <a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a> database
+ Returns : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a></pre><pre> </pre><div id="codesection-dbc" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dbc-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dbc-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dbc-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->db && $self->db->dbc;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4c9739f352e4eea538b17bb88de70285"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Int Bio::EnsEMBL::Hive::Process::debug </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : debug
+ Function: Gets/sets flag for debug level. Set through Worker/runWorker.pl
+ Subclasses should treat as a read_only variable.
+ Returns : integer</pre><pre> </pre><div id="codesection-debug" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-debug-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-debug-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-debug-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_debug'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_debug'</span>}=0 unless(defined($self->{<span class="stringliteral">'_debug'</span>})); </div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_debug'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2344d158b5ca1a21fa9975fd424a3e6b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::enter_status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-enter_status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-enter_status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-enter_status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-enter_status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a> {</div>
+<div class="line"> my ($self, $status) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $job = $self->input_job();</div>
+<div class="line"></div>
+<div class="line"> $job->update_status( $status );</div>
+<div class="line"></div>
+<div class="line"> my $status_msg = <span class="stringliteral">'Job '</span>.$job->dbID.<span class="stringliteral">' : '</span>.$status;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $worker = $self->worker) {</div>
+<div class="line"> $worker->enter_status( $status, $status_msg );</div>
+<div class="line"> } elsif($self->debug) {</div>
+<div class="line"> print STDERR <span class="stringliteral">"Standalone$status_msg\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2172d0e9d3014f2ef8f117176904fde3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Boolean Bio::EnsEMBL::Hive::Process::execute_writes </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : execute_writes
+ Usage : $self->execute_writes( 1 );
+ Function: getter/setter for whether we want the 'write_output' method to be run
+ Returns : boolean</pre><pre> </pre><div id="codesection-execute_writes" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-execute_writes-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-execute_writes-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-execute_writes-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_execute_writes'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_execute_writes'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="acdd4d38526457335f615330593ab9329"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : fetch_input
+ Function: sublcass can implement functions related to data fetching.
+ Typical acivities would be to parse $self->input_id and read
+ configuration information from $self->analysis. Subclasses
+ may also want to fetch data from databases or from files
+ within this function.</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> 1;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aaa5d456135299916bbb43f4c8300a404"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::input_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-input_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-input_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-input_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-input_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->input_job->input_id(@_);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="abaf96e66f6740ec51a294e4164363166"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> Bio::EnsEMBL::Hive::Process::input_job </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : input_job
+ Function: Returns the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">AnalysisJob</a> to be run by this process
+ Subclasses should treat this as a read_only object.
+ Returns : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> object</pre><pre> </pre><div id="codesection-input_job" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-input_job-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-input_job-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-input_job-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> {</div>
+<div class="line"> my( $self, $job ) = @_;</div>
+<div class="line"> <span class="keywordflow">if</span>($job) {</div>
+<div class="line"> <span class="keywordflow">throw</span>(<span class="stringliteral">"Not a Bio::EnsEMBL::Hive::AnalysisJob object"</span>)</div>
+<div class="line"> unless ($job->isa(<span class="stringliteral">"Bio::EnsEMBL::Hive::AnalysisJob"</span>));</div>
+<div class="line"> $self->{<span class="stringliteral">'_input_job'</span>} = $job;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_input_job'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1c6fcf03a764b66577f4e33477525401"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::life_cycle </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-life_cycle" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-life_cycle-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-life_cycle-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-life_cycle-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a> {</div>
+<div class="line"> my ($self, $worker) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $job = $self->input_job();</div>
+<div class="line"> my $partial_stopwatch = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a1cbc5b3e6c40f0a5862e55e228dc34a3">new</a>();</div>
+<div class="line"> my %job_partial_timing = ();</div>
+<div class="line"></div>
+<div class="line"> $job->autoflow(1);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $self->can(<span class="stringliteral">'pre_cleanup'</span>) and $job->retry_count()>0 ) {</div>
+<div class="line"> $self->enter_status(<span class="stringliteral">'PRE_CLEANUP'</span>);</div>
+<div class="line"> $self->pre_cleanup;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->enter_status(<span class="stringliteral">'FETCH_INPUT'</span>);</div>
+<div class="line"> $partial_stopwatch->restart();</div>
+<div class="line"> $self->fetch_input;</div>
+<div class="line"> $job_partial_timing{<span class="stringliteral">'FETCH_INPUT'</span>} = $partial_stopwatch->get_elapsed();</div>
+<div class="line"></div>
+<div class="line"> $self->enter_status(<span class="stringliteral">'RUN'</span>);</div>
+<div class="line"> $partial_stopwatch->restart();</div>
+<div class="line"> $self->run;</div>
+<div class="line"> $job_partial_timing{<span class="stringliteral">'RUN'</span>} = $partial_stopwatch->get_elapsed();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->execute_writes) {</div>
+<div class="line"> $self->enter_status(<span class="stringliteral">'WRITE_OUTPUT'</span>);</div>
+<div class="line"> $partial_stopwatch->restart();</div>
+<div class="line"> $self->write_output;</div>
+<div class="line"> $job_partial_timing{<span class="stringliteral">'WRITE_OUTPUT'</span>} = $partial_stopwatch->get_elapsed();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $job->autoflow ) {</div>
+<div class="line"> print STDERR <span class="stringliteral">"\njob "</span>.$job->dbID.<span class="stringliteral">" : AUTOFLOW input->output\n"</span> <span class="keywordflow">if</span>($self->debug);</div>
+<div class="line"> $job->dataflow_output_id();</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> print STDERR <span class="stringliteral">"\n!!! *no* WRITE_OUTPUT requested, so there will be no AUTOFLOW\n"</span> <span class="keywordflow">if</span>($self->debug); </div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $self->can(<span class="stringliteral">'post_cleanup'</span>) ) { # Todo: may need to <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> it after the eval, to clean up the memory even after partially failed attempts?</div>
+<div class="line"> $self->enter_status(<span class="stringliteral">'POST_CLEANUP'</span>);</div>
+<div class="line"> $self->post_cleanup;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my @zombie_funnel_dataflow_rule_ids = keys %{$job->fan_cache};</div>
+<div class="line"> <span class="keywordflow">if</span>( scalar(@zombie_funnel_dataflow_rule_ids) ) {</div>
+<div class="line"> $job->transient_error(0);</div>
+<div class="line"> die <span class="stringliteral">"There are cached semaphored fans for which a funnel job (dataflow_rule_id(s) "</span>.join(<span class="charliteral">','</span>,@zombie_funnel_dataflow_rule_ids).<span class="stringliteral">") has never been dataflown"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> \%job_partial_timing;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae2f3da1c5a538fc990739595101bbfc5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my ($class, @args) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = bless {}, $class;</div>
+<div class="line"></div>
+<div class="line"> my ($analysis) = rearrange([qw( ANALYSIS )], @args);</div>
+<div class="line"> $self->analysis($analysis) <span class="keywordflow">if</span>($analysis);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a6217efee02c3fc309ae8705356e5d8dd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::param </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-param" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->input_job->param(@_);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab30a44eca469388da3db6df134ea1559"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::param_defaults </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : param_defaults
+ Function: sublcass can define defaults for all params used by the RunnableDB/Process</pre><pre> </pre><div id="codesection-param_defaults" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_defaults-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_defaults-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_defaults-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> {};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a472fd524e446e292b836f7f73af250e9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::param_is_defined </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-param_is_defined" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_is_defined-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_is_defined-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_is_defined-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->input_job->param_is_defined(@_);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac4d8269232076e9956fbf09e32680c48"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::param_required </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-param_required" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_required-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_required-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_required-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $prev_transient_error = $self->input_job->transient_error(); # make a note of previously set transience status</div>
+<div class="line"> $self->input_job->transient_error(0); # make sure <span class="keywordflow">if</span> we die in <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> it is not <span class="keyword">transient</span></div>
+<div class="line"></div>
+<div class="line"> my $value = $self->input_job->param_required(@_);</div>
+<div class="line"></div>
+<div class="line"> $self->input_job->transient_error($prev_transient_error); # restore the previous transience status</div>
+<div class="line"> <span class="keywordflow">return</span> $value;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a43ada6306f2f629c9d727ea5a0146f89"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::param_substitute </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-param_substitute" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_substitute-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_substitute-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_substitute-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->input_job->param_substitute(@_);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a346410a6c7d0e5f2541bc304048efdb9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : run
+ Function: sublcass can implement functions related to process execution.
+ Typical activities include running external programs or running
+ algorithms by calling perl methods. <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Process</a> may also choose to
+ parse results into memory if an external program was used.</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> 1;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab6663081a21ccab06ee06c3d3d920846"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::strict_hash_format </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : strict_hash_format
+ Function: if a subclass wants more flexibility in parsing job.input_id and analysis.parameters,
+ it should redefine this method to return 0</pre><pre> </pre><div id="codesection-strict_hash_format" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-strict_hash_format-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-strict_hash_format-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-strict_hash_format-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> 1;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a5fef0ffecdd8b254a622f83baa8e03e3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::warning </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-warning" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-warning-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-warning-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-warning-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->input_job->warning(@_);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9d01ac47d41d31f30aca69b0220e0d9d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> Bio::EnsEMBL::Hive::Process::worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : worker
+ Usage : my $worker = $self->worker;
+ Function: returns the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Worker</a> object this <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Process</a> is run by
+ Returns : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></pre><pre> </pre><div id="codesection-worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_worker'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_worker'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3ee5bd7ae4938b858a48b3812814a0a1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::worker_temp_directory </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : worker_temp_directory
+ Function: Returns a path to a directory on the local /tmp disk
+ which the subclass can use as temporary file space.
+ This directory is made the first time the function is called.
+ It persists for as long as the worker is alive. This allows
+ multiple jobs run by the worker to potentially share temp data.
+ For example the worker (which is a single <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Analysis</a>) might need
+ to dump a datafile file which is needed by all jobs run through
+ this analysis. The process can first check the worker_temp_directory
+ for the file and dump it if it is missing. This way the first job
+ run by the worker will do the dump, but subsequent jobs can reuse the
+ file.
+ Usage : $tmp_dir = $self->worker_temp_directory;
+ Returns : <string> path to a local (/tmp) directory</pre><pre> </pre><div id="codesection-worker_temp_directory" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-worker_temp_directory-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-worker_temp_directory-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-worker_temp_directory-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> unless(defined($self->{<span class="stringliteral">'_tmp_dir'</span>}) and (-e $self->{<span class="stringliteral">'_tmp_dir'</span>})) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_tmp_dir'</span>} = $self->worker_temp_directory_name();</div>
+<div class="line"> mkdir($self->{<span class="stringliteral">'_tmp_dir'</span>}, 0777);</div>
+<div class="line"> <span class="keywordflow">throw</span>(<span class="stringliteral">"unable to create a writable directory "</span>.$self->{<span class="stringliteral">'_tmp_dir'</span>}) unless(-w $self->{<span class="stringliteral">'_tmp_dir'</span>});</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_tmp_dir'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab007327305a8dc5294ff757cb3d50559"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::worker_temp_directory_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-worker_temp_directory_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-worker_temp_directory_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-worker_temp_directory_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-worker_temp_directory_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $username = $ENV{<span class="stringliteral">'USER'</span>};</div>
+<div class="line"> my $worker_id = $self->worker ? $self->worker->dbID : <span class="stringliteral">"standalone.$$"</span>;</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">"/tmp/worker_${username}.${worker_id}/"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1c9525d489a6ef446c834ef3c08927a3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Process::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : write_output
+ Function: sublcass can implement functions related to storing results.
+ Typical activities including writing results into database tables
+ or into files on a shared filesystem.</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> 1;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_process_8pm.html">Process.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Process</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+  <span id="projectnumber">1.9</span>
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+<div class="title">Bio::EnsEMBL::Hive::Queen Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a020be70f3da4eca961fef537e68daca6">check_for_dead_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a8ec0da9cd78a6fc994786f65b8710a7d">check_in_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#afbb012326e074b38548ac7341404774b">count_running_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">create_new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a9cd9baa52f9e7a2240ffb979518cfee1">create_new_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">default_input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ab0c7e6cbb62054c0076d73a52efe9141">default_insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">default_overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a545edfa6d9aa715376d5ed7d20767755">default_table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a1ec8aba875ab47959d2714b32b04a5d2">fetch_all_dead_workers_with_jobs</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a47b088cb6be9493e6853b5ee0b20b522">fetch_overdue_workers</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#abe36b590f923d7e82d3577f484bd6056">get_hive_current_load</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#afdadb6fce4eb7469f6de433612867dd5">get_num_failed_analyses</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a51b365aa339df1f733167970be158c63">get_remaining_jobs_show_hive_progress</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ad5392456810e1f4bb16291b54a731c0a">get_workers_rank</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">insertion_method</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">mark_stored</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a422e896db7c973b0385bbafd2c8aa556">monitor</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#af9d2e010bf4d53356d2efde2367c5472">object_class</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ad396c5be7d6806c71b5740054325d5e6">print_analysis_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#af91dbe0832893ec7ec3ecc8a7f7164dd">print_running_worker_counts</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ab4f2cf470e0b3bbe732dd50c22e4deca">register_all_workers_dead</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a1dc35ff50f5375e8796f12d17b372773">register_worker_death</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a46f196406a5bd9c452a5f94361a2eebd">reset_job_by_dbID_and_sync</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#abe0354cbdbf898d95cf08cb2d167ba38">safe_synchronize_AnalysisStats</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">slicer</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#adcc937a7a48d51f801d65757bc55bda2">specialize_new_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a2f39e9a7a7eacf12c8c6262f32b7ffce">synchronize_AnalysisStats</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a2892c256744ac4bdd4f90b9bcc238735">synchronize_hive</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Bio::EnsEMBL::Hive::Queen</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">table_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="entry"></td></tr>
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diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Queen Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::Queen:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen_inherit__map" alt="Inheritance graph"/></div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::Queen:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen_coll__map" alt="Collaboration graph"/></div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a545edfa6d9aa715376d5ed7d20767755"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a545edfa6d9aa715376d5ed7d20767755">default_table_name</a> ()</td></tr>
+<tr class="separator:a545edfa6d9aa715376d5ed7d20767755"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab0c7e6cbb62054c0076d73a52efe9141"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ab0c7e6cbb62054c0076d73a52efe9141">default_insertion_method</a> ()</td></tr>
+<tr class="separator:ab0c7e6cbb62054c0076d73a52efe9141"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:af9d2e010bf4d53356d2efde2367c5472"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#af9d2e010bf4d53356d2efde2367c5472">object_class</a> ()</td></tr>
+<tr class="separator:af9d2e010bf4d53356d2efde2367c5472"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9cd9baa52f9e7a2240ffb979518cfee1"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a9cd9baa52f9e7a2240ffb979518cfee1">create_new_worker</a> ()</td></tr>
+<tr class="separator:a9cd9baa52f9e7a2240ffb979518cfee1"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adcc937a7a48d51f801d65757bc55bda2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#adcc937a7a48d51f801d65757bc55bda2">specialize_new_worker</a> ()</td></tr>
+<tr class="separator:adcc937a7a48d51f801d65757bc55bda2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1dc35ff50f5375e8796f12d17b372773"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a1dc35ff50f5375e8796f12d17b372773">register_worker_death</a> ()</td></tr>
+<tr class="separator:a1dc35ff50f5375e8796f12d17b372773"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a020be70f3da4eca961fef537e68daca6"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a020be70f3da4eca961fef537e68daca6">check_for_dead_workers</a> ()</td></tr>
+<tr class="separator:a020be70f3da4eca961fef537e68daca6"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ec0da9cd78a6fc994786f65b8710a7d"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a8ec0da9cd78a6fc994786f65b8710a7d">check_in_worker</a> ()</td></tr>
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+<tr class="memitem:a46f196406a5bd9c452a5f94361a2eebd"><td class="memItemLeft" align="right" valign="top">public void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a46f196406a5bd9c452a5f94361a2eebd">reset_job_by_dbID_and_sync</a> ()</td></tr>
+<tr class="separator:a46f196406a5bd9c452a5f94361a2eebd"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a47b088cb6be9493e6853b5ee0b20b522"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a47b088cb6be9493e6853b5ee0b20b522">fetch_overdue_workers</a> ()</td></tr>
+<tr class="separator:a47b088cb6be9493e6853b5ee0b20b522"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1ec8aba875ab47959d2714b32b04a5d2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a1ec8aba875ab47959d2714b32b04a5d2">fetch_all_dead_workers_with_jobs</a> ()</td></tr>
+<tr class="separator:a1ec8aba875ab47959d2714b32b04a5d2"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a2892c256744ac4bdd4f90b9bcc238735"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:abe0354cbdbf898d95cf08cb2d167ba38"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2f39e9a7a7eacf12c8c6262f32b7ffce"><td class="memItemLeft" align="right" valign="top">public Newly </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a2f39e9a7a7eacf12c8c6262f32b7ffce">synchronize_AnalysisStats</a> ()</td></tr>
+<tr class="separator:a2f39e9a7a7eacf12c8c6262f32b7ffce"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afdadb6fce4eb7469f6de433612867dd5"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#afdadb6fce4eb7469f6de433612867dd5">get_num_failed_analyses</a> ()</td></tr>
+<tr class="separator:afdadb6fce4eb7469f6de433612867dd5"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abe36b590f923d7e82d3577f484bd6056"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#abe36b590f923d7e82d3577f484bd6056">get_hive_current_load</a> ()</td></tr>
+<tr class="separator:abe36b590f923d7e82d3577f484bd6056"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afbb012326e074b38548ac7341404774b"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#afbb012326e074b38548ac7341404774b">count_running_workers</a> ()</td></tr>
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+<tr class="memitem:a51b365aa339df1f733167970be158c63"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a51b365aa339df1f733167970be158c63">get_remaining_jobs_show_hive_progress</a> ()</td></tr>
+<tr class="separator:a51b365aa339df1f733167970be158c63"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad396c5be7d6806c71b5740054325d5e6"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ad396c5be7d6806c71b5740054325d5e6">print_analysis_status</a> ()</td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td></tr>
+<tr class="memitem:a834186b707376a4ead29771860ab440f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a834186b707376a4ead29771860ab440f">object_class</a> ()</td></tr>
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+<tr class="memitem:af1b4e5cdd9865d10338aafe4c6d047c0 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">slicer</a> ()</td></tr>
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+<tr class="memitem:a02d847dd4df770edb4bdbc5ed309a2d5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">objectify</a> ()</td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td></tr>
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+<tr class="memitem:a1f8bbd7bad6d23b679d4c07ab4121085 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">overflow_limit</a> ()</td></tr>
+<tr class="separator:a1f8bbd7bad6d23b679d4c07ab4121085 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac7e056384281180e1b314889fc7c317f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">input_column_mapping</a> ()</td></tr>
+<tr class="separator:ac7e056384281180e1b314889fc7c317f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:acd1bde351fcbdfddf8fa9896c8716514 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ada55ab8c29c95535953efb0ca8c1d805 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">column_set</a> ()</td></tr>
+<tr class="separator:ada55ab8c29c95535953efb0ca8c1d805 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae98ea2fa8c6a85c6df918b9816bd6cbf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">primary_key</a> ()</td></tr>
+<tr class="separator:ae98ea2fa8c6a85c6df918b9816bd6cbf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae47ff32866fc8b69d8463680b5ead1d2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">updatable_column_list</a> ()</td></tr>
+<tr class="separator:ae47ff32866fc8b69d8463680b5ead1d2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">autoinc_id</a> ()</td></tr>
+<tr class="separator:a7da3298fc1c03c9e7e07123fb710e9a5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">_table_info_loader</a> ()</td></tr>
+<tr class="separator:a348c46fdc789f2eb970dfcc5260aaa28 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">count_all</a> ()</td></tr>
+<tr class="separator:a5675f57702aa4cae6bfc1e39eb420bde inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">fetch_all</a> ()</td></tr>
+<tr class="separator:a18c6bfae797d67669e16242c2390c379 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">primary_key_constraint</a> ()</td></tr>
+<tr class="separator:aadc8dac52ad2c57bff954060d60af436 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a> ()</td></tr>
+<tr class="separator:a29854e14eb6854bc6871db82fdb89d1f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1e7b244d27dcc1244453f725d81d3e54 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">remove_all</a> ()</td></tr>
+<tr class="separator:a1e7b244d27dcc1244453f725d81d3e54 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">remove</a> ()</td></tr>
+<tr class="separator:ab19a4a6d447c8661574a97ae159234f3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> ()</td></tr>
+<tr class="separator:ab8f4cc3813b7d1ad259b02e4a24112f2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">check_object_present_in_db</a> ()</td></tr>
+<tr class="separator:a73ed3c029cb8e6ba86cfd3159de577b2 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">store</a> ()</td></tr>
+<tr class="separator:a23e67bcbf6294126212da34c0c5a2a90 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">DESTROY</a> ()</td></tr>
+<tr class="separator:aeac6bf08072f89a153165ea39b8ed7a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">AUTOLOAD</a> ()</td></tr>
+<tr class="separator:a4805f85a21ec6b85814f32312ee36711 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ The Queen of the Hive based job control system is responsible to 'birthing' the
+ correct number of workers of the right type so that they can find jobs to do.
+ It will also free up jobs of Workers that died unexpectantly so that other workers
+ can claim them to do.
+
+ Hive based processing is a concept based on a more controlled version
+ of an autonomous agent type system. Each worker is not told what to do
+ (like a centralized control system - like the current pipeline system)
+ but rather queries a central database for jobs (give me jobs).
+
+ Each worker is linked to an analysis_id, registers its self on creation
+ into the Hive, creates a RunnableDB instance of the Analysis->module,
+ gets $analysis->stats->batch_size jobs from the job table, does its work,
+ creates the next layer of job entries by interfacing to
+ the DataflowRuleAdaptor to determine the analyses it needs to pass its
+ output data to and creates jobs on the next analysis database.
+ It repeats this cycle until it has lived its lifetime or until there are no
+ more jobs left.
+ The lifetime limit is just a safety limit to prevent these from 'infecting'
+ a system.
+
+ The Queens job is to simply birth Workers of the correct analysis_id to get the
+ work down. The only other thing the Queen does is free up jobs that were
+ claimed by Workers that died unexpectantly so that other workers can take
+ over the work.
+
+ The Beekeeper is in charge of interfacing between the Queen and a compute resource
+ or 'compute farm'. Its job is to query Queens if they need any workers and to
+ send the requested number of workers to open machines via the runWorker.pl script.
+ It is also responsible for interfacing with the Queen to identify worker which died
+ unexpectantly.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a020be70f3da4eca961fef537e68daca6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::check_for_dead_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-check_for_dead_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-check_for_dead_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-check_for_dead_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-check_for_dead_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a020be70f3da4eca961fef537e68daca6">check_for_dead_workers</a> { # scans the whole Valley <span class="keywordflow">for</span> lost Workers (but ignores unreachagle ones)</div>
+<div class="line"> my ($self, $valley, $check_buried_in_haste) = @_;</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"GarbageCollector:\tChecking for lost Workers...\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $last_few_seconds = 5; # FIXME: It is probably a good idea to expose <span class="keyword">this</span> parameter <span class="keywordflow">for</span> easier tuning.</div>
+<div class="line"> my $queen_overdue_workers = $self->fetch_overdue_workers( $last_few_seconds ); # check the workers we have not seen active during the $last_few_seconds</div>
+<div class="line"> my %mt_and_pid_to_worker_status = ();</div>
+<div class="line"> my %worker_status_counts = ();</div>
+<div class="line"> my %mt_and_pid_to_lost_worker = ();</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"GarbageCollector:\t[Queen:] out of "</span>.scalar(@$queen_overdue_workers).<span class="stringliteral">" Workers that haven't checked in during the last $last_few_seconds seconds...\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $worker (@$queen_overdue_workers) {</div>
+<div class="line"></div>
+<div class="line"> my $meadow_type = $worker->meadow_type;</div>
+<div class="line"> <span class="keywordflow">if</span>(my $meadow = $valley->find_available_meadow_responsible_for_worker($worker)) {</div>
+<div class="line"> $mt_and_pid_to_worker_status{$meadow_type} ||= $meadow->status_of_all_our_workers;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $worker_status_counts{$meadow_type}{<span class="stringliteral">'UNREACHABLE'</span>}++;</div>
+<div class="line"></div>
+<div class="line"> next; # Worker is unreachable from <span class="keyword">this</span> Valley</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $process_id = $worker->process_id;</div>
+<div class="line"> <span class="keywordflow">if</span>(my $status = $mt_and_pid_to_worker_status{$meadow_type}{$process_id}) { # can be RUN|PEND|xSUSP</div>
+<div class="line"> $worker_status_counts{$meadow_type}{$status}++;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $worker_status_counts{$meadow_type}{<span class="stringliteral">'LOST'</span>}++;</div>
+<div class="line"></div>
+<div class="line"> $mt_and_pid_to_lost_worker{$meadow_type}{$process_id} = $worker;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # just a quick summary report:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">foreach</span> my $meadow_type (keys %worker_status_counts) {</div>
+<div class="line"> warn <span class="stringliteral">"GarbageCollector:\t[$meadow_type Meadow:]\t"</span>.join(<span class="stringliteral">', '</span>, map { <span class="stringliteral">"$_:$worker_status_counts{$meadow_type}{$_}"</span> } keys %{$worker_status_counts{$meadow_type}}).<span class="stringliteral">"\n\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>(my ($meadow_type, $pid_to_lost_worker) = each %mt_and_pid_to_lost_worker) {</div>
+<div class="line"> my $this_meadow = $valley->available_meadow_hash->{$meadow_type};</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $lost_this_meadow = scalar(keys %$pid_to_lost_worker) ) {</div>
+<div class="line"> warn <span class="stringliteral">"GarbageCollector:\tDiscovered $lost_this_meadow lost $meadow_type Workers\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $wpid_to_cod = {};</div>
+<div class="line"> <span class="keywordflow">if</span>($this_meadow->can(<span class="stringliteral">'find_out_causes'</span>)) {</div>
+<div class="line"> $wpid_to_cod = $this_meadow->find_out_causes( keys %$pid_to_lost_worker );</div>
+<div class="line"> my $lost_with_known_cod = scalar(keys %$wpid_to_cod);</div>
+<div class="line"> warn <span class="stringliteral">"GarbageCollector:\tFound why $lost_with_known_cod of $meadow_type Workers died\n"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"GarbageCollector:\t$meadow_type meadow does not support post-mortem examination\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> warn <span class="stringliteral">"GarbageCollector:\tReleasing the jobs\n"</span>;</div>
+<div class="line"> <span class="keywordflow">while</span>(my ($process_id, $worker) = each %$pid_to_lost_worker) {</div>
+<div class="line"> $worker->cause_of_death( $wpid_to_cod->{$process_id} || <span class="stringliteral">'UNKNOWN'</span>);</div>
+<div class="line"> $self->register_worker_death($worker);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # the following bit is completely Meadow-agnostic and only restores database integrity:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>($check_buried_in_haste) {</div>
+<div class="line"> warn <span class="stringliteral">"GarbageCollector:\tChecking for Workers buried in haste...\n"</span>;</div>
+<div class="line"> my $buried_in_haste_list = $self->fetch_all_dead_workers_with_jobs();</div>
+<div class="line"> <span class="keywordflow">if</span>(my $bih_number = scalar(@$buried_in_haste_list)) {</div>
+<div class="line"> warn <span class="stringliteral">"GarbageCollector:\tfound $bih_number jobs, reclaiming.\n\n"</span>;</div>
+<div class="line"> <span class="keywordflow">if</span>($bih_number) {</div>
+<div class="line"> my $job_adaptor = $self->db->get_AnalysisJobAdaptor();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $worker (@$buried_in_haste_list) {</div>
+<div class="line"> $job_adaptor->release_undone_jobs_from_worker($worker);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"GarbageCollector:\tfound none\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8ec0da9cd78a6fc994786f65b8710a7d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::check_in_worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-check_in_worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-check_in_worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-check_in_worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-check_in_worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a8ec0da9cd78a6fc994786f65b8710a7d">check_in_worker</a> {</div>
+<div class="line"> my ($self, $worker) = @_;</div>
+<div class="line"></div>
+<div class="line"> $self->dbc->do(<span class="stringliteral">"UPDATE worker SET last_check_in=CURRENT_TIMESTAMP, status='"</span>.$worker->status.<span class="stringliteral">"', work_done='"</span>.$worker->work_done.<span class="stringliteral">"' WHERE worker_id='"</span>.$worker->dbID.<span class="stringliteral">"'"</span>);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="afbb012326e074b38548ac7341404774b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::count_running_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-count_running_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-count_running_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-count_running_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-count_running_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#afbb012326e074b38548ac7341404774b">count_running_workers</a> {</div>
+<div class="line"> my ($self, $analysis_id) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->count_all( <span class="stringliteral">"status!='DEAD'"</span>.($analysis_id ? <span class="stringliteral">" AND analysis_id=$analysis_id"</span> : <span class="stringliteral">''</span>) );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9cd9baa52f9e7a2240ffb979518cfee1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> Bio::EnsEMBL::Hive::Queen::create_new_worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: Creates an entry in the worker table,
+ populates some non-storable attributes
+ and returns a <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Worker</a> object based on that insert.
+ This guarantees that each worker registered in this <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Queen</a>'s hive is properly registered.
+ Returntype : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a>
+ Caller : <a class="el" href="run_worker_8pl.html">runWorker.pl</a></pre><pre> </pre><div id="codesection-create_new_worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-create_new_worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-create_new_worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-create_new_worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a9cd9baa52f9e7a2240ffb979518cfee1">create_new_worker</a> {</div>
+<div class="line"> my ($self, @args) = @_;</div>
+<div class="line"></div>
+<div class="line"> my ($meadow_type, $meadow_name, $process_id, $exec_host, $resource_class_id, $resource_class_name,</div>
+<div class="line"> $no_write, $debug, $worker_log_dir, $hive_log_dir, $job_limit, $life_span, $no_cleanup, $retry_throwing_jobs, $can_respecialize) =</div>
+<div class="line"></div>
+<div class="line"> rearrange([qw(meadow_type meadow_name process_id exec_host resource_class_id resource_class_name</div>
+<div class="line"> no_write debug worker_log_dir hive_log_dir job_limit life_span no_cleanup retry_throwing_jobs can_respecialize) ], @args);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $prev_worker_incarnation (@{ $self->fetch_all( <span class="stringliteral">"status!='DEAD' AND meadow_type='$meadow_type' AND meadow_name='$meadow_name' AND process_id='$process_id'"</span> ) }) {</div>
+<div class="line"><span class="preprocessor"> # so far 'RELOCATED events' has been detected on LSF 9.0 in response to sending signal #99 or #100</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # Since I don't know how to avoid them, I am trying to register them when they happen.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # The following snippet buries the previous incarnation of the Worker before starting a new one.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # FIXME: if GarabageCollector (beekeeper -dead) gets to these processes first, it will register them as DEAD/UNKNOWN.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # LSF 9.0 does not report "rescheduling" events in the output of 'bacct', but does mention them in 'bhist'.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # So parsing 'bhist' output would probably yield the most accurate & confident registration of these events.</span></div>
+<div class="line"><span class="preprocessor"></span> $prev_worker_incarnation->cause_of_death( <span class="stringliteral">'RELOCATED'</span> );</div>
+<div class="line"> $self->register_worker_death( $prev_worker_incarnation );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( defined($resource_class_name) ) {</div>
+<div class="line"> my $rc = $self->db->get_ResourceClassAdaptor->fetch_by_name($resource_class_name)</div>
+<div class="line"> or die <span class="stringliteral">"resource_class with name='$resource_class_name' could not be fetched from the database"</span>;</div>
+<div class="line"></div>
+<div class="line"> $resource_class_id = $rc->dbID;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $sql = q{INSERT INTO worker (born, last_check_in, meadow_type, meadow_name, host, process_id, resource_class_id)</div>
+<div class="line"> VALUES (CURRENT_TIMESTAMP, CURRENT_TIMESTAMP, ?, ?, ?, ?, ?)};</div>
+<div class="line"></div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute($meadow_type, $meadow_name, $exec_host, $process_id, $resource_class_id);</div>
+<div class="line"> my $worker_id = $self->dbc->db_handle->last_insert_id(undef, undef, 'worker', 'worker_id')</div>
+<div class="line"> or die "Could not insert a new worker";</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"></div>
+<div class="line"> my $worker = $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">fetch_by_dbID</a>($worker_id)</div>
+<div class="line"> or die "Could not fetch worker with dbID=$worker_id";</div>
+<div class="line"></div>
+<div class="line"> if($hive_log_dir or $worker_log_dir) {</div>
+<div class="line"> my $dir_revhash = dir_revhash($worker_id);</div>
+<div class="line"> $worker_log_dir ||= $hive_log_dir .<span class="charliteral">'/'</span>. ($dir_revhash ? <span class="stringliteral">"$dir_revhash/"</span> : <span class="stringliteral">''</span>) .<span class="stringliteral">'worker_id_'</span>.$worker_id;</div>
+<div class="line"></div>
+<div class="line"> eval {</div>
+<div class="line"> make_path( $worker_log_dir );</div>
+<div class="line"> 1;</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab0c7e6cbb62054c0076d73a52efe9141"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::default_insertion_method </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_insertion_method" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_insertion_method-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_insertion_method-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_insertion_method-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ab0c7e6cbb62054c0076d73a52efe9141">default_insertion_method</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'INSERT'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a545edfa6d9aa715376d5ed7d20767755"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::default_table_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_table_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_table_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_table_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_table_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a545edfa6d9aa715376d5ed7d20767755">default_table_name</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'worker'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1ec8aba875ab47959d2714b32b04a5d2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::fetch_all_dead_workers_with_jobs </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_all_dead_workers_with_jobs" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_all_dead_workers_with_jobs-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_all_dead_workers_with_jobs-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_all_dead_workers_with_jobs-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a1ec8aba875ab47959d2714b32b04a5d2">fetch_all_dead_workers_with_jobs</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_all( <span class="stringliteral">"JOIN job j USING(worker_id) WHERE worker.status='DEAD' AND j.status NOT IN ('DONE', 'READY', 'FAILED', 'PASSED_ON') GROUP BY worker_id"</span> );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a47b088cb6be9493e6853b5ee0b20b522"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::fetch_overdue_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_overdue_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_overdue_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_overdue_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_overdue_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a47b088cb6be9493e6853b5ee0b20b522">fetch_overdue_workers</a> {</div>
+<div class="line"> my ($self,$overdue_secs) = @_;</div>
+<div class="line"></div>
+<div class="line"> $overdue_secs = 3600 unless(defined($overdue_secs));</div>
+<div class="line"></div>
+<div class="line"> my $constraint = <span class="stringliteral">"status!='DEAD' AND "</span>.{</div>
+<div class="line"> <span class="stringliteral">'mysql'</span> => <span class="stringliteral">"(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(last_check_in)) > $overdue_secs"</span>,</div>
+<div class="line"> <span class="stringliteral">'sqlite'</span> => <span class="stringliteral">"(strftime('%s','now')-strftime('%s',last_check_in)) > $overdue_secs"</span>,</div>
+<div class="line"> <span class="stringliteral">'pgsql'</span> => <span class="stringliteral">"EXTRACT(EPOCH FROM CURRENT_TIMESTAMP - last_check_in) > $overdue_secs"</span>,</div>
+<div class="line"> }->{ $self->dbc->driver };</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->fetch_all( $constraint );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="abe36b590f923d7e82d3577f484bd6056"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::get_hive_current_load </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_hive_current_load" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_hive_current_load-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_hive_current_load-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_hive_current_load-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#abe36b590f923d7e82d3577f484bd6056">get_hive_current_load</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> my $sql = qq{</div>
+<div class="line"> SELECT sum(1/hive_capacity)</div>
+<div class="line"> FROM worker w</div>
+<div class="line"> JOIN analysis_stats USING(analysis_id)</div>
+<div class="line"> WHERE w.status!='DEAD'</div>
+<div class="line"> AND hive_capacity IS NOT NULL</div>
+<div class="line"> AND hive_capacity>0</div>
+<div class="line"> };</div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"> my ($load)=$sth->fetchrow_array();</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"> return ($load || 0);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="afdadb6fce4eb7469f6de433612867dd5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Int Bio::EnsEMBL::Hive::Queen::get_num_failed_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a> object (optional)
+ Example :</pre><div class="fragment"><div class="line"><span class="keywordflow">if</span>( $self->get_num_failed_analyses( $my_analysis )) { do_something; }</div>
+</div><!-- fragment --> <pre> Example :</pre><div class="fragment"><div class="line">my $num_failed_analyses = $self->get_num_failed_analyses();</div>
+</div><!-- fragment --> <pre> Description: Reports all failed analyses and returns
+ either the number of total failed (if no $filter_analysis was provided)
+ or 1/0, depending on whether $filter_analysis failed or not.
+ Returntype : int
+ Exceptions : none
+ Caller : general</pre><pre> </pre><div id="codesection-get_num_failed_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_num_failed_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_num_failed_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_num_failed_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#afdadb6fce4eb7469f6de433612867dd5">get_num_failed_analyses</a> {</div>
+<div class="line"> my ($self, $filter_analysis) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $failed_analyses = $self->db->get_AnalysisAdaptor->fetch_all_failed_analyses();</div>
+<div class="line"></div>
+<div class="line"> my $filter_analysis_failed = 0;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $failed_analysis (@$failed_analyses) {</div>
+<div class="line"> print <span class="stringliteral">"\t##########################################################\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\t# Too many jobs in analysis '"</span>.$failed_analysis->logic_name.<span class="stringliteral">"' FAILED #\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\t##########################################################\n\n"</span>;</div>
+<div class="line"> <span class="keywordflow">if</span>($filter_analysis and ($filter_analysis->dbID == $failed_analysis)) {</div>
+<div class="line"> $filter_analysis_failed = 1;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $filter_analysis ? $filter_analysis_failed : scalar(@$failed_analyses);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a51b365aa339df1f733167970be158c63"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::get_remaining_jobs_show_hive_progress </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_remaining_jobs_show_hive_progress" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_remaining_jobs_show_hive_progress-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_remaining_jobs_show_hive_progress-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_remaining_jobs_show_hive_progress-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a51b365aa339df1f733167970be158c63">get_remaining_jobs_show_hive_progress</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> my $sql = <span class="stringliteral">"SELECT sum(done_job_count), sum(failed_job_count), sum(total_job_count), "</span>.</div>
+<div class="line"> <span class="stringliteral">"sum(ready_job_count * analysis_stats.avg_msec_per_job)/1000/60/60 "</span>.</div>
+<div class="line"> <span class="stringliteral">"FROM analysis_stats"</span>;</div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"> my ($done, $failed, $total, $cpuhrs) = $sth->fetchrow_array();</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"></div>
+<div class="line"> $done ||= 0;</div>
+<div class="line"> $failed ||= 0;</div>
+<div class="line"> $total ||= 0;</div>
+<div class="line"> my $completed = $total</div>
+<div class="line"> ? ((100.0 * ($done+$failed))/$total)</div>
+<div class="line"> : 0.0;</div>
+<div class="line"> my $remaining = $total - $done - $failed;</div>
+<div class="line"> warn sprintf(<span class="stringliteral">"hive %1.3f%% complete (< %1.3f CPU_hrs) (%d todo + %d done + %d failed = %d total)\n"</span>,</div>
+<div class="line"> $completed, $cpuhrs, $remaining, $done, $failed, $total);</div>
+<div class="line"> <span class="keywordflow">return</span> $remaining;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad5392456810e1f4bb16291b54a731c0a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::get_workers_rank </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_workers_rank" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_workers_rank-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_workers_rank-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_workers_rank-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ad5392456810e1f4bb16291b54a731c0a">get_workers_rank</a> {</div>
+<div class="line"> my ($self, $worker) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->count_all( <span class="stringliteral">"status!='DEAD' AND analysis_id="</span>.$worker->analysis_id.<span class="stringliteral">" AND worker_id<"</span>.$worker->dbID );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a422e896db7c973b0385bbafd2c8aa556"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::monitor </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg[1] : --none--
+ Example :</pre><div class="fragment"><div class="line">$queen->monitor();</div>
+</div><!-- fragment --> <pre> Description: Monitors current throughput and store the result in the monitor
+ table
+ Exceptions : none
+ Caller : beekeepers and other external processes</pre><pre> </pre><div id="codesection-monitor" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-monitor-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-monitor-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-monitor-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a422e896db7c973b0385bbafd2c8aa556">monitor</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> my $sql = qq{</div>
+<div class="line"> INSERT INTO <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a422e896db7c973b0385bbafd2c8aa556">monitor</a></div>
+<div class="line"> SELECT CURRENT_TIMESTAMP, count(*),</div>
+<div class="line"> } . {</div>
+<div class="line"> <span class="stringliteral">'mysql'</span> => qq{ sum(work_done/(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(born))),</div>
+<div class="line"> sum(work_done/(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(born)))/count(*), },</div>
+<div class="line"> <span class="stringliteral">'sqlite'</span> => qq{ sum(work_done/(strftime(<span class="stringliteral">'%s'</span>,<span class="stringliteral">'now'</span>)-strftime(<span class="stringliteral">'%s'</span>,born))),</div>
+<div class="line"> sum(work_done/(strftime(<span class="stringliteral">'%s'</span>,<span class="stringliteral">'now'</span>)-strftime(<span class="stringliteral">'%s'</span>,born)))/count(*), },</div>
+<div class="line"> <span class="stringliteral">'pgsql'</span> => qq{ sum(work_done/(EXTRACT(EPOCH FROM CURRENT_TIMESTAMP - born))),</div>
+<div class="line"> sum(work_done/(EXTRACT(EPOCH FROM CURRENT_TIMESTAMP - born)))/count(*), },</div>
+<div class="line"> }->{ $self->dbc->driver }. qq{</div>
+<div class="line"> group_concat(DISTINCT logic_name)</div>
+<div class="line"> FROM worker w</div>
+<div class="line"> LEFT JOIN analysis_base USING (analysis_id)</div>
+<div class="line"> WHERE w.status!='DEAD'</div>
+<div class="line"> };</div>
+<div class="line"> </div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af9d2e010bf4d53356d2efde2367c5472"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::object_class </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-object_class" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-object_class-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-object_class-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-object_class-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#af9d2e010bf4d53356d2efde2367c5472">object_class</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'Bio::EnsEMBL::Hive::Worker'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad396c5be7d6806c71b5740054325d5e6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::print_analysis_status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-print_analysis_status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-print_analysis_status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-print_analysis_status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-print_analysis_status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ad396c5be7d6806c71b5740054325d5e6">print_analysis_status</a> {</div>
+<div class="line"> my ($self, $filter_analysis) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $analysis (sort {$a->dbID <=> $b->dbID} @$list_of_analyses) {</div>
+<div class="line"> print $analysis->stats->toString . <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af91dbe0832893ec7ec3ecc8a7f7164dd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::print_running_worker_counts </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-print_running_worker_counts" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-print_running_worker_counts-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-print_running_worker_counts-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-print_running_worker_counts-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#af91dbe0832893ec7ec3ecc8a7f7164dd">print_running_worker_counts</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> my $sql = qq{</div>
+<div class="line"> SELECT logic_name, count(*)</div>
+<div class="line"> FROM worker w</div>
+<div class="line"> JOIN analysis_base a USING(analysis_id)</div>
+<div class="line"> WHERE w.status!='DEAD'</div>
+<div class="line"> GROUP BY a.analysis_id</div>
+<div class="line"> };</div>
+<div class="line"></div>
+<div class="line"> my $total_workers = 0;</div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"></div>
+<div class="line"> print "\n===== Stats of live Workers according to the Queen: ======\n";</div>
+<div class="line"> while((my $logic_name, my $worker_count)=$sth->fetchrow_array()) {</div>
+<div class="line"> printf(<span class="stringliteral">"%30s : %d workers\n"</span>, $logic_name, $worker_count);</div>
+<div class="line"> $total_workers += $worker_count;</div>
+<div class="line"> }</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"> printf(<span class="stringliteral">"%30s : %d workers\n\n"</span>, <span class="stringliteral">'======= TOTAL ======='</span>, $total_workers);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab4f2cf470e0b3bbe732dd50c22e4deca"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::register_all_workers_dead </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Example :</pre><div class="fragment"><div class="line">$queen->register_all_workers_dead();</div>
+</div><!-- fragment --> <pre> Description: Registers all workers dead
+ Exceptions : none
+ Caller : beekeepers and other external processes</pre><pre> </pre><div id="codesection-register_all_workers_dead" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-register_all_workers_dead-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-register_all_workers_dead-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-register_all_workers_dead-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ab4f2cf470e0b3bbe732dd50c22e4deca">register_all_workers_dead</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> my $all_workers_considered_alive = $self->fetch_all( <span class="stringliteral">"status!='DEAD'"</span> );</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $worker (@{$all_workers_considered_alive}) {</div>
+<div class="line"> $worker->cause_of_death( <span class="stringliteral">'UNKNOWN'</span> ); # well, maybe we could have investigated further...</div>
+<div class="line"> $self->register_worker_death($worker);</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1dc35ff50f5375e8796f12d17b372773"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::register_worker_death </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-register_worker_death" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-register_worker_death-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-register_worker_death-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-register_worker_death-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a1dc35ff50f5375e8796f12d17b372773">register_worker_death</a> {</div>
+<div class="line"> my ($self, $worker, $self_burial) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> unless($worker);</div>
+<div class="line"></div>
+<div class="line"> my $cod = $worker->cause_of_death() || <span class="stringliteral">'UNKNOWN'</span>; # make sure we <span class="keywordflow">do</span> not attempt to insert a <span class="keywordtype">void</span></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # FIXME: make it possible to set the 'died' timestamp if we have detected it from logs:</span></div>
+<div class="line"><span class="preprocessor"></span> my $sql = qq{UPDATE worker SET died=CURRENT_TIMESTAMP</div>
+<div class="line"> } . ( $self_burial ? <span class="stringliteral">',last_check_in=CURRENT_TIMESTAMP '</span> : <span class="stringliteral">''</span>) . qq{</div>
+<div class="line"> ,status=<span class="stringliteral">'DEAD'</span></div>
+<div class="line"> ,work_done=<span class="stringliteral">'}. $worker->work_done . qq{'</span></div>
+<div class="line"> ,cause_of_death=<span class="stringliteral">'$cod'</span></div>
+<div class="line"> WHERE worker_id=<span class="stringliteral">'}. $worker->dbID . qq{'</span>};</div>
+<div class="line"> $self->dbc->do( $sql );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $analysis_id = $worker->analysis_id) {</div>
+<div class="line"> my $analysis_stats_adaptor = $self->db->get_AnalysisStatsAdaptor;</div>
+<div class="line"></div>
+<div class="line"> unless( $self->db->hive_use_triggers() ) {</div>
+<div class="line"> $analysis_stats_adaptor->decrease_running_workers($worker->analysis_id);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> unless( $cod eq <span class="stringliteral">'NO_WORK'</span></div>
+<div class="line"> or $cod eq <span class="stringliteral">'JOB_LIMIT'</span></div>
+<div class="line"> or $cod eq <span class="stringliteral">'HIVE_OVERLOAD'</span></div>
+<div class="line"> or $cod eq <span class="stringliteral">'LIFESPAN'</span></div>
+<div class="line"> ) {</div>
+<div class="line"> $self->db->get_AnalysisJobAdaptor->release_undone_jobs_from_worker($worker);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # re-sync the analysis_stats when a worker dies as part of dynamic sync system</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>($self->safe_synchronize_AnalysisStats($worker->analysis->stats)->status ne <span class="stringliteral">'DONE'</span>) {</div>
+<div class="line"><span class="preprocessor"> # since I'm dying I should make sure there is someone to take my place after I'm gone ...</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # above synch still sees me as a 'living worker' so I need to compensate for that</span></div>
+<div class="line"><span class="preprocessor"></span> $analysis_stats_adaptor->increase_required_workers($worker->analysis_id);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a46f196406a5bd9c452a5f94361a2eebd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public void Bio::EnsEMBL::Hive::Queen::reset_job_by_dbID_and_sync </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1]: int $job_id
+ Example:
+ my $job = $queen->reset_job_by_dbID_and_sync($job_id);
+ Description:
+ For the specified job_id it will fetch just that job,
+ reset it completely as if it has never run, and return it.
+ Specifying a specific job bypasses the safety checks,
+ thus multiple workers could be running the
+ same job simultaneously (use only for debugging).
+ Returntype : none
+ Exceptions :
+ Caller : <a class="el" href="beekeeper_8pl.html">beekeeper.pl</a></pre><pre> </pre><div id="codesection-reset_job_by_dbID_and_sync" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-reset_job_by_dbID_and_sync-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-reset_job_by_dbID_and_sync-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-reset_job_by_dbID_and_sync-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a46f196406a5bd9c452a5f94361a2eebd">reset_job_by_dbID_and_sync</a> {</div>
+<div class="line"> my ($self, $job_id) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $job_adaptor = $self->db->get_AnalysisJobAdaptor;</div>
+<div class="line"> my $job = $job_adaptor->reset_or_grab_job_by_dbID($job_id); </div>
+<div class="line"></div>
+<div class="line"> my $stats = $self->db->get_AnalysisStatsAdaptor->fetch_by_analysis_id($job->analysis_id);</div>
+<div class="line"> $self->synchronize_AnalysisStats($stats);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="abe0354cbdbf898d95cf08cb2d167ba38"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::safe_synchronize_AnalysisStats </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a> object
+ Example :</pre><div class="fragment"><div class="line">$self->safe_synchronize_AnalysisStats($stats);</div>
+</div><!-- fragment --> <pre> Description: Prewrapper around synchronize_AnalysisStats that does
+ checks and grabs sync_lock before proceeding with sync.
+ Used by distributed worker sync system to avoid contention.
+ Exceptions : none
+ Caller : general</pre><pre> </pre><div id="codesection-safe_synchronize_AnalysisStats" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-safe_synchronize_AnalysisStats-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-safe_synchronize_AnalysisStats-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-safe_synchronize_AnalysisStats-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#abe0354cbdbf898d95cf08cb2d167ba38">safe_synchronize_AnalysisStats</a> {</div>
+<div class="line"> my ($self, $stats) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $max_refresh_attempts = 5;</div>
+<div class="line"> <span class="keywordflow">while</span>($stats->sync_lock and $max_refresh_attempts--) { # another Worker/Beekeeper is synching <span class="keyword">this</span> analysis right now</div>
+<div class="line"> sleep(1);</div>
+<div class="line"> $stats->refresh(); # just <span class="keywordflow">try</span> to avoid collision</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $stats <span class="keywordflow">if</span>($stats->status eq <span class="stringliteral">'DONE'</span>);</div>
+<div class="line"> <span class="keywordflow">return</span> $stats <span class="keywordflow">if</span>(($stats->status eq <span class="stringliteral">'WORKING'</span>) and</div>
+<div class="line"> ($stats->seconds_since_last_update < 3*60));</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # try to claim the sync_lock</span></div>
+<div class="line"><span class="preprocessor"></span> my $sql = <span class="stringliteral">"UPDATE analysis_stats SET status='SYNCHING', sync_lock=1 "</span>.</div>
+<div class="line"> <span class="stringliteral">"WHERE sync_lock=0 and analysis_id="</span> . $stats->analysis_id;</div>
+<div class="line"> my $row_count = $self->dbc->do($sql); </div>
+<div class="line"> <span class="keywordflow">return</span> $stats unless($row_count == 1); # <span class="keywordflow">return</span> the un-updated status <span class="keywordflow">if</span> locked</div>
+<div class="line"> </div>
+<div class="line"><span class="preprocessor"> # if we managed to obtain the lock, let's go and perform the sync:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->synchronize_AnalysisStats($stats);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $stats;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="adcc937a7a48d51f801d65757bc55bda2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::specialize_new_worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: If analysis_id or logic_name is specified it will try to specialize the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Worker</a> into this analysis.
+ If not specified the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Queen</a> will analyze the hive and pick the most suitable analysis.
+ Caller : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></pre><pre> </pre><div id="codesection-specialize_new_worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-specialize_new_worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-specialize_new_worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-specialize_new_worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#adcc937a7a48d51f801d65757bc55bda2">specialize_new_worker</a> {</div>
+<div class="line"> my ($self, $worker, @args) = @_;</div>
+<div class="line"></div>
+<div class="line"> my ($analysis_id, $logic_name, $job_id, $force) =</div>
+<div class="line"> rearrange([qw(analysis_id logic_name job_id force) ], @args);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( scalar( grep {defined($_)} ($analysis_id, $logic_name, $job_id) ) > 1) {</div>
+<div class="line"> die <span class="stringliteral">"At most one of the options {-analysis_id, -logic_name, -job_id} can be set to pre-specialize a Worker"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my ($analysis, $stats, $special_batch);</div>
+<div class="line"> my $analysis_stats_adaptor = $self->db->get_AnalysisStatsAdaptor;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($job_id or $analysis_id or $logic_name) { # probably pre-specialized from command-line</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($job_id) {</div>
+<div class="line"> print <span class="stringliteral">"resetting and fetching job for job_id '$job_id'\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $job_adaptor = $self->db->get_AnalysisJobAdaptor;</div>
+<div class="line"></div>
+<div class="line"> my $job = $job_adaptor->fetch_by_dbID( $job_id )</div>
+<div class="line"> or die <span class="stringliteral">"Could not fetch job with dbID='$job_id'"</span>;</div>
+<div class="line"> my $job_status = $job->status();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($job_status =~/(CLAIMED|PRE_CLEANUP|FETCH_INPUT|RUN|WRITE_OUTPUT|POST_CLEANUP)/ ) {</div>
+<div class="line"> die <span class="stringliteral">"Job with dbID='$job_id' is already in progress, cannot run"</span>; # FIXME: <span class="keywordflow">try</span> GC first, then complain</div>
+<div class="line"> } elsif($job_status =~/(DONE|SEMAPHORED)/ and !$force) {</div>
+<div class="line"> die <span class="stringliteral">"Job with dbID='$job_id' is $job_status, please use -force 1 to override"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(($job_status eq <span class="stringliteral">'DONE'</span>) and $job->semaphored_job_id) {</div>
+<div class="line"> warn <span class="stringliteral">"Increasing the semaphore count of the dependent job"</span>;</div>
+<div class="line"> $job_adaptor->increase_semaphore_count_for_jobid( $job->semaphored_job_id );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $worker_id = $worker->dbID;</div>
+<div class="line"> <span class="keywordflow">if</span>($job = $job_adaptor->reset_or_grab_job_by_dbID($job_id, $worker_id)) {</div>
+<div class="line"> $special_batch = [ $job ];</div>
+<div class="line"> $analysis_id = $job->analysis_id;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> die <span class="stringliteral">"Could not claim job with dbID='$job_id' for worker with dbID='$worker_id'"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($logic_name) {</div>
+<div class="line"> $analysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($logic_name)</div>
+<div class="line"> or die <span class="stringliteral">"analysis with name='$logic_name' could not be fetched from the database"</span>;</div>
+<div class="line"></div>
+<div class="line"> $analysis_id = $analysis->dbID;</div>
+<div class="line"></div>
+<div class="line"> } elsif($analysis_id) {</div>
+<div class="line"> $analysis = $self->db->get_AnalysisAdaptor->fetch_by_dbID($analysis_id)</div>
+<div class="line"> or die <span class="stringliteral">"analysis with dbID='$analysis_id' could not be fetched from the database"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $worker->resource_class_id</div>
+<div class="line"> and $worker->resource_class_id != $analysis->resource_class_id) {</div>
+<div class="line"> die <span class="stringliteral">"resource_class of analysis "</span>.$analysis->logic_name.<span class="stringliteral">" is incompatible with this Worker's resource_class"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $stats = $analysis_stats_adaptor->fetch_by_analysis_id($analysis_id);</div>
+<div class="line"> $self->safe_synchronize_AnalysisStats($stats);</div>
+<div class="line"></div>
+<div class="line"> unless($special_batch or $force) { # <span class="keywordflow">do</span> we really need to run <span class="keyword">this</span> analysis?</div>
+<div class="line"> <span class="keywordflow">if</span>($self->get_hive_current_load() >= 1.1) {</div>
+<div class="line"> $worker->cause_of_death(<span class="stringliteral">'HIVE_OVERLOAD'</span>);</div>
+<div class="line"> die <span class="stringliteral">"Hive is overloaded, can't specialize a worker"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">if</span>($stats->status eq <span class="stringliteral">'BLOCKED'</span>) {</div>
+<div class="line"> die <span class="stringliteral">"Analysis is BLOCKED, can't specialize a worker"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">if</span>($stats->num_required_workers <= 0) {</div>
+<div class="line"> die <span class="stringliteral">"Analysis doesn't require extra workers at the moment"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">if</span>($stats->status eq <span class="stringliteral">'DONE'</span>) {</div>
+<div class="line"> die <span class="stringliteral">"Analysis is DONE, and doesn't require workers"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"><span class="preprocessor"> # probably scheduled by beekeeper.pl:</span></div>
+<div class="line"><span class="preprocessor"></span> } elsif( $stats = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ab56e0d78a8774c93dc262a5c63812891">Bio::EnsEMBL::Hive::Scheduler::suggest_analysis_to_specialize_by_rc_id_meadow_type</a>($self, $worker->resource_class_id, $worker->meadow_type) ) {</div>
+<div class="line"></div>
+<div class="line"> $worker->analysis( undef ); # make sure we reset anything that was there before</div>
+<div class="line"> $analysis_id = $stats->analysis_id;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $worker->cause_of_death(<span class="stringliteral">'NO_ROLE'</span>);</div>
+<div class="line"> die <span class="stringliteral">"No analysis suitable for the worker was found\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # now set it in the $worker:</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> $worker->analysis_id( $analysis_id );</div>
+<div class="line"></div>
+<div class="line"> $self->update_analysis_id( $worker ); # autoloaded</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($special_batch) {</div>
+<div class="line"> $worker->special_batch( $special_batch );</div>
+<div class="line"> } <span class="keywordflow">else</span> { # count it as autonomous worker sharing the load of that analysis:</div>
+<div class="line"></div>
+<div class="line"> $stats->update_status(<span class="stringliteral">'WORKING'</span>);</div>
+<div class="line"></div>
+<div class="line"> $analysis_stats_adaptor->decrease_required_workers($worker->analysis_id);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # The following increment used to be done only when no specific task was given to the worker,</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # thereby excluding such "special task" workers from being counted in num_running_workers.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # However this may be tricky to emulate by triggers that know nothing about "special tasks",</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # so I am (temporarily?) simplifying the accounting algorithm.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span> unless( $self->db->hive_use_triggers() ) {</div>
+<div class="line"> $analysis_stats_adaptor->increase_running_workers($worker->analysis_id);</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2f39e9a7a7eacf12c8c6262f32b7ffce"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Newly Bio::EnsEMBL::Hive::Queen::synchronize_AnalysisStats </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a> object
+ Example :</pre><div class="fragment"><div class="line">$self->synchronize($analysisStats);</div>
+</div><!-- fragment --> <pre> Description: Queries the job and worker tables to get summary counts
+ and rebuilds the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">AnalysisStats</a> object. Then updates the
+ analysis_stats table with the new summary info
+ Returntype : newly synced <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">Bio::EnsEMBL::Hive::AnalysisStats</a> object
+ Exceptions : none
+ Caller : general</pre><pre> </pre><div id="codesection-synchronize_AnalysisStats" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-synchronize_AnalysisStats-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-synchronize_AnalysisStats-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-synchronize_AnalysisStats-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a2f39e9a7a7eacf12c8c6262f32b7ffce">synchronize_AnalysisStats</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> my $analysisStats = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $analysisStats unless($analysisStats);</div>
+<div class="line"> <span class="keywordflow">return</span> $analysisStats unless($analysisStats->analysis_id);</div>
+<div class="line"></div>
+<div class="line"> $analysisStats->refresh(); ## Need to <span class="keyword">get</span> the <span class="keyword">new</span> hive_capacity <span class="keywordflow">for</span> dynamic analyses</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"> unless($self->db->hive_use_triggers()) {</div>
+<div class="line"> $analysisStats->total_job_count(0);</div>
+<div class="line"> $analysisStats->semaphored_job_count(0);</div>
+<div class="line"> $analysisStats->ready_job_count(0);</div>
+<div class="line"> $analysisStats->done_job_count(0);</div>
+<div class="line"> $analysisStats->failed_job_count(0);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # ask for analysis_id to force MySQL to use existing index on (analysis_id, status)</span></div>
+<div class="line"><span class="preprocessor"></span> my $sql = <span class="stringliteral">"SELECT analysis_id, status, count(*) FROM job WHERE analysis_id=? GROUP BY analysis_id, status"</span>;</div>
+<div class="line"> my $sth = $self->prepare($sql);</div>
+<div class="line"> $sth->execute($analysisStats->analysis_id);</div>
+<div class="line"></div>
+<div class="line"> my $done_here = 0;</div>
+<div class="line"> my $done_elsewhere = 0;</div>
+<div class="line"> my $total_job_count = 0;</div>
+<div class="line"> <span class="keywordflow">while</span> (my ($dummy_analysis_id, $status, $job_count)=$sth->fetchrow_array()) {</div>
+<div class="line"><span class="preprocessor"> # print STDERR "$status: $job_count\n";</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> $total_job_count += $job_count;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($status eq <span class="stringliteral">'READY'</span>) {</div>
+<div class="line"> $analysisStats->ready_job_count($job_count);</div>
+<div class="line"> } elsif($status eq <span class="stringliteral">'SEMAPHORED'</span>) {</div>
+<div class="line"> $analysisStats->semaphored_job_count($job_count);</div>
+<div class="line"> } elsif($status eq <span class="stringliteral">'DONE'</span>) {</div>
+<div class="line"> $done_here = $job_count;</div>
+<div class="line"> } elsif($status eq <span class="stringliteral">'PASSED_ON'</span>) {</div>
+<div class="line"> $done_elsewhere = $job_count;</div>
+<div class="line"> } elsif ($status eq <span class="stringliteral">'FAILED'</span>) {</div>
+<div class="line"> $analysisStats->failed_job_count($job_count);</div>
+<div class="line"> }</div>
+<div class="line"> } # /<span class="keywordflow">while</span></div>
+<div class="line"> $sth->finish;</div>
+<div class="line"></div>
+<div class="line"> $analysisStats->total_job_count( $total_job_count );</div>
+<div class="line"> $analysisStats->done_job_count( $done_here + $done_elsewhere );</div>
+<div class="line"> } # unless($self->db->hive_use_triggers())</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"> # compute the number of total required workers <span class="keywordflow">for</span> <span class="keyword">this</span> analysis (taking into account the jobs that are already running)</div>
+<div class="line"> my $analysis = $analysisStats->get_analysis();</div>
+<div class="line"> my $scheduling_allowed = ( !defined( $analysisStats->hive_capacity ) or $analysisStats->hive_capacity )</div>
+<div class="line"> && ( !defined( $analysis->analysis_capacity ) or $analysis->analysis_capacity );</div>
+<div class="line"> my $required_workers = $scheduling_allowed</div>
+<div class="line"> && POSIX::ceil( $analysisStats->ready_job_count() / $analysisStats->get_or_estimate_batch_size() );</div>
+<div class="line"> $analysisStats->num_required_workers( $required_workers );</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"> $analysisStats->check_blocking_control_rules();</div>
+<div class="line"></div>
+<div class="line"> if($analysisStats->status ne 'BLOCKED') {</div>
+<div class="line"> $analysisStats->determine_status();</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # $analysisStats->sync_lock(0); ## do we perhaps need it here?</span></div>
+<div class="line"><span class="preprocessor"></span> $analysisStats->update; #<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">update</a> and release sync_lock</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $analysisStats;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2892c256744ac4bdd4f90b9bcc238735"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Queen::synchronize_hive </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : $filter_analysis (optional)
+ Example :</pre><div class="fragment"><div class="line">$queen->synchronize_hive();</div>
+</div><!-- fragment --> <pre> Description: Runs through all analyses in the system and synchronizes
+ the analysis_stats summary with the states in the job
+ and worker tables. Then follows by checking all the blocking rules
+ and blocks/unblocks analyses as needed.
+ Exceptions : none
+ Caller : general</pre><pre> </pre><div id="codesection-synchronize_hive" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-synchronize_hive-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-synchronize_hive-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-synchronize_hive-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a2892c256744ac4bdd4f90b9bcc238735">synchronize_hive</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> my $filter_analysis = shift; # optional parameter</div>
+<div class="line"></div>
+<div class="line"> my $start_time = time();</div>
+<div class="line"></div>
+<div class="line"> my $list_of_analyses = $filter_analysis ? [$filter_analysis] : $self->db->get_AnalysisAdaptor->fetch_all;</div>
+<div class="line"></div>
+<div class="line"> print STDERR <span class="stringliteral">"\nSynchronizing the hive ("</span>.scalar(@$list_of_analyses).<span class="stringliteral">" analyses this time):\n"</span>;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $analysis (@$list_of_analyses) {</div>
+<div class="line"> $self->synchronize_AnalysisStats($analysis->stats);</div>
+<div class="line"> print STDERR ( ($analysis->stats()->status eq <span class="stringliteral">'BLOCKED'</span>) ? <span class="charliteral">'x'</span> : <span class="charliteral">'o'</span>);</div>
+<div class="line"> }</div>
+<div class="line"> print STDERR <span class="stringliteral">"\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> print STDERR <span class="stringliteral">''</span>.((time() - $start_time)).<span class="stringliteral">" seconds to synchronize_hive\n\n"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_queen_8pm.html">Queen.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Queen</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
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+<meta name="generator" content="Doxygen 1.8.6"/>
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+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::ResourceClass Member List</div> </div>
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+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html">Bio::EnsEMBL::Hive::ResourceClass</a>, including all inherited members.</p>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a4483fbceef09b5b032c54b797fdb73d9">name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html">Bio::EnsEMBL::Hive::ResourceClass</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a76ab34ac067611e361c72614a8156cb7">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html">Bio::EnsEMBL::Hive::ResourceClass</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a1bb8f3a9ff04edf71733a8cca5622080">toString</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html">Bio::EnsEMBL::Hive::ResourceClass</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html
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+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Bio::EnsEMBL::Hive::ResourceClass Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<script type="text/javascript" src="navtree.js"></script>
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+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
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+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
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+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::ResourceClass Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::ResourceClass:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class_inherit__map" alt="Inheritance graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class_inherit__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class_inherit__map">
+</map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::ResourceClass:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class_coll__map">
+</map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a76ab34ac067611e361c72614a8156cb7"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a76ab34ac067611e361c72614a8156cb7">new</a> ()</td></tr>
+<tr class="separator:a76ab34ac067611e361c72614a8156cb7"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4483fbceef09b5b032c54b797fdb73d9"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a4483fbceef09b5b032c54b797fdb73d9">name</a> ()</td></tr>
+<tr class="separator:a4483fbceef09b5b032c54b797fdb73d9"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1bb8f3a9ff04edf71733a8cca5622080"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a1bb8f3a9ff04edf71733a8cca5622080">toString</a> ()</td></tr>
+<tr class="separator:a1bb8f3a9ff04edf71733a8cca5622080"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A data container object (the only methods are getters/setters) that corresponds to a row in 'resource_class' table:
+
+ CREATE TABLE resource_class (
+ resource_class_id int(10) unsigned NOT NULL AUTO_INCREMENT, # unique internal id
+ name varchar(40) NOT NULL,
+
+ PRIMARY KEY(resource_class_id)
+ );
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a4483fbceef09b5b032c54b797fdb73d9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::ResourceClass::name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a4483fbceef09b5b032c54b797fdb73d9">name</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_name'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_name'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a76ab34ac067611e361c72614a8156cb7"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::ResourceClass::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = $class->SUPER::new( @_ ); # deal with Storable stuff</div>
+<div class="line"></div>
+<div class="line"> my ($name) =</div>
+<div class="line"> rearrange([qw(<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a4483fbceef09b5b032c54b797fdb73d9">name</a>) ], @_);</div>
+<div class="line"></div>
+<div class="line"> $self->name($name) <span class="keywordflow">if</span>($name);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1bb8f3a9ff04edf71733a8cca5622080"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::ResourceClass::toString </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-toString" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-toString-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-toString-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-toString-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a1bb8f3a9ff04edf71733a8cca5622080">toString</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> (ref($self).<span class="stringliteral">': '</span>.join(<span class="stringliteral">', '</span>, map { $_.<span class="stringliteral">'="'</span>.$self->$_().<span class="charliteral">'"'</span> } qw(dbID <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a4483fbceef09b5b032c54b797fdb73d9">name</a>) ));</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_resource_class_8pm.html">ResourceClass.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html">ResourceClass</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class =
+[
+ [ "name", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a4483fbceef09b5b032c54b797fdb73d9", null ],
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+ [ "toString", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a1bb8f3a9ff04edf71733a8cca5622080", null ]
+];
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
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+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
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+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
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+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
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+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::ResourceDescription Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html">Bio::EnsEMBL::Hive::ResourceDescription</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a253a528483f463acf6db1e49f54c75a2">adaptor</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html">Bio::EnsEMBL::Hive::ResourceDescription</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a73ad6041bffcd835a77d9086b2ea1695">meadow_type</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html">Bio::EnsEMBL::Hive::ResourceDescription</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a182572a7a902208f7b78653dbca05fa4">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html">Bio::EnsEMBL::Hive::ResourceDescription</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a5c5bf7acac77e65b07761146d39bcc24">resource_class_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html">Bio::EnsEMBL::Hive::ResourceDescription</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a2e0e47ea126a9a4ce7d1340700919239">submission_cmd_args</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html">Bio::EnsEMBL::Hive::ResourceDescription</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#aff13953b8d3b80fcb2b72a8f03457259">toString</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html">Bio::EnsEMBL::Hive::ResourceDescription</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a1b975bd9bfad96e24af7bc859a28d116">worker_cmd_args</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html">Bio::EnsEMBL::Hive::ResourceDescription</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html
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@@ -0,0 +1,374 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Bio::EnsEMBL::Hive::ResourceDescription Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
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+ $(document).ready(initResizable);
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+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+</script>
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+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+
+<div class="header">
+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::ResourceDescription Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a182572a7a902208f7b78653dbca05fa4"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a182572a7a902208f7b78653dbca05fa4">new</a> ()</td></tr>
+<tr class="separator:a182572a7a902208f7b78653dbca05fa4"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a253a528483f463acf6db1e49f54c75a2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a253a528483f463acf6db1e49f54c75a2">adaptor</a> ()</td></tr>
+<tr class="separator:a253a528483f463acf6db1e49f54c75a2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5c5bf7acac77e65b07761146d39bcc24"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a5c5bf7acac77e65b07761146d39bcc24">resource_class_id</a> ()</td></tr>
+<tr class="separator:a5c5bf7acac77e65b07761146d39bcc24"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a73ad6041bffcd835a77d9086b2ea1695"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a73ad6041bffcd835a77d9086b2ea1695">meadow_type</a> ()</td></tr>
+<tr class="separator:a73ad6041bffcd835a77d9086b2ea1695"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2e0e47ea126a9a4ce7d1340700919239"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a2e0e47ea126a9a4ce7d1340700919239">submission_cmd_args</a> ()</td></tr>
+<tr class="separator:a2e0e47ea126a9a4ce7d1340700919239"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1b975bd9bfad96e24af7bc859a28d116"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a1b975bd9bfad96e24af7bc859a28d116">worker_cmd_args</a> ()</td></tr>
+<tr class="separator:a1b975bd9bfad96e24af7bc859a28d116"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aff13953b8d3b80fcb2b72a8f03457259"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#aff13953b8d3b80fcb2b72a8f03457259">toString</a> ()</td></tr>
+<tr class="separator:aff13953b8d3b80fcb2b72a8f03457259"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A data container object (the only methods are getters/setters) that corresponds to a row in 'resource_description' table:
+
+ CREATE TABLE resource_description (
+ resource_class_id int(10) unsigned NOT NULL,
+ meadow_type varchar(40) NOT NULL,
+ submission_cmd_args VARCHAR(255) NOT NULL DEFAULT '',
+ worker_cmd_args VARCHAR(255) NOT NULL DEFAULT '',
+
+ PRIMARY KEY(resource_class_id, meadow_type)
+ ) ENGINE=InnoDB;
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a253a528483f463acf6db1e49f54c75a2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::ResourceDescription::adaptor </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-adaptor" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-adaptor-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-adaptor-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-adaptor-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a253a528483f463acf6db1e49f54c75a2">adaptor</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_adaptor'</span>} = shift @_;</div>
+<div class="line"> weaken $self->{<span class="stringliteral">'_adaptor'</span>};</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_adaptor'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a73ad6041bffcd835a77d9086b2ea1695"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::ResourceDescription::meadow_type </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-meadow_type" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-meadow_type-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-meadow_type-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-meadow_type-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a73ad6041bffcd835a77d9086b2ea1695">meadow_type</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_meadow_type'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_meadow_type'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a182572a7a902208f7b78653dbca05fa4"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::ResourceDescription::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = bless {}, $class;</div>
+<div class="line"></div>
+<div class="line"> my ($adaptor, $resource_class_id, $meadow_type, $submission_cmd_args, $worker_cmd_args) =</div>
+<div class="line"> rearrange([qw(<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a253a528483f463acf6db1e49f54c75a2">adaptor</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a5c5bf7acac77e65b07761146d39bcc24">resource_class_id</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a73ad6041bffcd835a77d9086b2ea1695">meadow_type</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a2e0e47ea126a9a4ce7d1340700919239">submission_cmd_args</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a1b975bd9bfad96e24af7bc859a28d116">worker_cmd_args</a>) ], @_);</div>
+<div class="line"></div>
+<div class="line"> $self->adaptor($adaptor) <span class="keywordflow">if</span>(defined($adaptor));</div>
+<div class="line"> $self->resource_class_id($resource_class_id);</div>
+<div class="line"> $self->meadow_type($meadow_type);</div>
+<div class="line"> $self->submission_cmd_args($submission_cmd_args);</div>
+<div class="line"> $self->worker_cmd_args($worker_cmd_args);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a5c5bf7acac77e65b07761146d39bcc24"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::ResourceDescription::resource_class_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-resource_class_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-resource_class_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-resource_class_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-resource_class_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a5c5bf7acac77e65b07761146d39bcc24">resource_class_id</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_resource_class_id'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_resource_class_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2e0e47ea126a9a4ce7d1340700919239"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::ResourceDescription::submission_cmd_args </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-submission_cmd_args" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-submission_cmd_args-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-submission_cmd_args-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-submission_cmd_args-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a2e0e47ea126a9a4ce7d1340700919239">submission_cmd_args</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_submission_cmd_args'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_submission_cmd_args'</span>} || <span class="stringliteral">''</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aff13953b8d3b80fcb2b72a8f03457259"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::ResourceDescription::toString </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-toString" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-toString-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-toString-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-toString-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#aff13953b8d3b80fcb2b72a8f03457259">toString</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> (ref($self).<span class="stringliteral">': '</span>.join(<span class="stringliteral">', '</span>, map { $_.<span class="stringliteral">'="'</span>.$self->$_().<span class="charliteral">'"'</span> } qw(<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a5c5bf7acac77e65b07761146d39bcc24">resource_class_id</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a73ad6041bffcd835a77d9086b2ea1695">meadow_type</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a2e0e47ea126a9a4ce7d1340700919239">submission_cmd_args</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a1b975bd9bfad96e24af7bc859a28d116">worker_cmd_args</a>) ));</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1b975bd9bfad96e24af7bc859a28d116"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::ResourceDescription::worker_cmd_args </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-worker_cmd_args" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-worker_cmd_args-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-worker_cmd_args-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-worker_cmd_args-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a1b975bd9bfad96e24af7bc859a28d116">worker_cmd_args</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_worker_cmd_args'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_worker_cmd_args'</span>} || <span class="stringliteral">''</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_resource_description_8pm.html">ResourceDescription.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html">ResourceDescription</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.js b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.js
new file mode 100644
index 0000000000000000000000000000000000000000..43d52f52369779529c394ef8ee7f7555fa6adb07
--- /dev/null
+++ b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.js
@@ -0,0 +1,10 @@
+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description =
+[
+ [ "adaptor", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a253a528483f463acf6db1e49f54c75a2", null ],
+ [ "meadow_type", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a73ad6041bffcd835a77d9086b2ea1695", null ],
+ [ "new", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a182572a7a902208f7b78653dbca05fa4", null ],
+ [ "resource_class_id", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a5c5bf7acac77e65b07761146d39bcc24", null ],
+ [ "submission_cmd_args", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a2e0e47ea126a9a4ce7d1340700919239", null ],
+ [ "toString", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#aff13953b8d3b80fcb2b72a8f03457259", null ],
+ [ "worker_cmd_args", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a1b975bd9bfad96e24af7bc859a28d116", null ]
+];
\ No newline at end of file
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper-members.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper-members.html
new file mode 100644
index 0000000000000000000000000000000000000000..e2b568740306d8e6736c180ca60d2d4ea52a3e3a
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@@ -0,0 +1,154 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a8e55c7699aa239e5c5550427bed3eed9">_get_table_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#ae38dde4f24511a8913461f18ae56067b">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a66b12a83a4107e2f9758fba932642f7b">mysql_conn_from_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a0a727e827af0f003386490d0aa3b2af9">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper:</div>
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+</div>
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
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+<tr class="memitem:ae38dde4f24511a8913461f18ae56067b"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#ae38dde4f24511a8913461f18ae56067b">fetch_input</a> ()</td></tr>
+<tr class="separator:ae38dde4f24511a8913461f18ae56067b"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8e55c7699aa239e5c5550427bed3eed9"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a8e55c7699aa239e5c5550427bed3eed9">_get_table_list</a> ()</td></tr>
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+<tr class="memitem:a0a727e827af0f003386490d0aa3b2af9"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a0a727e827af0f003386490d0aa3b2af9">run</a> ()</td></tr>
+<tr class="separator:a0a727e827af0f003386490d0aa3b2af9"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a66b12a83a4107e2f9758fba932642f7b"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a66b12a83a4107e2f9758fba932642f7b">mysql_conn_from_dbc</a> ()</td></tr>
+<tr class="separator:a66b12a83a4107e2f9758fba932642f7b"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td></tr>
+<tr class="memitem:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a> ()</td></tr>
+<tr class="separator:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a> ()</td></tr>
+<tr class="separator:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a> ()</td></tr>
+<tr class="separator:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a> ()</td></tr>
+<tr class="separator:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a> ()</td></tr>
+<tr class="separator:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a> ()</td></tr>
+<tr class="separator:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> ()</td></tr>
+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
+<tr class="separator:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
+<tr class="separator:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">standaloneJob.pl RunnableDB/DatabaseDumper.pm -exclude_ehive 1 -exclude_list 1 \</div>
+<div class="line"> -table_list <span class="stringliteral">"['peptide_align_%']"</span> -src_db_conn mysql:<span class="comment">//ensro@127.0.0.1:4313/mm14_compara_homology_67 -output_file ~/dump1.sql</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+This is a Runnable to dump the tables of a database (by default,
+all of them).
+
+The following parameters are accepted:
+
+ - src_db_conn : the connection parameters to the database to be
+ dumped (by default, the current eHive database if available)
+
+ - exclude_ehive [boolean=0] : do we exclude the eHive-specific tables
+ from the dump
+
+ - table_list [string or array of strings]: the list of tables
+ to include in the dump. The '%' wildcard is accepted.
+
+ - exclude_list [boolean=0] : do we consider 'table_list' as a list
+ of tables to be excluded from the dump (instead of included)
+
+ - output_file [string] : the file to write the dump to. If the filename
+ ends with ".gz", the file is compressed with "gzip" (default parameters)
+
+ - output_db [string] : URL of a database to write the dump to. In this
+ mode, the Runnable acts like MySQLTransfer
+
+If "table_list" is undefined or maps to an empty list, the list
+of tables to be dumped is decided accordingly to "exclude_list" (EL)
+and "exclude_ehive" (EH). "exclude_list" controls the whole list of
+non-eHive tables.
+
+EL EH List of tables to dump
+
+0 0 => all the tables
+0 1 => all the tables, except the eHive ones
+1 0 => all the tables, except the non-eHive ones = only the eHive tables
+1 1 => both eHive and non-eHive tables are excluded = nothing is dumped
+
+If "table_list" is defined to non-empty list T, the table of decision is:
+
+EL EH List of tables to dump
+
+0 0 => all the tables in T + the eHive tables
+0 1 => all the tables in T
+1 0 => all the tables, except the ones in T
+1 1 => all the tables, except the ones in T and the eHive ones
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a8e55c7699aa239e5c5550427bed3eed9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper::_get_table_list </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_get_table_list" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_get_table_list-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_get_table_list-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_get_table_list-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a8e55c7699aa239e5c5550427bed3eed9">_get_table_list</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $table_list = $self->param(<span class="stringliteral">'table_list'</span>) || <span class="stringliteral">''</span>;</div>
+<div class="line"> my @newtables = ();</div>
+<div class="line"> my $dbc = $self->param(<span class="stringliteral">'src_dbc'</span>);</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $initable (ref($table_list) eq <span class="stringliteral">'ARRAY'</span> ? @$table_list : split(<span class="charliteral">' '</span>, $table_list)) {</div>
+<div class="line"> <span class="keywordflow">if</span> ($initable =~ /%/) {</div>
+<div class="line"> $initable =~ s/_/\\_/g;</div>
+<div class="line"> my $sth = $dbc->db_handle->table_info(undef, undef, $initable, undef);</div>
+<div class="line"> push @newtables, map( {$_->[2]} @{$sth->fetchall_arrayref});</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> push @newtables, $initable;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> \@newtables;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae38dde4f24511a8913461f18ae56067b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#ae38dde4f24511a8913461f18ae56067b">fetch_input</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # The final list of tables</span></div>
+<div class="line"><span class="preprocessor"></span> my @tables = ();</div>
+<div class="line"> $self->param(<span class="stringliteral">'tables'</span>, \@tables);</div>
+<div class="line"> my @ignores = ();</div>
+<div class="line"> $self->param(<span class="stringliteral">'ignores'</span>, \@ignores);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Would be good to have this from eHive</span></div>
+<div class="line"><span class="preprocessor"></span> my @ehive_tables = qw(hive_meta worker dataflow_rule analysis_base analysis_ctrl_rule job accu log_message job_file analysis_data resource_description analysis_stats analysis_stats_monitor monitor msg progress resource_class);</div>
+<div class="line"> $self->param(<span class="stringliteral">'nb_ehive_tables'</span>, scalar(@ehive_tables));</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Connection parameters</span></div>
+<div class="line"><span class="preprocessor"></span> my $src_db_conn = $self->param(<span class="stringliteral">'src_db_conn'</span>);</div>
+<div class="line"> my $src_dbc = $src_db_conn ? go_figure_dbc($src_db_conn) : $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>;</div>
+<div class="line"> $self->param(<span class="stringliteral">'src_dbc'</span>, $src_dbc);</div>
+<div class="line"></div>
+<div class="line"> $self->input_job->transient_error(0);</div>
+<div class="line"> die <span class="stringliteral">'Only the "mysql" driver is supported.'</span> <span class="keywordflow">if</span> $src_dbc->driver ne <span class="stringliteral">'mysql'</span>;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Get the table list in either "tables" or "ignores"</span></div>
+<div class="line"><span class="preprocessor"></span> my $table_list = $self->_get_table_list;</div>
+<div class="line"> print <span class="stringliteral">"table_list: "</span>, scalar(@$table_list), <span class="stringliteral">" "</span>, join(<span class="charliteral">'/'</span>, @$table_list), <span class="stringliteral">"\n"</span> <span class="keywordflow">if</span> $self->debug;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span> ($self->param(<span class="stringliteral">'exclude_list'</span>)) {</div>
+<div class="line"> push @ignores, @$table_list;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> push @tables, @$table_list;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # eHive tables are dumped unless exclude_ehive is defined</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span> ($self->param(<span class="stringliteral">'exclude_ehive'</span>)) {</div>
+<div class="line"> push @ignores, @ehive_tables;</div>
+<div class="line"> } elsif (scalar(@$table_list) and not $self->param(<span class="stringliteral">'exclude_list'</span>)) {</div>
+<div class="line"> push @tables, @ehive_tables;</div>
+<div class="line"> } elsif (not scalar(@$table_list) and $self->param(<span class="stringliteral">'exclude_list'</span>)) {</div>
+<div class="line"> push @tables, @ehive_tables;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Output file / output database</span></div>
+<div class="line"><span class="preprocessor"></span> $self->param(<span class="stringliteral">'output_file'</span>) || $self->param(<span class="stringliteral">'output_db'</span>) || die <span class="stringliteral">'One of the parameters "output_file" and "output_db" is mandatory'</span>;</div>
+<div class="line"> unless ($self->param(<span class="stringliteral">'output_file'</span>)) {</div>
+<div class="line"> $self->param(<span class="stringliteral">'real_output_db'</span>, go_figure_dbc( $self->param(<span class="stringliteral">'output_db'</span>) ) );</div>
+<div class="line"> die <span class="stringliteral">'Only the "mysql" driver is supported.'</span> <span class="keywordflow">if</span> $self->param(<span class="stringliteral">'real_output_db'</span>)->driver ne <span class="stringliteral">'mysql'</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->input_job->transient_error(1);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a66b12a83a4107e2f9758fba932642f7b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper::mysql_conn_from_dbc </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-mysql_conn_from_dbc" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-mysql_conn_from_dbc-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-mysql_conn_from_dbc-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-mysql_conn_from_dbc-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a66b12a83a4107e2f9758fba932642f7b">mysql_conn_from_dbc</a> {</div>
+<div class="line"> my ($self, $dbc) = @_; </div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'--host='</span>.$dbc->host.<span class="stringliteral">' --port='</span>.$dbc->port.<span class="stringliteral">" --user='"</span>.$dbc->username.<span class="stringliteral">"' --password='"</span>.$dbc->password.<span class="stringliteral">"' "</span>.$dbc->dbname;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0a727e827af0f003386490d0aa3b2af9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a0a727e827af0f003386490d0aa3b2af9">run</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $src_dbc = $self->param(<span class="stringliteral">'src_dbc'</span>);</div>
+<div class="line"> my $tables = $self->param(<span class="stringliteral">'tables'</span>);</div>
+<div class="line"> my $ignores = $self->param(<span class="stringliteral">'ignores'</span>);</div>
+<div class="line"></div>
+<div class="line"> print <span class="stringliteral">"tables: "</span>, scalar(@$tables), <span class="stringliteral">" "</span>, join(<span class="charliteral">'/'</span>, @$tables), <span class="stringliteral">"\n"</span> <span class="keywordflow">if</span> $self->debug;</div>
+<div class="line"> print <span class="stringliteral">"ignores: "</span>, scalar(@$ignores), <span class="stringliteral">" "</span>, join(<span class="charliteral">'/'</span>, @$ignores), <span class="stringliteral">"\n"</span> <span class="keywordflow">if</span> $self->debug;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # We have to exclude everything</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">return</span> <span class="keywordflow">if</span> ($self->param(<span class="stringliteral">'exclude_ehive'</span>) and $self->param(<span class="stringliteral">'exclude_list'</span>) and scalar(@$ignores) == $self->param(<span class="stringliteral">'nb_ehive_tables'</span>));</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # mysqldump command</span></div>
+<div class="line"><span class="preprocessor"></span> my $output = <span class="stringliteral">""</span>;</div>
+<div class="line"> <span class="keywordflow">if</span> ($self->param(<span class="stringliteral">'output_file'</span>)) {</div>
+<div class="line"> <span class="keywordflow">if</span> (lc $self->param(<span class="stringliteral">'output_file'</span>) =~ /\.gz$/) {</div>
+<div class="line"> $output = sprintf(<span class="stringliteral">' | gzip > %s'</span>, $self->param(<span class="stringliteral">'output_file'</span>));</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $output = sprintf(<span class="stringliteral">'> %s'</span>, $self->param(<span class="stringliteral">'output_file'</span>));</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $output = sprintf(<span class="stringliteral">' | mysql %s'</span>, $self->mysql_conn_from_dbc($self->param(<span class="stringliteral">'real_output_db'</span>)));</div>
+<div class="line"> };</div>
+<div class="line"></div>
+<div class="line"> my $cmd = join(<span class="charliteral">' '</span>, </div>
+<div class="line"> <span class="stringliteral">'mysqldump'</span>,</div>
+<div class="line"> $self->mysql_conn_from_dbc($src_dbc),</div>
+<div class="line"> <span class="stringliteral">'--skip-lock-tables'</span>,</div>
+<div class="line"> @$tables,</div>
+<div class="line"> (map {sprintf(<span class="stringliteral">'--ignore-table=%s.%s'</span>, $src_dbc->dbname, $_)} @$ignores),</div>
+<div class="line"> $output</div>
+<div class="line"> );</div>
+<div class="line"> print <span class="stringliteral">"$cmd\n"</span> <span class="keywordflow">if</span> $self->debug;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # We have to skip the dump</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">return</span> <span class="keywordflow">if</span> ($self->param(<span class="stringliteral">'skip_dump'</span>));</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # OK, we can dump</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>(my $return_value = system($cmd)) {</div>
+<div class="line"> die <span class="stringliteral">"system( $cmd ) failed: $return_value"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/<a class="el" href="_database_dumper_8pm.html">DatabaseDumper.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html">DatabaseDumper</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper =
+[
+ [ "_get_table_list", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a8e55c7699aa239e5c5550427bed3eed9", null ],
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+ [ "run", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a0a727e827af0f003386490d0aa3b2af9", null ]
+];
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+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a>, including all inherited members.</p>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a4be920b14ab4f65812887f02751e1a10">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a></td><td class="entry"></td></tr>
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+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::Dummy Class Reference</div> </div>
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+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::Dummy:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy_inherit__map" alt="Inheritance graph"/></div>
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::RunnableDB::Dummy:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy_coll__map">
+<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html" title="Bio::EnsEMBL::Hive\l::Process" alt="" coords="13,97,155,138"/></map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:aaeefc3b5e868e3302698ff162baf5b64"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#aaeefc3b5e868e3302698ff162baf5b64">strict_hash_format</a> ()</td></tr>
+<tr class="separator:aaeefc3b5e868e3302698ff162baf5b64"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a87f4c403bf90241054674b689d01dd33"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a87f4c403bf90241054674b689d01dd33">param_defaults</a> ()</td></tr>
+<tr class="separator:a87f4c403bf90241054674b689d01dd33"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0574c8877209e27b076ef7afe573baa2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a0574c8877209e27b076ef7afe573baa2">fetch_input</a> ()</td></tr>
+<tr class="separator:a0574c8877209e27b076ef7afe573baa2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4be920b14ab4f65812887f02751e1a10"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a4be920b14ab4f65812887f02751e1a10">run</a> ()</td></tr>
+<tr class="separator:a4be920b14ab4f65812887f02751e1a10"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a091a7496c19f579499f04ee9c7f78c77"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a091a7496c19f579499f04ee9c7f78c77">write_output</a> ()</td></tr>
+<tr class="separator:a091a7496c19f579499f04ee9c7f78c77"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td></tr>
+<tr class="memitem:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a> ()</td></tr>
+<tr class="separator:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a> ()</td></tr>
+<tr class="separator:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a> ()</td></tr>
+<tr class="separator:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a> ()</td></tr>
+<tr class="separator:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a> ()</td></tr>
+<tr class="separator:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a> ()</td></tr>
+<tr class="separator:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> ()</td></tr>
+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
+<tr class="separator:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
+<tr class="separator:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">standaloneJob.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> <span class="stringliteral">"{}"</span></div>
+<div class="line"></div>
+<div class="line">standaloneJob.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> <span class="stringliteral">"{take_time=>3}"</span></div>
+<div class="line"></div>
+<div class="line">standaloneJob.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a> -<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> <span class="stringliteral">"{take_time=>'rand(3)+1'}"</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A job of 'Bio::EnsEMBL::Hive::RunnableDB::Dummy' analysis does not do any work by itself,
+ but it benefits from the side-effects that are associated with having an analysis.
+
+ For example, if a dataflow rule is linked to the analysis then
+ every job that is created or flown into this analysis will be dataflown further according to this rule.
+
+ param('take_time'): How much time to spend sleeping (floating point seconds);
+ can be given by a runtime-evaluated formula; useful for testing.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a0574c8877209e27b076ef7afe573baa2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::Dummy::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a0574c8877209e27b076ef7afe573baa2">fetch_input()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to read in parameters and load data.
+ Here we simply override this method so that nothing is done.</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a0574c8877209e27b076ef7afe573baa2">fetch_input</a> {</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a87f4c403bf90241054674b689d01dd33"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::Dummy::param_defaults </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a87f4c403bf90241054674b689d01dd33">param_defaults()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that defines module defaults for parameters.</pre><pre> </pre><div id="codesection-param_defaults" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_defaults-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_defaults-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_defaults-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a87f4c403bf90241054674b689d01dd33">param_defaults</a> {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'take_time'</span> => 0, # how much time <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a4be920b14ab4f65812887f02751e1a10">run</a>() method will spend in sleeping state</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4be920b14ab4f65812887f02751e1a10"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::Dummy::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a4be920b14ab4f65812887f02751e1a10">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to perform the main bulk of the job (minus input and output).
+ Since this Runnable is a <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html">Dummy</a>, it does nothing. But it can also optionally sleep for param('take_time') seconds.</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a4be920b14ab4f65812887f02751e1a10">run</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $take_time = eval $self->param(<span class="stringliteral">'take_time'</span>);</div>
+<div class="line"> <span class="keywordflow">if</span>($take_time) {</div>
+<div class="line"> print <span class="stringliteral">"Sleeping for '$take_time' seconds...\n"</span>;</div>
+<div class="line"> usleep( $take_time*1000000 );</div>
+<div class="line"> print <span class="stringliteral">"Done.\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aaeefc3b5e868e3302698ff162baf5b64"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::Dummy::strict_hash_format </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-strict_hash_format" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-strict_hash_format-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-strict_hash_format-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-strict_hash_format-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#aaeefc3b5e868e3302698ff162baf5b64">strict_hash_format</a> { # allow <span class="keyword">this</span> Runnable to parse parameters in its own way (don<span class="stringliteral">'t complain)</span></div>
+<div class="line"><span class="stringliteral"> return 0;</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a091a7496c19f579499f04ee9c7f78c77"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::Dummy::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a091a7496c19f579499f04ee9c7f78c77">write_output()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to deal with job's output after the execution.
+ Here we simply override this method so that nothing is done.</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a091a7496c19f579499f04ee9c7f78c77">write_output</a> {</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/<a class="el" href="_dummy_8pm.html">Dummy.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html">Dummy</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::FailureTest Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>, including all inherited members.</p>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a9ca1fe4defa82d28bc60b64fb4c9cf71">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a76caed50af47567cd2fd93ea4b7b3f8a">grab_memory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#aebd3288a79a288b73f8527c86fcd6fd9">param_defaults</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a071768efd731a484438461e833bae07f">post_cleanup</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a6d7e5437a262f09e5e9cc37965f07ed1">pre_cleanup</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a525479b5642b24c86208663fa2fd7d4a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a0b3680ba302807ee3b9fc34de7b1449d">write_output</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::FailureTest Class Reference</div> </div>
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+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::FailureTest:</div>
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+<tr class="memitem:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> ()</td></tr>
+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
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+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
+<tr class="separator:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">This is a RunnableDB module that implements <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> interface</div>
+<div class="line">and is ran by Workers during the execution of eHive pipelines.</div>
+<div class="line">It is not generally supposed to be instantiated and used outside of <span class="keyword">this</span> framework.</div>
+<div class="line"></div>
+<div class="line">Please refer to <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> documentation to understand the basics of the RunnableDB interface.</div>
+<div class="line"></div>
+<div class="line">Please refer to Bio::EnsEMBL::Hive::PipeConfig::* pipeline configuration files to understand how to configure pipelines.</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This RunnableDB module is used to test failure of jobs in the hive system.
+
+ It is intended for development/training purposes only.
+
+ Available parameters:
+
+ param('value'): is essentially your job's number.
+ If you are intending to create 100 jobs, let the param('value') take consecutive values from 1 to 100.
+
+ param('divisor'): defines the failure rate for this particular analysis. If the modulo (value % divisor) is 0, the job will fail.
+ For example, if param('divisor')==5, jobs with 5, 10, 15, 20, 25,... param('value') will fail.
+
+ param('state'): defines the state in which the jobs of this analysis may be failing.
+
+ param('lethal_after'): makes jobs' failures lethal when 'value' is greater than this parameter
+
+ param('time_FETCH_INPUT'): time in seconds that the job will spend sleeping in FETCH_INPUT state.
+
+ param('time_RUN'): time in seconds that the job will spend sleeping in RUN state.
+
+ param('time_WRITE_OUTPUT'): time in seconds that the job will spend sleeping in WRITE_OUTPUT state.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="add6d6e854b8d35f11810311490b17ab9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FailureTest::dangerous_math </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: an internal subroutine that will first sleep for some predefined time,
+ and then either return or crash if $value is an integral multiple of $divisor.</pre><pre> </pre><div id="codesection-dangerous_math" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dangerous_math-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dangerous_math-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dangerous_math-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#add6d6e854b8d35f11810311490b17ab9">dangerous_math</a> {</div>
+<div class="line"> my ($self, $current_state) = @_;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # First, sleep as required:</span></div>
+<div class="line"><span class="preprocessor"></span> my $seconds_to_sleep = $self->param(<span class="stringliteral">'time_'</span>.$current_state);</div>
+<div class="line"> sleep( $seconds_to_sleep );</div>
+<div class="line"></div>
+<div class="line"> my $state = $self->param(<span class="stringliteral">'state'</span>);</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="keywordflow">if</span>($current_state ne $state);</div>
+<div class="line"></div>
+<div class="line"> my $value = $self->param(<span class="stringliteral">'value'</span>) or die <span class="stringliteral">"param('value') has to be a nonzero integer"</span>;</div>
+<div class="line"> my $divisor = $self->param(<span class="stringliteral">'divisor'</span>) or die <span class="stringliteral">"param('divisor') has to be a nonzero integer"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($value % $divisor == 0) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $lethal_after = $self->param(<span class="stringliteral">'lethal_after'</span>)) {</div>
+<div class="line"> <span class="keywordflow">if</span>($value>$lethal_after) { # take the Worker with us into the grave</div>
+<div class="line"> $self->input_job->lethal_for_worker(1);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> die <span class="stringliteral">"Preprogrammed death since $value is a multiple of $divisor"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9ca1fe4defa82d28bc60b64fb4c9cf71"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FailureTest::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a9ca1fe4defa82d28bc60b64fb4c9cf71">fetch_input()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to read in parameters and load data.
+ Here it only calls <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#add6d6e854b8d35f11810311490b17ab9">dangerous_math()</a> subroutine.</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a9ca1fe4defa82d28bc60b64fb4c9cf71">fetch_input</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $self->dangerous_math(<span class="stringliteral">'FETCH_INPUT'</span>);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a76caed50af47567cd2fd93ea4b7b3f8a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FailureTest::grab_memory </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-grab_memory" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-grab_memory-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-grab_memory-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-grab_memory-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a76caed50af47567cd2fd93ea4b7b3f8a">grab_memory</a> {</div>
+<div class="line"> my ($self, $grab_mln) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $elements = $grab_mln*1_000_000;</div>
+<div class="line"> my $estimated_megs = $grab_mln*69 + 23; # empirically found by running on farm3, may differ elsewhere</div>
+<div class="line"></div>
+<div class="line"> $|=1;</div>
+<div class="line"></div>
+<div class="line"> $self->warning(<span class="stringliteral">"Allocating $elements elements, which should map to approximately $estimated_megs megabytes"</span>);</div>
+<div class="line"></div>
+<div class="line"> my @mem = (1..$elements);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> \@mem;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aebd3288a79a288b73f8527c86fcd6fd9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FailureTest::param_defaults </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#aebd3288a79a288b73f8527c86fcd6fd9">param_defaults()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that defines module defaults for parameters.</pre><pre> </pre><div id="codesection-param_defaults" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_defaults-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_defaults-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_defaults-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#aebd3288a79a288b73f8527c86fcd6fd9">param_defaults</a> {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'value'</span> => 1, # normally you generate a batch of jobs with different values of <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>(<span class="stringliteral">'value'</span>)</div>
+<div class="line"> <span class="stringliteral">'divisor'</span> => 2, # but the same <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>(<span class="stringliteral">'divisor'</span>) and see how every <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>('divisor')'s job will crash</div>
+<div class="line"> 'state' => 'RUN', <span class="preprocessor"># the state in which the process may commit apoptosis ('FETCH_INPUT', 'RUN' or 'WRITE_OUTPUT')</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'lethal_after'</span> => 0, # If value is above <span class="keyword">this</span> (nonzero) threshold, job<span class="stringliteral">'s death becomes lethal to the worker.</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> '</span>time_FETCH_INPUT<span class="stringliteral">' => 0, # how much time fetch_input() will spend in sleeping state</span></div>
+<div class="line"><span class="stringliteral"> '</span>time_RUN<span class="stringliteral">' => 1, # how much time run() will spend in sleeping state</span></div>
+<div class="line"><span class="stringliteral"> '</span>time_WRITE_OUTPUT<span class="stringliteral">' => 0, # how much time write_output() will spend in sleeping state</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> '</span>grab_mln<span class="stringliteral">' => 0, # how many millions of numeric elements to allocate</span></div>
+<div class="line"><span class="stringliteral"> };</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a071768efd731a484438461e833bae07f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FailureTest::post_cleanup </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : post_cleanup
+ Function: sublcass can implement functions related to cleaning up after running one job
+ (destroying non-trivial data structures in memory).
+ Here we just define it to see when the job gets into this state.</pre><pre> </pre><div id="codesection-post_cleanup" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-post_cleanup-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-post_cleanup-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-post_cleanup-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a071768efd731a484438461e833bae07f">post_cleanup</a> {</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a6d7e5437a262f09e5e9cc37965f07ed1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FailureTest::pre_cleanup </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : pre_cleanup
+ Function: sublcass can implement functions related to cleaning up the database/filesystem after the previous unsuccessful run.
+ Here we just define it to see when the job gets into this state.</pre><pre> </pre><div id="codesection-pre_cleanup" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pre_cleanup-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pre_cleanup-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pre_cleanup-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a6d7e5437a262f09e5e9cc37965f07ed1">pre_cleanup</a> {</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a525479b5642b24c86208663fa2fd7d4a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FailureTest::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a525479b5642b24c86208663fa2fd7d4a">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to perform the main bulk of the job (minus input and output).
+ Here it only calls <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#add6d6e854b8d35f11810311490b17ab9">dangerous_math()</a> subroutine.</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a525479b5642b24c86208663fa2fd7d4a">run</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $mem_ref;</div>
+<div class="line"> <span class="keywordflow">if</span>(my $grab_mln = $self->param(<span class="stringliteral">'grab_mln'</span>)) {</div>
+<div class="line"> $mem_ref = $self->grab_memory( $grab_mln );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->dangerous_math(<span class="stringliteral">'RUN'</span>);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0b3680ba302807ee3b9fc34de7b1449d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FailureTest::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a0b3680ba302807ee3b9fc34de7b1449d">write_output()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to deal with job's output after the execution.
+ Here it only calls <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#add6d6e854b8d35f11810311490b17ab9">dangerous_math()</a> subroutine.</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a0b3680ba302807ee3b9fc34de7b1449d">write_output</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $self->dangerous_math(<span class="stringliteral">'WRITE_OUTPUT'</span>);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/<a class="el" href="_failure_test_8pm.html">FailureTest.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html">FailureTest</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory Member List</div> </div>
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+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a364bc206bd7c1d93307258ff83b3fcce">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a2291deabf24d52906b30ec18d2dbb126">param_defaults</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#ad2334d5ffe5a01936cb8c9c365da979c">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#aac3d886006c17c1e6578d622455bda2f">write_output</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory-members.html">List of all members</a> </div>
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+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::FastaFactory:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::RunnableDB::FastaFactory:</div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a2291deabf24d52906b30ec18d2dbb126"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a2291deabf24d52906b30ec18d2dbb126">param_defaults</a> ()</td></tr>
+<tr class="separator:a2291deabf24d52906b30ec18d2dbb126"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a364bc206bd7c1d93307258ff83b3fcce"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a364bc206bd7c1d93307258ff83b3fcce">fetch_input</a> ()</td></tr>
+<tr class="separator:a364bc206bd7c1d93307258ff83b3fcce"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad2334d5ffe5a01936cb8c9c365da979c"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#ad2334d5ffe5a01936cb8c9c365da979c">run</a> ()</td></tr>
+<tr class="separator:ad2334d5ffe5a01936cb8c9c365da979c"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aac3d886006c17c1e6578d622455bda2f"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#aac3d886006c17c1e6578d622455bda2f">write_output</a> ()</td></tr>
+<tr class="separator:aac3d886006c17c1e6578d622455bda2f"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td></tr>
+<tr class="memitem:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a> ()</td></tr>
+<tr class="separator:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a> ()</td></tr>
+<tr class="separator:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a> ()</td></tr>
+<tr class="separator:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a> ()</td></tr>
+<tr class="separator:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a> ()</td></tr>
+<tr class="separator:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a> ()</td></tr>
+<tr class="separator:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> ()</td></tr>
+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
+<tr class="separator:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
+<tr class="separator:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">standaloneJob.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a> --inputfile reference.fasta --max_chunk_length 600000</div>
+<div class="line"></div>
+<div class="line">standaloneJob.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a> \</div>
+<div class="line"> --inputfile reference.fasta \</div>
+<div class="line"> --max_chunk_length 700000 \</div>
+<div class="line"> --output_prefix ref_chunk \</div>
+<div class="line"> --flow_into <span class="stringliteral">"{ 2 => ['mysql://ensadmin:${ENSADMIN_PSW}@127.0.0.1/lg4_split_fasta/analysis?logic_name=blast']}"</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is a Bioinformatics-specific "Factory" Runnable that splits a given Fasta file into smaller chunks
+ and dataflows one job per chunk.
+
+ The following parameters are supported:
+
+ param('inputfile'); # The original Fasta file: 'inputfile' => 'my_sequences.fasta'
+
+ param('max_chunk_length'); # Maximum total length of sequences in a chunk: 'max_chunk_length' => '200000'
+
+ param('output_prefix'); # A common prefix for output files: 'output_prefix' => 'my_special_chunk_'
+
+ param('output_suffix'); # A common suffix for output files: 'output_suffix' => '.nt'
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a364bc206bd7c1d93307258ff83b3fcce"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FastaFactory::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a364bc206bd7c1d93307258ff83b3fcce">fetch_input()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to read in parameters and load data.
+ Here we only check the existence of 'inputfile' parameter and try to parse it (all other parameters have defaults).</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a364bc206bd7c1d93307258ff83b3fcce">fetch_input</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $inputfile = $self->param_required(<span class="stringliteral">'inputfile'</span>);</div>
+<div class="line"> die <span class="stringliteral">"Cannot read '$inputfile'"</span> unless(-r $inputfile);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($inputfile=~/\.(?:gz|Z)$/) {</div>
+<div class="line"> $inputfile = <span class="stringliteral">"gunzip -c $inputfile |"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> my $input_seqio = Bio::SeqIO->new(-file => $inputfile) || die <span class="stringliteral">"Could not open or parse '$inputfile', please investigate"</span>;</div>
+<div class="line"></div>
+<div class="line"> $self->param(<span class="stringliteral">'input_seqio'</span>, $input_seqio);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2291deabf24d52906b30ec18d2dbb126"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FastaFactory::param_defaults </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a2291deabf24d52906b30ec18d2dbb126">param_defaults()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that defines module defaults for parameters.</pre><pre> </pre><div id="codesection-param_defaults" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_defaults-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_defaults-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_defaults-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a2291deabf24d52906b30ec18d2dbb126">param_defaults</a> {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'max_chunk_length'</span> => 100000,</div>
+<div class="line"> <span class="stringliteral">'output_prefix'</span> => <span class="stringliteral">'my_chunk_'</span>,</div>
+<div class="line"> <span class="stringliteral">'output_suffix'</span> => <span class="stringliteral">'.fasta'</span>,</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad2334d5ffe5a01936cb8c9c365da979c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FastaFactory::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#ad2334d5ffe5a01936cb8c9c365da979c">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to perform the main bulk of the job (minus input and output).
+ Because we want to stream the data more efficiently, all functionality is in <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#aac3d886006c17c1e6578d622455bda2f">write_output()</a>;</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#ad2334d5ffe5a01936cb8c9c365da979c">run</a> {</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aac3d886006c17c1e6578d622455bda2f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::FastaFactory::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#aac3d886006c17c1e6578d622455bda2f">write_output()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to deal with job's output after the execution.
+ The main bulk of this Runnable's functionality is here.
+ Iterates through all sequences in input_seqio, splits them into separate files ("chunks") using a cut-off length and dataflows one job per chunk.</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#aac3d886006c17c1e6578d622455bda2f">write_output</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $input_seqio = $self->param(<span class="stringliteral">'input_seqio'</span>);</div>
+<div class="line"> my $max_chunk_length = $self->param(<span class="stringliteral">'max_chunk_length'</span>);</div>
+<div class="line"> my $output_prefix = $self->param(<span class="stringliteral">'output_prefix'</span>);</div>
+<div class="line"> my $output_suffix = $self->param(<span class="stringliteral">'output_suffix'</span>);</div>
+<div class="line"></div>
+<div class="line"> my $chunk_number = 1; # counts the chunks</div>
+<div class="line"> my $chunk_length = 0; # total length of the current chunk</div>
+<div class="line"> my $chunk_size = 0; # number of sequences in the current chunk</div>
+<div class="line"> my $chunk_name = $output_prefix.$chunk_number.$output_suffix;</div>
+<div class="line"> my $chunk_seqio = Bio::SeqIO->new(-file => <span class="charliteral">'>'</span>.$chunk_name, -format => <span class="stringliteral">'fasta'</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span> (my $seq_object = $input_seqio->next_seq) {</div>
+<div class="line"> <span class="keywordflow">if</span>((my $seq_length = $seq_object->length()) + $chunk_length <= $max_chunk_length) {</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # add to the current chunk:</span></div>
+<div class="line"><span class="preprocessor"></span> $chunk_seqio->write_seq( $seq_object );</div>
+<div class="line"> $chunk_length += $seq_length;</div>
+<div class="line"> $chunk_size += 1;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # dataflow the current chunk:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->dataflow_output_id( {</div>
+<div class="line"> <span class="stringliteral">'chunk_name'</span> => $chunk_name,</div>
+<div class="line"> <span class="stringliteral">'chunk_number'</span> => $chunk_number,</div>
+<div class="line"> <span class="stringliteral">'chunk_length'</span> => $chunk_length,</div>
+<div class="line"> <span class="stringliteral">'chunk_size'</span> => $chunk_size</div>
+<div class="line"> }, 2);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # start writing to the next one:</span></div>
+<div class="line"><span class="preprocessor"></span> $chunk_length = 0;</div>
+<div class="line"> $chunk_size = 0;</div>
+<div class="line"> $chunk_number++;</div>
+<div class="line"> $chunk_name = $output_prefix.$chunk_number.$output_suffix;</div>
+<div class="line"> $chunk_seqio = Bio::SeqIO->new(-file => <span class="charliteral">'>'</span>.$chunk_name, -format => <span class="stringliteral">'fasta'</span>);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($chunk_size) { # flush the last chunk:</div>
+<div class="line"></div>
+<div class="line"> $self->dataflow_output_id( {</div>
+<div class="line"> <span class="stringliteral">'chunk_name'</span> => $chunk_name,</div>
+<div class="line"> <span class="stringliteral">'chunk_number'</span> => $chunk_number,</div>
+<div class="line"> <span class="stringliteral">'chunk_length'</span> => $chunk_length,</div>
+<div class="line"> <span class="stringliteral">'chunk_size'</span> => $chunk_size</div>
+<div class="line"> }, 2);</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/<a class="el" href="_fasta_factory_8pm.html">FastaFactory.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html">FastaFactory</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a051cdcc9af5a857e02f899adf0736c46">_fisher_yates_shuffle_in_place</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a046e795740452e442df65849921da767">_get_rows_from_list</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#ac5c6183dcd03bbfdb054253cbd4b7405">_get_rows_from_open</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a66dd4176925958a32b1e09ec6b381f6e">_get_rows_from_query</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a1d866fc6d59bb185b2a7630583b6a93a">_substitute_minibatched_rows</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a32b9467b5a794591dd41d0c471c1dab6">_substitute_rows</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a80bb69bad70a8a048e373c72621bd7f9">param_defaults</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a8f3a3f15b7d15493a3e0522a27a2edf5">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#adcb45127a2af2a4015d59e590e1eb061">write_output</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a></td><td class="entry"></td></tr>
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+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::JobFactory Class Reference</div> </div>
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+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::JobFactory:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory_inherit__map" alt="Inheritance graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory_inherit__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory_inherit__map">
+<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html" title="Bio::EnsEMBL::Hive\l::Process" alt="" coords="22,97,164,138"/></map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::RunnableDB::JobFactory:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory_coll__map">
+<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html" title="Bio::EnsEMBL::Hive\l::Process" alt="" coords="22,97,164,138"/></map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a80bb69bad70a8a048e373c72621bd7f9"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a80bb69bad70a8a048e373c72621bd7f9">param_defaults</a> ()</td></tr>
+<tr class="separator:a80bb69bad70a8a048e373c72621bd7f9"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8f3a3f15b7d15493a3e0522a27a2edf5"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a8f3a3f15b7d15493a3e0522a27a2edf5">run</a> ()</td></tr>
+<tr class="separator:a8f3a3f15b7d15493a3e0522a27a2edf5"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adcb45127a2af2a4015d59e590e1eb061"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#adcb45127a2af2a4015d59e590e1eb061">write_output</a> ()</td></tr>
+<tr class="separator:adcb45127a2af2a4015d59e590e1eb061"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a046e795740452e442df65849921da767"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a046e795740452e442df65849921da767">_get_rows_from_list</a> ()</td></tr>
+<tr class="separator:a046e795740452e442df65849921da767"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a66dd4176925958a32b1e09ec6b381f6e"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a66dd4176925958a32b1e09ec6b381f6e">_get_rows_from_query</a> ()</td></tr>
+<tr class="separator:a66dd4176925958a32b1e09ec6b381f6e"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac5c6183dcd03bbfdb054253cbd4b7405"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#ac5c6183dcd03bbfdb054253cbd4b7405">_get_rows_from_open</a> ()</td></tr>
+<tr class="separator:ac5c6183dcd03bbfdb054253cbd4b7405"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a32b9467b5a794591dd41d0c471c1dab6"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a32b9467b5a794591dd41d0c471c1dab6">_substitute_rows</a> ()</td></tr>
+<tr class="separator:a32b9467b5a794591dd41d0c471c1dab6"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1d866fc6d59bb185b2a7630583b6a93a"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a1d866fc6d59bb185b2a7630583b6a93a">_substitute_minibatched_rows</a> ()</td></tr>
+<tr class="separator:a1d866fc6d59bb185b2a7630583b6a93a"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a051cdcc9af5a857e02f899adf0736c46"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a051cdcc9af5a857e02f899adf0736c46">_fisher_yates_shuffle_in_place</a> ()</td></tr>
+<tr class="separator:a051cdcc9af5a857e02f899adf0736c46"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td></tr>
+<tr class="memitem:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a> ()</td></tr>
+<tr class="separator:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a> ()</td></tr>
+<tr class="separator:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a> ()</td></tr>
+<tr class="separator:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a> ()</td></tr>
+<tr class="separator:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a> ()</td></tr>
+<tr class="separator:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a> ()</td></tr>
+<tr class="separator:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> ()</td></tr>
+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
+<tr class="separator:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
+<tr class="separator:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">standaloneJob.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a> \</div>
+<div class="line"> --inputcmd <span class="stringliteral">'cd ${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/modules/Bio/EnsEMBL/Hive/RunnableDB; ls -1 *.pm'</span> \</div>
+<div class="line"> --flow_into <span class="stringliteral">"{ 2 => { 'mysql://ensadmin:${ENSADMIN_PSW}@127.0.0.1:2914/lg4_compara_families_70/meta' => {'meta_key'=>'module_name','meta_value'=>'#_0#'} } }"</span><span class="stringliteral">"</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is a generic RunnableDB module for creating batches of similar jobs using dataflow mechanism
+ (a fan of jobs is created in one branch and the funnel in another).
+ Make sure you wire this buliding block properly from outside.
+
+ You can supply as parameter one of 4 sources of ids from which the batches will be generated:
+
+ param('inputlist'); The list is explicitly given in the parameters, can be abbreviated: 'inputlist' => ['a'..'z']
+
+ param('inputfile'); The list is contained in a file whose name is supplied as parameter: 'inputfile' => 'myfile.txt'
+
+ param('inputquery'); The list is generated by an SQL query (against the production database by default) : 'inputquery' => 'SELECT object_id FROM object WHERE x=y'
+
+ param('inputcmd'); The list is generated by running a system command: 'inputcmd' => 'find /tmp/big_directory -type f'
+
+ NB for developpers: fetch_input() method is intentionally missing from JobFactory.pm .
+ If JobFactory is subclassed (say, by a Compara RunnableDB) the child class's should use fetch_input()
+ to set $self->param('inputlist') to whatever list of ids specific to that particular type of data (slices, members, etc).
+ The rest functionality will be taken care for by the parent class code.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a051cdcc9af5a857e02f899adf0736c46"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::RunnableDB::JobFactory::_fisher_yates_shuffle_in_place </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: a private function (not a method) that shuffles a list of ids</pre><pre> </pre><div id="codesection-_fisher_yates_shuffle_in_place" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_fisher_yates_shuffle_in_place-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_fisher_yates_shuffle_in_place-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_fisher_yates_shuffle_in_place-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a051cdcc9af5a857e02f899adf0736c46">_fisher_yates_shuffle_in_place</a> {</div>
+<div class="line"> my $array = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">for</span>(my $upper=scalar(@$array);--$upper;) {</div>
+<div class="line"> my $lower=int(rand($upper+1));</div>
+<div class="line"> next <span class="keywordflow">if</span> $lower == $upper;</div>
+<div class="line"> @$array[$lower,$upper] = @$array[$upper,$lower];</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a046e795740452e442df65849921da767"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::RunnableDB::JobFactory::_get_rows_from_list </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: a private method that ensures the list is 2D</pre><pre> </pre><div id="codesection-_get_rows_from_list" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_get_rows_from_list-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_get_rows_from_list-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_get_rows_from_list-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a046e795740452e442df65849921da767">_get_rows_from_list</a> {</div>
+<div class="line"> my ($self, $inputlist) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ref($inputlist->[0])</div>
+<div class="line"> ? $inputlist</div>
+<div class="line"> : [ map { [ $_ ] } @$inputlist ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac5c6183dcd03bbfdb054253cbd4b7405"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::RunnableDB::JobFactory::_get_rows_from_open </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: a private method that loads ids from a given file or command pipe</pre><pre> </pre><div id="codesection-_get_rows_from_open" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_get_rows_from_open-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_get_rows_from_open-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_get_rows_from_open-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#ac5c6183dcd03bbfdb054253cbd4b7405">_get_rows_from_open</a> {</div>
+<div class="line"> my ($self, $input_file_or_pipe, $delimiter, $parse_header) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->debug()) {</div>
+<div class="line"> warn qq{input_file_or_pipe = <span class="stringliteral">"$input_file_or_pipe"</span>\n};</div>
+<div class="line"> }</div>
+<div class="line"> my @rows = ();</div>
+<div class="line"> open(FILE, $input_file_or_pipe) or die "Could not open '$input_file_or_pipe' because: $!";</div>
+<div class="line"> while(my $line = <FILE>) {</div>
+<div class="line"> chomp $line;</div>
+<div class="line"></div>
+<div class="line"> push @rows, [ defined($delimiter) ? split(/$delimiter/, $line) : $line ];</div>
+<div class="line"> }</div>
+<div class="line"> close FILE;</div>
+<div class="line"></div>
+<div class="line"> my $column_names_from_data = $parse_header ? shift @rows : 0;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> (\@rows, $column_names_from_data);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a66dd4176925958a32b1e09ec6b381f6e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::RunnableDB::JobFactory::_get_rows_from_query </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: a private method that loads ids from a given sql query</pre><pre> param('db_conn'): An optional hash to pass in connection parameters to the database upon which the query will have to be run.</pre><pre> </pre><div id="codesection-_get_rows_from_query" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_get_rows_from_query-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_get_rows_from_query-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_get_rows_from_query-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a66dd4176925958a32b1e09ec6b381f6e">_get_rows_from_query</a> {</div>
+<div class="line"> my ($self, $inputquery) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->debug()) {</div>
+<div class="line"> warn qq{inputquery = <span class="stringliteral">"$inputquery"</span>\n};</div>
+<div class="line"> }</div>
+<div class="line"> my @rows = ();</div>
+<div class="line"> my $sth = $self->data_dbc()->prepare($inputquery);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"> my @column_names_from_data = @{$sth->{NAME}}; # tear it off the original reference to gain some freedom</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span> (my @cols = $sth->fetchrow_array()) {</div>
+<div class="line"> push @rows, \@cols;</div>
+<div class="line"> }</div>
+<div class="line"> $sth->finish();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> (\@rows, \@column_names_from_data);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1d866fc6d59bb185b2a7630583b6a93a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::RunnableDB::JobFactory::_substitute_minibatched_rows </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: a private method that minibatches a list and transforms every minibatch using param-substitution</pre><pre> </pre><div id="codesection-_substitute_minibatched_rows" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_substitute_minibatched_rows-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_substitute_minibatched_rows-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_substitute_minibatched_rows-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a1d866fc6d59bb185b2a7630583b6a93a">_substitute_minibatched_rows</a> {</div>
+<div class="line"> my ($self, $rows, $column_names, $step, $key_column) = @_;</div>
+<div class="line"></div>
+<div class="line"> my @ranges = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>(@$rows) {</div>
+<div class="line"> my $start_row = shift @$rows;</div>
+<div class="line"> my $range_start = $start_row->[$key_column];</div>
+<div class="line"></div>
+<div class="line"> my $range_end = $range_start;</div>
+<div class="line"> my $range_count = 1;</div>
+<div class="line"> my $next_row = $start_row; # safety, in <span class="keywordflow">case</span> the <span class="keyword">internal</span> <span class="keywordflow">while</span> doesn<span class="stringliteral">'t execute even once</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> while($range_count<$step && @$rows) {</span></div>
+<div class="line"><span class="stringliteral"> $next_row = shift @$rows;</span></div>
+<div class="line"><span class="stringliteral"> my $next_value = $next_row->[$key_column];</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $predicted_next = $range_end;</span></div>
+<div class="line"><span class="stringliteral"> if(++$predicted_next eq $next_value) {</span></div>
+<div class="line"><span class="stringliteral"> $range_end = $next_value;</span></div>
+<div class="line"><span class="stringliteral"> $range_count++;</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> unshift @$rows, $next_row;</span></div>
+<div class="line"><span class="stringliteral"> last;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $job_range = {</span></div>
+<div class="line"><span class="stringliteral"> '</span>_range_start<span class="stringliteral">' => $range_start,</span></div>
+<div class="line"><span class="stringliteral"> '</span>_range_end<span class="stringliteral">' => $range_end,</span></div>
+<div class="line"><span class="stringliteral"> '</span>_range_count<span class="stringliteral">' => $range_count,</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $column_names</span></div>
+<div class="line"><span class="stringliteral"> ? map { ('</span>_start_<span class="stringliteral">'.$column_names->[$_] => $start_row->[$_], '</span>_end_<span class="stringliteral">'.$column_names->[$_] => $next_row->[$_]) } (0..scalar(@$start_row)-1)</span></div>
+<div class="line"><span class="stringliteral"> : map { ("_start_$_" => $start_row->[$_], "_end_$_" => $next_row->[$_]) } (0..scalar(@$start_row)-1)</span></div>
+<div class="line"><span class="stringliteral"> };</span></div>
+<div class="line"><span class="stringliteral"> push @ranges, $job_range;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> return \@ranges;</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a32b9467b5a794591dd41d0c471c1dab6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::RunnableDB::JobFactory::_substitute_rows </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: a private method that goes through a list and transforms every row into a hash</pre><pre> </pre><div id="codesection-_substitute_rows" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_substitute_rows-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_substitute_rows-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_substitute_rows-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a32b9467b5a794591dd41d0c471c1dab6">_substitute_rows</a> {</div>
+<div class="line"> my ($self, $rows, $column_names) = @_;</div>
+<div class="line"></div>
+<div class="line"> my @hashes = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $row (@$rows) {</div>
+<div class="line"> my $job_param_hash = $column_names</div>
+<div class="line"> ? { map { ($column_names->[$_] => $row->[$_]) } (0..scalar(@$row)-1) }</div>
+<div class="line"> : { <span class="charliteral">'_'</span> => $row, map { (<span class="stringliteral">"_$_"</span> => $row->[$_]) } (0..scalar(@$row)-1) };</div>
+<div class="line"></div>
+<div class="line"> push @hashes, $job_param_hash;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> \@hashes;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a80bb69bad70a8a048e373c72621bd7f9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::JobFactory::param_defaults </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-param_defaults" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_defaults-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_defaults-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_defaults-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a80bb69bad70a8a048e373c72621bd7f9">param_defaults</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'column_names'</span> => 0,</div>
+<div class="line"> <span class="stringliteral">'delimiter'</span> => undef,</div>
+<div class="line"> <span class="stringliteral">'randomize'</span> => 0,</div>
+<div class="line"> <span class="stringliteral">'step'</span> => 0,</div>
+<div class="line"> <span class="stringliteral">'key_column'</span> => 0,</div>
+<div class="line"> <span class="stringliteral">'input_id'</span> => 0, # <span class="keyword">this</span> parameter is no longer supported and should stay at 0</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'inputlist'</span> => undef,</div>
+<div class="line"> <span class="stringliteral">'inputfile'</span> => undef,</div>
+<div class="line"> <span class="stringliteral">'inputquery'</span> => undef,</div>
+<div class="line"> <span class="stringliteral">'inputcmd'</span> => undef,</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'fan_branch_code'</span> => 2,</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8f3a3f15b7d15493a3e0522a27a2edf5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::JobFactory::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a8f3a3f15b7d15493a3e0522a27a2edf5">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to perform the main bulk of the job (minus input and output).</pre><pre> param('column_names'): Controls the column names that come out of the parser: 0 = "no names", 1 = "parse names from data", arrayref = "take names from this array"</pre><pre> param('delimiter'): If you set it your lines in file/cmd mode will be split into columns that you can use individually when constructing the input_id_template hash.</pre><pre> param('randomize'): Shuffles the rows before creating jobs - can sometimes lead to better overall performance of the pipeline. Doesn't make any sence for minibatches (step>1).</pre><pre> param('step'): The requested size of the minibatch (1 by default). The real size of a range may be smaller than the requested size.</pre><pre> param('key_column'): If every line of your input is a list (it happens, for example, when your SQL returns multiple columns or you have set the 'delimiter' in file/cmd mode)
+ this is the way to say which column is undergoing 'ranging'</pre><pre> # The following 4 parameters are mutually exclusive and define the source of ids for the jobs:</pre><pre> param('inputlist'); The list is explicitly given in the parameters, can be abbreviated: 'inputlist' => ['a'..'z']</pre><pre> param('inputfile'); The list is contained in a file whose name is supplied as parameter: 'inputfile' => 'myfile.txt'</pre><pre> param('inputquery'); The list is generated by an SQL query (against the production database by default) : 'inputquery' => 'SELECT object_id FROM object WHERE x=y'</pre><pre> param('inputcmd'); The list is generated by running a system command: 'inputcmd' => 'find /tmp/big_directory -type f'</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a8f3a3f15b7d15493a3e0522a27a2edf5">run</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $column_names = $self->param(<span class="stringliteral">'column_names'</span>); # can be 0 (no names), 1 (names from data) or an arrayref (names from <span class="keyword">this</span> array)</div>
+<div class="line"> my $delimiter = $self->param(<span class="stringliteral">'delimiter'</span>);</div>
+<div class="line"></div>
+<div class="line"> my $randomize = $self->param(<span class="stringliteral">'randomize'</span>);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # minibatching-related:</span></div>
+<div class="line"><span class="preprocessor"></span> my $step = $self->param(<span class="stringliteral">'step'</span>);</div>
+<div class="line"> my $key_column = $self->param(<span class="stringliteral">'key_column'</span>);</div>
+<div class="line"></div>
+<div class="line"> my $inputlist = $self->param(<span class="stringliteral">'inputlist'</span>);</div>
+<div class="line"> my $inputfile = $self->param(<span class="stringliteral">'inputfile'</span>);</div>
+<div class="line"> my $inputquery = $self->param(<span class="stringliteral">'inputquery'</span>);</div>
+<div class="line"> my $inputcmd = $self->param(<span class="stringliteral">'inputcmd'</span>);</div>
+<div class="line"></div>
+<div class="line"> my $parse_column_names = $column_names && (ref($column_names) ne 'ARRAY');</div>
+<div class="line"></div>
+<div class="line"> my ($rows, $column_names_from_data) =</div>
+<div class="line"> $inputlist ? $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a046e795740452e442df65849921da767">_get_rows_from_list</a>( $inputlist )</div>
+<div class="line"> : $inputquery ? $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a66dd4176925958a32b1e09ec6b381f6e">_get_rows_from_query</a>( $inputquery )</div>
+<div class="line"> : $inputfile ? $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#ac5c6183dcd03bbfdb054253cbd4b7405">_get_rows_from_open</a>( $inputfile , $delimiter, $parse_column_names )</div>
+<div class="line"> : $inputcmd ? $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#ac5c6183dcd03bbfdb054253cbd4b7405">_get_rows_from_open</a>( "$inputcmd |", $delimiter, $parse_column_names )</div>
+<div class="line"> : die "range of values should be defined by setting 'inputlist', 'inputquery', 'inputfile' or 'inputcmd'";</div>
+<div class="line"></div>
+<div class="line"> if( $column_names_from_data <span class="preprocessor"># column data is available</span></div>
+<div class="line"><span class="preprocessor"></span> and ( defined($column_names) ? (ref($column_names) ne <span class="stringliteral">'ARRAY'</span>) : 1 ) <span class="preprocessor"># and is badly needed</span></div>
+<div class="line"><span class="preprocessor"></span> ) {</div>
+<div class="line"> $column_names = $column_names_from_data;</div>
+<div class="line"> }</div>
+<div class="line"><span class="preprocessor"> # after this point $column_names should either contain a list or be false</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line"> <span class="keywordflow">if</span>( $self->param(<span class="stringliteral">'input_id'</span>) ) {</div>
+<div class="line"> die <span class="stringliteral">"'input_id' is no longer supported, please reconfigure as the input_id_template of the dataflow_rule"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($randomize) {</div>
+<div class="line"> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a051cdcc9af5a857e02f899adf0736c46">_fisher_yates_shuffle_in_place</a>($rows);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $output_ids = $step</div>
+<div class="line"> ? $self->_substitute_minibatched_rows($rows, $column_names, $step, $key_column)</div>
+<div class="line"> : $self->_substitute_rows($rows, $column_names);</div>
+<div class="line"></div>
+<div class="line"> $self->param(<span class="stringliteral">'output_ids'</span>, $output_ids);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="adcb45127a2af2a4015d59e590e1eb061"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::JobFactory::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#adcb45127a2af2a4015d59e590e1eb061">write_output()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to deal with job's output after the execution.
+ Here we rely on the dataflow mechanism to create jobs.</pre><pre> param('fan_branch_code'): defines the branch where the fan of jobs is created (2 by default).</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#adcb45127a2af2a4015d59e590e1eb061">write_output</a> { # nothing to write out, but some dataflow to perform:</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $output_ids = $self->param(<span class="stringliteral">'output_ids'</span>);</div>
+<div class="line"> my $fan_branch_code = $self->param(<span class="stringliteral">'fan_branch_code'</span>);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # "fan out" into fan_branch_code:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->dataflow_output_id($output_ids, $fan_branch_code);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/<a class="el" href="_job_factory_8pm.html">JobFactory.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">JobFactory</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+[
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+ [ "_substitute_rows", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a32b9467b5a794591dd41d0c471c1dab6", null ],
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+ [ "run", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a8f3a3f15b7d15493a3e0522a27a2edf5", null ],
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+];
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+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether Member List</div> </div>
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+<div class="contents">
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+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a>, including all inherited members.</p>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a18e25e086249fc4775be954efe8efaef">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#ad709c3f522582c4965ce53adb1499e15">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a></td><td class="entry"></td></tr>
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together_inherit__map" alt="Inheritance graph"/></div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a4d6debc4b842ca5cdde9707783c62f20"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a4d6debc4b842ca5cdde9707783c62f20">param_defaults</a> ()</td></tr>
+<tr class="separator:a4d6debc4b842ca5cdde9707783c62f20"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td></tr>
+<tr class="memitem:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a> ()</td></tr>
+<tr class="separator:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a> ()</td></tr>
+<tr class="separator:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a> ()</td></tr>
+<tr class="separator:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a> ()</td></tr>
+<tr class="separator:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> ()</td></tr>
+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
+<tr class="separator:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
+<tr class="separator:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">Please refer to <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a> pipeline configuration file</div>
+<div class="line">to understand how <span class="keyword">this</span> particular example pipeline is configured and ran.</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ 'LongMult::AddTogether' is the final step of the pipeline that, naturally, adds the products together
+ and stores the result in 'final_result' database table.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a58596178ed9c2bb86dbaca822ce0f29a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether::_add_together </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: this is a private function (not a method) that adds all the products with a shift</pre><pre> </pre><div id="codesection-_add_together" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_add_together-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_add_together-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_add_together-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a58596178ed9c2bb86dbaca822ce0f29a">_add_together</a> {</div>
+<div class="line"> my ($b_multiplier, $partial_product) = @_;</div>
+<div class="line"></div>
+<div class="line"> my @accu = ();</div>
+<div class="line"></div>
+<div class="line"> my @b_digits = reverse split(<span class="comment">//, $b_multiplier);</span></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $b_index (0..(@b_digits-1)) {</div>
+<div class="line"> my $b_digit = $b_digits[$b_index];</div>
+<div class="line"> my $product = $partial_product->{$b_digit};</div>
+<div class="line"></div>
+<div class="line"> my @p_digits = reverse split(<span class="comment">//, $product);</span></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $p_index (0..(@p_digits-1)) {</div>
+<div class="line"> $accu[$b_index+$p_index] += $p_digits[$p_index];</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $a_index (0..(@accu-1)) {</div>
+<div class="line"> my $a_digit = $accu[$a_index];</div>
+<div class="line"> my $carry = int($a_digit/10);</div>
+<div class="line"> $accu[$a_index] = $a_digit % 10;</div>
+<div class="line"> $accu[$a_index+1] += $carry;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # get rid of the leading zero</span></div>
+<div class="line"><span class="preprocessor"></span> unless($accu[@accu-1]) {</div>
+<div class="line"> pop @accu;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> join(<span class="stringliteral">''</span>, reverse @accu);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a18e25e086249fc4775be954efe8efaef"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a18e25e086249fc4775be954efe8efaef">fetch_input()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to read in parameters and load data.
+ Here all relevant partial products are fetched from the 'partial_product' accumulator and stored in a hash for future use.</pre><pre> param('a_multiplier'): The first long number (a string of digits - doesn't have to fit a register).</pre><pre> param('b_multiplier'): The second long number (also a string of digits).</pre><pre> param('take_time'): How much time to spend sleeping (seconds).</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a18e25e086249fc4775be954efe8efaef">fetch_input</a> { # fetch all the (relevant) precomputed products</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $a_multiplier = $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a>('a_multiplier');</div>
+<div class="line"> my $partial_product = $self->param('partial_product');</div>
+<div class="line"></div>
+<div class="line"> $partial_product->{1} = $a_multiplier;</div>
+<div class="line"> $partial_product->{0} = 0;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4d6debc4b842ca5cdde9707783c62f20"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether::param_defaults </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a4d6debc4b842ca5cdde9707783c62f20">param_defaults()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that defines module defaults for parameters.</pre><pre> </pre><div id="codesection-param_defaults" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_defaults-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_defaults-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_defaults-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a4d6debc4b842ca5cdde9707783c62f20">param_defaults</a> {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'partial_product'</span> => { }, # to be used when b_multiplier only contains digits <span class="charliteral">'0'</span> and <span class="charliteral">'1'</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'take_time'</span> => 0, # how much time <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#ad709c3f522582c4965ce53adb1499e15">run</a>() method will spend in sleeping state</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad709c3f522582c4965ce53adb1499e15"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#ad709c3f522582c4965ce53adb1499e15">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to perform the main bulk of the job (minus input and output).
+ The only thing we do here is make a call to the function that will add together the intermediate results.</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#ad709c3f522582c4965ce53adb1499e15">run</a> { # call the <span class="keyword">function</span> that will compute the stuff</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $b_multiplier = $self->param_required(<span class="stringliteral">'b_multiplier'</span>);</div>
+<div class="line"> my $partial_product = $self->param(<span class="stringliteral">'partial_product'</span>);</div>
+<div class="line"></div>
+<div class="line"> $self->param(<span class="stringliteral">'result'</span>, <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a58596178ed9c2bb86dbaca822ce0f29a">_add_together</a>($b_multiplier, $partial_product));</div>
+<div class="line"></div>
+<div class="line"> sleep( $self->param(<span class="stringliteral">'take_time'</span>) );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a51b40c598bc04b4df6e78c5fd1189fc5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a51b40c598bc04b4df6e78c5fd1189fc5">write_output()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to deal with job's output after the execution.
+ Dataflows both original multipliers and the final result down branch-1, which will be routed into 'final_result' table.</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a51b40c598bc04b4df6e78c5fd1189fc5">write_output</a> { # store and dataflow</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $self->dataflow_output_id({</div>
+<div class="line"> <span class="stringliteral">'result'</span> => $self->param(<span class="stringliteral">'result'</span>),</div>
+<div class="line"> }, 1);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/<a class="el" href="_add_together_8pm.html">AddTogether.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
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+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory</a>, including all inherited members.</p>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a8ef4b1260e767a0d1392e05c8753c59f">write_output</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory</a></td><td class="entry"></td></tr>
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+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
+<tr class="separator:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
+<tr class="separator:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">Please refer to <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a> pipeline configuration file</div>
+<div class="line">to understand how <span class="keyword">this</span> particular example pipeline is configured and ran.</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ 'LongMult::DigitFactory' is the first step of the LongMult example pipeline that multiplies two long numbers.
+
+ It takes apart the second multiplier and creates several 'LongMult::PartMultiply' jobs
+ that correspond to the different digits of the second multiplier.
+
+ It also "flows into" one 'LongMult::AddTogether' job that will wait until 'LongMult::PartMultiply' jobs
+ complete and will arrive at the final result.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="adf959e0495247f1455195ab4d5761725"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#adf959e0495247f1455195ab4d5761725">fetch_input()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to read in parameters and load data.
+ Here the task of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#adf959e0495247f1455195ab4d5761725">fetch_input()</a> is to read in the two multipliers, split the second one into digits and create a set of input_ids that will be used later.</pre><pre> param('b_multiplier'): The second long number (a string of digits - doesn't have to fit a register)</pre><pre> param('take_time'): How much time to spend sleeping (seconds).</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#adf959e0495247f1455195ab4d5761725">fetch_input</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $b_multiplier = $self->param_required(<span class="stringliteral">'b_multiplier'</span>);</div>
+<div class="line"></div>
+<div class="line"> my %digit_hash = ();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $digit (split(<span class="comment">//,$b_multiplier)) {</span></div>
+<div class="line"> next <span class="keywordflow">if</span> (($digit eq <span class="charliteral">'0'</span>) or ($digit eq <span class="charliteral">'1'</span>));</div>
+<div class="line"> $digit_hash{$digit}++;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # parameter hashes of partial multiplications to be computed:</span></div>
+<div class="line"><span class="preprocessor"></span> my @sub_tasks = map { { <span class="stringliteral">'digit'</span> => $_ } } keys %digit_hash;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # store them for future use:</span></div>
+<div class="line"><span class="preprocessor"></span> $self->param(<span class="stringliteral">'sub_tasks'</span>, \@sub_tasks);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac539ab7a01025992f908be787b08aebb"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory::param_defaults </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#ac539ab7a01025992f908be787b08aebb">param_defaults()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that defines module defaults for parameters.</pre><pre> </pre><div id="codesection-param_defaults" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_defaults-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_defaults-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_defaults-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#ac539ab7a01025992f908be787b08aebb">param_defaults</a> {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'take_time'</span> => 0, # how much time <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a12b9e75e3910ce20c4489fa8babe9b6a">run</a>() method will spend in sleeping state</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a12b9e75e3910ce20c4489fa8babe9b6a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a12b9e75e3910ce20c4489fa8babe9b6a">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to perform the main bulk of the job (minus input and output).
+ Here we don't have any real work to do, just input and output, so <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a12b9e75e3910ce20c4489fa8babe9b6a">run()</a> just spends some time waiting.</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a12b9e75e3910ce20c4489fa8babe9b6a">run</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> sleep( $self->param(<span class="stringliteral">'take_time'</span>) );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8ef4b1260e767a0d1392e05c8753c59f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a8ef4b1260e767a0d1392e05c8753c59f">write_output()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to deal with job's output after the execution.
+ Here we dataflow all the partial multiplication jobs whose input_ids were generated in <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#adf959e0495247f1455195ab4d5761725">fetch_input()</a> into the branch-2 ("fan out"),
+ and also dataflow the original task down branch-1 (create the "funnel job").</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a8ef4b1260e767a0d1392e05c8753c59f">write_output</a> { # nothing to write out, but some dataflow to perform:</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $sub_tasks = $self->param(<span class="stringliteral">'sub_tasks'</span>);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # "fan out" into branch#2 first, branch#1 will be created if we wire it (and we do)</span></div>
+<div class="line"><span class="preprocessor"></span> $self->dataflow_output_id($sub_tasks, 2);</div>
+<div class="line"></div>
+<div class="line"> $self->warning(scalar(@$sub_tasks).<span class="stringliteral">' multiplication jobs have been created'</span>); # <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> messages <span class="keyword">get</span> recorded into <span class="stringliteral">'log_message'</span> table</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor">## extra information sent to the funnel will extend its stack:</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"># $self->dataflow_output_id( { 'different_digits' => scalar(@$sub_tasks) } , 1);</span></div>
+<div class="line"><span class="preprocessor">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/<a class="el" href="_digit_factory_8pm.html">DigitFactory.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult.html">LongMult</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html">DigitFactory</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory =
+[
+ [ "fetch_input", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#adf959e0495247f1455195ab4d5761725", null ],
+ [ "param_defaults", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#ac539ab7a01025992f908be787b08aebb", null ],
+ [ "run", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a12b9e75e3910ce20c4489fa8babe9b6a", null ],
+ [ "write_output", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a8ef4b1260e767a0d1392e05c8753c59f", null ]
+];
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+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="dynsections.js"></script>
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+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aae56050726847606ccb5ea8c7516dc75">_rec_multiply</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aefd561f1a619b59d3b784bdb78a54439">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a4b5d3553e76345622fb3fddb0aac447f">param_defaults</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a5cfb529f37ccb583abe0a1518a86ab2c">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a8f715ad1e9dc777cb7dcbbbc6a35c24b">write_output</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a></td><td class="entry"></td></tr>
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply:</div>
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+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply:</div>
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+<tr class="memitem:a4b5d3553e76345622fb3fddb0aac447f"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a4b5d3553e76345622fb3fddb0aac447f">param_defaults</a> ()</td></tr>
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+<tr class="memitem:aefd561f1a619b59d3b784bdb78a54439"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aefd561f1a619b59d3b784bdb78a54439">fetch_input</a> ()</td></tr>
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+<tr class="memitem:aae56050726847606ccb5ea8c7516dc75"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aae56050726847606ccb5ea8c7516dc75">_rec_multiply</a> ()</td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td></tr>
+<tr class="memitem:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a> ()</td></tr>
+<tr class="separator:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a> ()</td></tr>
+<tr class="separator:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a> ()</td></tr>
+<tr class="separator:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a> ()</td></tr>
+<tr class="separator:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a> ()</td></tr>
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+<tr class="memitem:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a> ()</td></tr>
+<tr class="separator:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> ()</td></tr>
+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
+<tr class="separator:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
+<tr class="separator:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">Please refer to <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a> pipeline configuration file</div>
+<div class="line">to understand how <span class="keyword">this</span> particular example pipeline is configured and ran.</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ 'LongMult::PartMultiply' has a separate task of multiplying 'a_multiplier' by the given 'digit',
+ then it passes its partial_product on.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="aae56050726847606ccb5ea8c7516dc75"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply::_rec_multiply </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: this is a private function (not a method) that performs recursive multiplication of a long number by a digit with a carry.</pre><pre> </pre><div id="codesection-_rec_multiply" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_rec_multiply-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_rec_multiply-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_rec_multiply-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aae56050726847606ccb5ea8c7516dc75">_rec_multiply</a> {</div>
+<div class="line"> my ($a_multiplier, $digit, $carry) = @_;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # recursion end:</span></div>
+<div class="line"><span class="preprocessor"></span> unless($a_multiplier) {</div>
+<div class="line"> <span class="keywordflow">return</span> ($carry || <span class="stringliteral">''</span>);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # recursion step:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>($a_multiplier=~/^(\d*)(\d)$/) {</div>
+<div class="line"> my ($prefix, $last_digit) = ($1, $2);</div>
+<div class="line"></div>
+<div class="line"> my $this_product = $last_digit*$digit+$carry;</div>
+<div class="line"> my $this_result = $this_product % 10;</div>
+<div class="line"> my $this_carry = int($this_product / 10);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aae56050726847606ccb5ea8c7516dc75">_rec_multiply</a>($prefix, $digit, $this_carry).$this_result;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> die <span class="stringliteral">"'a_multiplier' has to be a decimal number"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aefd561f1a619b59d3b784bdb78a54439"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aefd561f1a619b59d3b784bdb78a54439">fetch_input()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to read in parameters and load data.
+ Here we have nothing to fetch.</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aefd561f1a619b59d3b784bdb78a54439">fetch_input</a> {</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4b5d3553e76345622fb3fddb0aac447f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply::param_defaults </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a4b5d3553e76345622fb3fddb0aac447f">param_defaults()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that defines module defaults for parameters.</pre><pre> </pre><div id="codesection-param_defaults" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_defaults-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_defaults-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_defaults-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a4b5d3553e76345622fb3fddb0aac447f">param_defaults</a> {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'take_time'</span> => 0, # how much time <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a5cfb529f37ccb583abe0a1518a86ab2c">run</a>() method will spend in sleeping state</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a5cfb529f37ccb583abe0a1518a86ab2c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a5cfb529f37ccb583abe0a1518a86ab2c">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to perform the main bulk of the job (minus input and output).
+ The only thing we do here is make a call to the recursive function that will compute the product.</pre><pre> param('a_multiplier'): The first long number (a string of digits - doesn't have to fit a register).</pre><pre> param('digit'): A decimal digit that is a part of the second multiplier.</pre><pre> param('take_time'): How much time to spend sleeping (seconds).</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a5cfb529f37ccb583abe0a1518a86ab2c">run</a> { # call the recursive <span class="keyword">function</span> that will compute the stuff</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $a_multiplier = $self->param_required(<span class="stringliteral">'a_multiplier'</span>);</div>
+<div class="line"> my $digit = $self->param_required(<span class="stringliteral">'digit'</span>);</div>
+<div class="line"></div>
+<div class="line"> $self->param(<span class="stringliteral">'partial_product'</span>, <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aae56050726847606ccb5ea8c7516dc75">_rec_multiply</a>($a_multiplier, $digit, 0) || 0);</div>
+<div class="line"></div>
+<div class="line"> sleep( $self->param(<span class="stringliteral">'take_time'</span>) );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8f715ad1e9dc777cb7dcbbbc6a35c24b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a8f715ad1e9dc777cb7dcbbbc6a35c24b">write_output()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to deal with job's output after the execution.
+ Dataflows the intermediate results down branch 1, which will be routed into 'partial_product' accumulator.</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a8f715ad1e9dc777cb7dcbbbc6a35c24b">write_output</a> { # but <span class="keyword">this</span> time we have something to store</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $self->dataflow_output_id( {</div>
+<div class="line"> <span class="stringliteral">'partial_product'</span> => $self->param(<span class="stringliteral">'partial_product'</span>)</div>
+<div class="line"> }, 1);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/<a class="el" href="_part_multiply_8pm.html">PartMultiply.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult.html">LongMult</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html">PartMultiply</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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@@ -0,0 +1,8 @@
+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply =
+[
+ [ "_rec_multiply", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aae56050726847606ccb5ea8c7516dc75", null ],
+ [ "fetch_input", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aefd561f1a619b59d3b784bdb78a54439", null ],
+ [ "param_defaults", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a4b5d3553e76345622fb3fddb0aac447f", null ],
+ [ "run", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a5cfb529f37ccb583abe0a1518a86ab2c", null ],
+ [ "write_output", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a8f715ad1e9dc777cb7dcbbbc6a35c24b", null ]
+];
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="dynsections.js"></script>
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+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
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+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
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+ alt=""/>
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+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#a2b25c050ce8cf7f5b8a12e0a21f2203d">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#aadc21d596971f8edf7410fbeec1f77ba">get_row_count</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#ab2382b362b1dd698c6c7b0a8d02acabe">mysql_conn_from_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#af07560dd3842fc50a1c2381ab0e338d0">param_defaults</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#af26f682eca96b51923aa75c501f21d02">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#a14ae8df5996542778d3e2ef9f64052a8">write_output</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a></td><td class="entry"></td></tr>
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+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer:</div>
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+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:af07560dd3842fc50a1c2381ab0e338d0"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#af07560dd3842fc50a1c2381ab0e338d0">param_defaults</a> ()</td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td></tr>
+<tr class="memitem:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a> ()</td></tr>
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+<tr class="memitem:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a> ()</td></tr>
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+<tr class="memitem:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a> ()</td></tr>
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+<tr class="memitem:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a> ()</td></tr>
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+<tr class="memitem:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a> ()</td></tr>
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+<tr class="memitem:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> ()</td></tr>
+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
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+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
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+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
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+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
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+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
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+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">standaloneJob.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a> --table meta_foo \</div>
+<div class="line"> --src_db_conn mysql:<span class="comment">//ensadmin:${ENSADMIN_PSW}@127.0.0.1:2913/lg4_compara_homology_merged_64 \</span></div>
+<div class="line"><span class="comment"> --dest_db_conn mysql://ensadmin:${ENSADMIN_PSW}@127.0.0.1:2912/lg4_compara_families_64</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This RunnableDB module lets you copy/merge rows from a table in one database into table with the same name in another.
+ There are three modes ('overwrite', 'topup' and 'insertignore') that do it very differently.
+ Also, 'where' parameter allows to select subset of rows to be copied/merged over.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a2b25c050ce8cf7f5b8a12e0a21f2203d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#a2b25c050ce8cf7f5b8a12e0a21f2203d">fetch_input()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to read in parameters and load data.
+ Here it parses parameters, creates up to two database handles and finds the pre-execution row counts filtered by '$where'.</pre><pre> param('src_db_conn'): connection parameters to the source database (if different from hive_db)</pre><pre> param('dest_db_conn'): connection parameters to the destination database (if different from hive_db - at least one of the two will have to be different)</pre><pre> param('mode'): 'overwrite' (default), 'topup' or 'insertignore'</pre><pre> param('where'): filter for rows to be copied/merged.</pre><pre> param('table'): table name to be copied/merged.</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#a2b25c050ce8cf7f5b8a12e0a21f2203d">fetch_input</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> my $src_db_conn = $self->param(<span class="stringliteral">'src_db_conn'</span>);</div>
+<div class="line"> my $dest_db_conn = $self->param(<span class="stringliteral">'dest_db_conn'</span>);</div>
+<div class="line"></div>
+<div class="line"> $self->input_job->transient_error(0);</div>
+<div class="line"> <span class="keywordflow">if</span>($src_db_conn eq $dest_db_conn) {</div>
+<div class="line"> die <span class="stringliteral">"Please either specify 'src_db_conn' or 'dest_db_conn' or make them different\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> my $table = $self->param(<span class="stringliteral">'table'</span>) or die <span class="stringliteral">"Please specify 'table' parameter\n"</span>;</div>
+<div class="line"> $self->input_job->transient_error(1);</div>
+<div class="line"></div>
+<div class="line"> my $src_dbc = $src_db_conn ? go_figure_dbc( $src_db_conn ) : $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>;</div>
+<div class="line"> my $dest_dbc = $dest_db_conn ? go_figure_dbc( $dest_db_conn ) : $self-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>;</div>
+<div class="line"></div>
+<div class="line"> $self->param(<span class="stringliteral">'src_dbc'</span>, $src_dbc);</div>
+<div class="line"> $self->param(<span class="stringliteral">'dest_dbc'</span>, $dest_dbc);</div>
+<div class="line"></div>
+<div class="line"> my $where = $self->param(<span class="stringliteral">'where'</span>);</div>
+<div class="line"></div>
+<div class="line"> $self->param(<span class="stringliteral">'src_before'</span>, $self->get_row_count($src_dbc, $table, $where) );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->param(<span class="stringliteral">'mode'</span>) ne <span class="stringliteral">'overwrite'</span>) {</div>
+<div class="line"> $self->param(<span class="stringliteral">'dest_before_all'</span>, $self->get_row_count($dest_dbc, $table) );</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aadc21d596971f8edf7410fbeec1f77ba"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::get_row_count </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_row_count" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_row_count-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_row_count-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_row_count-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#aadc21d596971f8edf7410fbeec1f77ba">get_row_count</a> {</div>
+<div class="line"> my ($self, $dbc, $table, $where) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $sql = <span class="stringliteral">"SELECT count(*) FROM $table"</span> . (defined($where) ? <span class="stringliteral">" WHERE $where"</span> : <span class="stringliteral">''</span>);</div>
+<div class="line"></div>
+<div class="line"> my $sth = $dbc->prepare($sql);</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"> my ($row_count) = $sth->fetchrow_array();</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $row_count;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab2382b362b1dd698c6c7b0a8d02acabe"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::mysql_conn_from_dbc </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-mysql_conn_from_dbc" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-mysql_conn_from_dbc-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-mysql_conn_from_dbc-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-mysql_conn_from_dbc-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#ab2382b362b1dd698c6c7b0a8d02acabe">mysql_conn_from_dbc</a> {</div>
+<div class="line"> my ($self, $dbc) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'--host='</span>.$dbc->host.<span class="stringliteral">' --port='</span>.$dbc->port.<span class="stringliteral">" --user='"</span>.$dbc->username.<span class="stringliteral">"' --password='"</span>.$dbc->password.<span class="stringliteral">"' "</span>.$dbc->dbname;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af07560dd3842fc50a1c2381ab0e338d0"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::param_defaults </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-param_defaults" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_defaults-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_defaults-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_defaults-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#af07560dd3842fc50a1c2381ab0e338d0">param_defaults</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'src_db_conn'</span> => <span class="stringliteral">''</span>,</div>
+<div class="line"> <span class="stringliteral">'dest_db_conn'</span> => <span class="stringliteral">''</span>,</div>
+<div class="line"> <span class="stringliteral">'mode'</span> => <span class="stringliteral">'overwrite'</span>,</div>
+<div class="line"> <span class="stringliteral">'table'</span> => <span class="stringliteral">''</span>,</div>
+<div class="line"> <span class="stringliteral">'where'</span> => undef,</div>
+<div class="line"> <span class="stringliteral">'filter_cmd'</span> => undef,</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af26f682eca96b51923aa75c501f21d02"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#af26f682eca96b51923aa75c501f21d02">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to perform the main bulk of the job (minus input and output).
+ Here the actual data transfer is attempted.</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#af26f682eca96b51923aa75c501f21d02">run</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> my $src_dbc = $self->param(<span class="stringliteral">'src_dbc'</span>);</div>
+<div class="line"> my $dest_dbc = $self->param(<span class="stringliteral">'dest_dbc'</span>);</div>
+<div class="line"></div>
+<div class="line"> my $mode = $self->param(<span class="stringliteral">'mode'</span>);</div>
+<div class="line"> my $table = $self->param(<span class="stringliteral">'table'</span>);</div>
+<div class="line"> my $where = $self->param(<span class="stringliteral">'where'</span>);</div>
+<div class="line"> my $filter_cmd = $self->param(<span class="stringliteral">'filter_cmd'</span>);</div>
+<div class="line"></div>
+<div class="line"> my $cmd = <span class="stringliteral">'mysqldump '</span></div>
+<div class="line"> . { <span class="stringliteral">'overwrite'</span> => <span class="stringliteral">''</span>, <span class="stringliteral">'topup'</span> => <span class="stringliteral">'--no-create-info '</span>, <span class="stringliteral">'insertignore'</span> => <span class="stringliteral">'--no-create-info --insert-ignore '</span> }->{$mode}</div>
+<div class="line"> . $self->mysql_conn_from_dbc($src_dbc)</div>
+<div class="line"> . <span class="stringliteral">" $table "</span></div>
+<div class="line"> . (defined($where) ? <span class="stringliteral">"--where '$where' "</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> . <span class="stringliteral">'| '</span></div>
+<div class="line"> . ($filter_cmd ? <span class="stringliteral">"$filter_cmd | "</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> . <span class="stringliteral">'mysql '</span></div>
+<div class="line"> . $self->mysql_conn_from_dbc($dest_dbc);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $return_value = system($cmd)) { # NB: unfortunately, <span class="keyword">this</span> code won<span class="stringliteral">'t catch many errors because of the pipe</span></div>
+<div class="line"><span class="stringliteral"> $return_value >>= 8;</span></div>
+<div class="line"><span class="stringliteral"> die "system( $cmd ) failed: $return_value";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a14ae8df5996542778d3e2ef9f64052a8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#a14ae8df5996542778d3e2ef9f64052a8">write_output()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to deal with job's output after the execution.
+ Here we compare the number of rows and detect problems.</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#a14ae8df5996542778d3e2ef9f64052a8">write_output</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> my $dest_dbc = $self->param(<span class="stringliteral">'dest_dbc'</span>);</div>
+<div class="line"></div>
+<div class="line"> my $mode = $self->param(<span class="stringliteral">'mode'</span>);</div>
+<div class="line"> my $table = $self->param(<span class="stringliteral">'table'</span>);</div>
+<div class="line"> my $where = $self->param(<span class="stringliteral">'where'</span>);</div>
+<div class="line"></div>
+<div class="line"> my $src_before = $self->param(<span class="stringliteral">'src_before'</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($mode eq <span class="stringliteral">'overwrite'</span>) {</div>
+<div class="line"> my $dest_after = $self->get_row_count($dest_dbc, $table, $where);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($src_before == $dest_after) {</div>
+<div class="line"> $self->warning(<span class="stringliteral">"Successfully copied $src_before '$table' rows"</span>);</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> die <span class="stringliteral">"Could not copy '$table' rows: $src_before rows from source copied into $dest_after rows in target\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"></div>
+<div class="line"> my $dest_row_increase = $self->get_row_count($dest_dbc, $table) - $self->param(<span class="stringliteral">'dest_before_all'</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($mode eq <span class="stringliteral">'topup'</span>) {</div>
+<div class="line"> <span class="keywordflow">if</span>($src_before <= $dest_row_increase) {</div>
+<div class="line"> $self->warning(<span class="stringliteral">"Cannot check success/failure in this mode, but the number of '$table' rows in target increased by $dest_row_increase (higher than $src_before)"</span>);</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> die <span class="stringliteral">"Could not add rows: $src_before '$table' rows from source copied into $dest_row_increase rows in target\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> } elsif($mode eq <span class="stringliteral">'insertignore'</span>) {</div>
+<div class="line"> $self->warning(<span class="stringliteral">"Cannot check success/failure in this mode, but the number of '$table' rows in target increased by $dest_row_increase"</span>);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/<a class="el" href="_my_s_q_l_transfer_8pm.html">MySQLTransfer.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html">MySQLTransfer</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer =
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+ [ "mysql_conn_from_dbc", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#ab2382b362b1dd698c6c7b0a8d02acabe", null ],
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+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
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+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
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+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#ae903a369bd861a15a9826fa15fa8fa08">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a53d7a4e8cce22cfbe0eb51f041604ed9">param_defaults</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a268d6080f03e8ae23d7b1f31baf91d1a">write_output</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
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+<tr class="memitem:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> ()</td></tr>
+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
+<tr class="separator:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
+<tr class="separator:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">This is a RunnableDB module that implements <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> interface</div>
+<div class="line">and is ran by Workers during the execution of eHive pipelines.</div>
+<div class="line">It is not generally supposed to be instantiated and used outside of <span class="keyword">this</span> framework.</div>
+<div class="line"></div>
+<div class="line">Please refer to <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> documentation to understand the basics of the RunnableDB interface.</div>
+<div class="line"></div>
+<div class="line">Please refer to Bio::EnsEMBL::Hive::PipeConfig::* pipeline configuration files to understand how to configure pipelines.</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This RunnableDB module will send you a short notification email message per each job.
+ You can either dataflow into it, or simply create standalone jobs.
+
+ Note: this module depends heavily on the implementation of your compute farm.
+ Sendmail may be unsupported, or supported differently.
+ Please make sure it works as intended before using this module in complex pipelines.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ae903a369bd861a15a9826fa15fa8fa08"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#ae903a369bd861a15a9826fa15fa8fa08">fetch_input()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to read in parameters and load data.
+ Here we have nothing to do.</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#ae903a369bd861a15a9826fa15fa8fa08">fetch_input</a> {</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a53d7a4e8cce22cfbe0eb51f041604ed9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail::param_defaults </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-param_defaults" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_defaults-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_defaults-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_defaults-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a53d7a4e8cce22cfbe0eb51f041604ed9">param_defaults</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'subject'</span> => <span class="stringliteral">'An automatic message from your pipeline'</span>,</div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4eab23c711954e76734d980c40819726"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a4eab23c711954e76734d980c40819726">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to perform the main bulk of the job (minus input and output).
+ Here the actual sending of the email message happens in <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a4eab23c711954e76734d980c40819726">run()</a> though one may argue it is technically 'output'.</pre><pre> param('email'): The email address to send the message to.</pre><pre> param('subject'): The (optional) 'Subject:' line.</pre><pre> param('text'): Text of the email message. It will undergo parameter substitution.</pre><pre> param('*'): Any other parameters can be freely used for parameter substitution.</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a4eab23c711954e76734d980c40819726">run</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> my $email = $self->param_required(<span class="stringliteral">'email'</span>);</div>
+<div class="line"> my $subject = $self->param_required(<span class="stringliteral">'subject'</span>);</div>
+<div class="line"> my $text = $self->param_required(<span class="stringliteral">'text'</span>);</div>
+<div class="line"></div>
+<div class="line"> open(SENDMAIL, <span class="stringliteral">"|sendmail $email"</span>);</div>
+<div class="line"> print SENDMAIL <span class="stringliteral">"Subject: $subject\n"</span>;</div>
+<div class="line"> print SENDMAIL <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print SENDMAIL <span class="stringliteral">"$text\n"</span>;</div>
+<div class="line"> close SENDMAIL;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a268d6080f03e8ae23d7b1f31baf91d1a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a268d6080f03e8ae23d7b1f31baf91d1a">write_output()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to deal with job's output after the execution.
+ Here we have nothing to do.</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a268d6080f03e8ae23d7b1f31baf91d1a">write_output</a> {</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/<a class="el" href="_notify_by_email_8pm.html">NotifyByEmail.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html">NotifyByEmail</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.js b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.js
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--- /dev/null
+++ b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.js
@@ -0,0 +1,7 @@
+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email =
+[
+ [ "fetch_input", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#ae903a369bd861a15a9826fa15fa8fa08", null ],
+ [ "param_defaults", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a53d7a4e8cce22cfbe0eb51f041604ed9", null ],
+ [ "run", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a4eab23c711954e76734d980c40819726", null ],
+ [ "write_output", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a268d6080f03e8ae23d7b1f31baf91d1a", null ]
+];
\ No newline at end of file
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@@ -0,0 +1,3 @@
+<map id="Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail" name="Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail">
+<area shape="rect" id="node2" href="$class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html" title="Bio::EnsEMBL::Hive\l::Process" alt="" coords="31,97,173,138"/>
+</map>
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@@ -0,0 +1,3 @@
+<map id="Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail" name="Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail">
+<area shape="rect" id="node2" href="$class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html" title="Bio::EnsEMBL::Hive\l::Process" alt="" coords="31,97,173,138"/>
+</map>
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@@ -0,0 +1,152 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#a8796e11e1db7a6fd716e684198dfc282">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#ac3261fa50430bea9fecee3755c4ea2fa">strict_hash_format</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#a8701139930a22ab99b38e5786d1cef68">write_output</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a></td><td class="entry"></td></tr>
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+ <div class="headertitle">
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+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
+<tr class="separator:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
+<tr class="separator:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">standaloneJob.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a> --db_conn mysql:<span class="comment">//ensadmin:${ENSADMIN_PSW}@127.0.0.1:2912/lg4_compara_families_64 \</span></div>
+<div class="line"><span class="comment"> --sql "INSERT INTO meta(meta_key,meta_value) VALUES ('Hello', 'world')"</span></div>
+<div class="line"></div>
+<div class="line">standaloneJob.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a> --db_conn mysql:<span class="comment">//ensadmin:${ENSADMIN_PSW}@127.0.0.1:2913/lg4_compara_homology_merged_64 \</span></div>
+<div class="line"><span class="comment"> --sql "[ 'CREATE TABLE meta_foo LIKE meta', 'INSERT INTO meta_foo SELECT * FROM meta' ]"</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This RunnableDB module acts as a wrapper for an SQL command
+ run against either the current hive database (default) or against one specified by 'db_conn' parameter
+ (--db_conn becomes obligatory in standalone mode, because there is no hive_db).
+ If you behave you may also use parameter substitution.
+
+ The SQL command(s) can be given using two different syntaxes:
+
+ 1) Sql command is stored in the input_id() or parameters() as the value corresponding to the 'sql' key.
+ THIS IS THE RECOMMENDED WAY as it allows to pass in other parameters and use the parameter substitution mechanism in its full glory.
+
+ 2) Sql command is stored in the 'input_id' field of the job table.
+ (only works with sql commands shorter than 255 bytes).
+ This is a legacy syntax. Most people tend to use it not realizing there are other possiblities.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a8796e11e1db7a6fd716e684198dfc282"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::SqlCmd::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#a8796e11e1db7a6fd716e684198dfc282">fetch_input()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to read in parameters and load data.
+ Here it deals with finding the sql command(s), doing parameter substitution, storing the result in a predefined place
+ and optionally connecting to another database (see param('db_conn')).</pre><pre> param('sql'): The recommended way of passing in the sql command(s).</pre><pre> param('db_conn'): An optional hash to pass in connection parameters to the database upon which the sql command(s) will have to be run.</pre><pre> param('*'): Any other parameters can be freely used for parameter substitution.</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#a8796e11e1db7a6fd716e684198dfc282">fetch_input</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # First, FIND the sql command</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span> my $sql = ($self->input_id()!~/^\{.*\}$/)</div>
+<div class="line"> ? $self->input_id() # assume the sql command is given in <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a></div>
+<div class="line"> : $self->param(<span class="stringliteral">'sql'</span>) # or defined as a hash value (in <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> or parameters)</div>
+<div class="line"> or die <span class="stringliteral">"Could not find the command defined in param('sql') or input_id()"</span>;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Store the sql command array:</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span> $self->param(<span class="stringliteral">'sqls'</span>, (ref($sql) eq <span class="stringliteral">'ARRAY'</span>) ? $sql : [$sql] ); </div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af2232b93770b96595d7e042964379e2c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::SqlCmd::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#af2232b93770b96595d7e042964379e2c">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to perform the main bulk of the job (minus input and output).
+ Here it actually runs the sql command(s). If a list of commands is given, they are run in succession within the same session
+ (so you can create a temporary tables and use it in another command within the same sql command list).</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#af2232b93770b96595d7e042964379e2c">run</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> my $sqls = $self->param(<span class="stringliteral">'sqls'</span>);</div>
+<div class="line"> my $data_dbc = $self->data_dbc();</div>
+<div class="line"></div>
+<div class="line"> my %output_id;</div>
+<div class="line"></div>
+<div class="line"> my $counter = 0;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $sql (@$sqls) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->debug()) {</div>
+<div class="line"> warn qq{sql = <span class="stringliteral">"$sql"</span>\n};</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $data_dbc->do( $sql ) or die <span class="stringliteral">"Could not run '$sql': "</span>.$data_dbc->db_handle->errstr;</div>
+<div class="line"></div>
+<div class="line"> my $insert_id_name = <span class="stringliteral">'_insert_id_'</span>.$counter++;</div>
+<div class="line"> my $insert_id_value = $data_dbc->db_handle->last_insert_id(undef, undef, undef, undef);</div>
+<div class="line"></div>
+<div class="line"> $output_id{$insert_id_name} = $insert_id_value;</div>
+<div class="line"> $self->param($insert_id_name, $insert_id_value); # <span class="keywordflow">for</span> templates</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->param(<span class="stringliteral">'output_id'</span>, \%output_id);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac3261fa50430bea9fecee3755c4ea2fa"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::SqlCmd::strict_hash_format </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#ac3261fa50430bea9fecee3755c4ea2fa">strict_hash_format()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to set the strictness level of the parameters' parser.
+ Here we return 0 in order to indicate that neither <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id()</a> nor parameters() is required to contain a hash.</pre><pre> </pre><div id="codesection-strict_hash_format" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-strict_hash_format-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-strict_hash_format-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-strict_hash_format-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#ac3261fa50430bea9fecee3755c4ea2fa">strict_hash_format</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> 0;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8701139930a22ab99b38e5786d1cef68"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::SqlCmd::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#a8701139930a22ab99b38e5786d1cef68">write_output()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to deal with job's output after the execution.
+ Here we only flow out the insert_ids.</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#a8701139930a22ab99b38e5786d1cef68">write_output</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> $self->dataflow_output_id( $self->param(<span class="stringliteral">'output_id'</span>), 2);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/<a class="el" href="_sql_cmd_8pm.html">SqlCmd.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html">SqlCmd</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd =
+[
+ [ "fetch_input", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#a8796e11e1db7a6fd716e684198dfc282", null ],
+ [ "run", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#af2232b93770b96595d7e042964379e2c", null ],
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+<head>
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="dynsections.js"></script>
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+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
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+ <span class="left">
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+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
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+ onblur="searchBox.OnSearchFieldFocus(false)"
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+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
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+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a1341a510369536f2cbcd09fdd2050bf2">_run_test</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a3d33b3c3256122e564dfffc8b745f5af">_validate_tests</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#acabf587c254445072170ed6c7858cbe3">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a454164834bbb0e68d7cd321a4416a506">param_defaults</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a7a00da78d95fdd5a586770e0c6ec1d6b">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck Class Reference</div> </div>
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+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck:</div>
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+</div>
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+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck:</div>
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+</div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
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+<tr class="memitem:a454164834bbb0e68d7cd321a4416a506"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a454164834bbb0e68d7cd321a4416a506">param_defaults</a> ()</td></tr>
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+<tr class="memitem:acabf587c254445072170ed6c7858cbe3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#acabf587c254445072170ed6c7858cbe3">fetch_input</a> ()</td></tr>
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+<tr class="memitem:a3d33b3c3256122e564dfffc8b745f5af"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a3d33b3c3256122e564dfffc8b745f5af">_validate_tests</a> ()</td></tr>
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+<tr class="memitem:a1341a510369536f2cbcd09fdd2050bf2"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a1341a510369536f2cbcd09fdd2050bf2">_run_test</a> ()</td></tr>
+<tr class="separator:a1341a510369536f2cbcd09fdd2050bf2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td></tr>
+<tr class="memitem:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a> ()</td></tr>
+<tr class="separator:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a> ()</td></tr>
+<tr class="separator:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a> ()</td></tr>
+<tr class="separator:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a> ()</td></tr>
+<tr class="separator:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a> ()</td></tr>
+<tr class="separator:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a> ()</td></tr>
+<tr class="separator:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> ()</td></tr>
+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
+<tr class="separator:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
+<tr class="separator:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
+<tr class="separator:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
+<tr class="separator:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
+<tr class="separator:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
+<tr class="separator:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">standaloneJob.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a> \</div>
+<div class="line"> -db_conn mysql:<span class="comment">//ensro@compara1/mm14_compara_homology_71 \</span></div>
+<div class="line"><span class="comment"> -description 'We expect at least 20,000 human genes' \</span></div>
+<div class="line"><span class="comment"> -query 'SELECT * FROM member WHERE genome_db_id = 90 AND source_name = "ENSEMBLGENE"' \</span></div>
+<div class="line"><span class="comment"> -expected_size '>= 20000'</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is a generic RunnableDB module for testing the size of the resultset of any SQL query.
+
+ The query is passed by the parameter 'inputquery' (param substituted)
+ The expected size is passed by the parameter 'expected_size' as a string "CONDITION VALUE" (CONDITION defaults to equality, VALUE defaults to 0).
+ Currently, CONDITION is one of: = == < <= > >= <> !=
+
+ TODO: implement a "expected_value" test
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a1341a510369536f2cbcd09fdd2050bf2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::_run_test </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Runs a single test, defined in a hash with the following keys:
+ description, query, reference_size, logical_test</pre><pre> </pre><div id="codesection-_run_test" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_run_test-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_run_test-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_run_test-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a1341a510369536f2cbcd09fdd2050bf2">_run_test</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $test = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $description = $test->{description};</div>
+<div class="line"> my $query = $test->{subst_query};</div>
+<div class="line"> my $reference_size = $test->{reference_size};</div>
+<div class="line"> my $logical_test = $test->{logical_test};</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Final semicolons are removed if present</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span> ($query =~ /(;\s*$)/) {</div>
+<div class="line"> $query =~ s/$1<span class="comment">//;</span></div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> print <span class="stringliteral">"Test description: $description\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"Checking whether the number of rows $logical_test $reference_size\n"</span>;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # This could benefit from 'switch' once we move to a more recent version of Perl</span></div>
+<div class="line"><span class="preprocessor"></span> my $maxrow = $reference_size;</div>
+<div class="line"> $maxrow++ <span class="keywordflow">if</span> grep {$_ eq $logical_test} qw(= == > <= <> !=);</div>
+<div class="line"></div>
+<div class="line"> $query .= <span class="stringliteral">" LIMIT $maxrow"</span> unless $query =~ /LIMIT/i;</div>
+<div class="line"> print <span class="stringliteral">"Query: $query\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> my $sth = $self->data_dbc()->prepare($query);</div>
+<div class="line"> $sth->{mysql_use_result} = 1 <span class="keywordflow">if</span> $self->data_dbc->driver eq <span class="stringliteral">'mysql'</span>;</div>
+<div class="line"> $sth->execute();</div>
+<div class="line"></div>
+<div class="line"> my $nrow = 0;</div>
+<div class="line"> <span class="keywordflow">while</span> (defined $sth->fetchrow_arrayref()) {</div>
+<div class="line"> $nrow++;</div>
+<div class="line"> }</div>
+<div class="line"> $sth->finish;</div>
+<div class="line"></div>
+<div class="line"> print <span class="stringliteral">"$nrow rows returned"</span>.($nrow == $maxrow ? <span class="stringliteral">" (test aborted, there could be more rows)"</span> : <span class="stringliteral">""</span>).<span class="stringliteral">"\n"</span>;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # This could benefit from 'switch' once we move to a more recent version of Perl</span></div>
+<div class="line"><span class="preprocessor"></span> my $success = 0;</div>
+<div class="line"> <span class="keywordflow">if</span> ($logical_test eq <span class="charliteral">'='</span> or $logical_test eq <span class="stringliteral">'=='</span>) {</div>
+<div class="line"> $success = 1 <span class="keywordflow">if</span> $nrow == $reference_size;</div>
+<div class="line"></div>
+<div class="line"> } elsif ($logical_test eq <span class="charliteral">'<'</span> or $logical_test eq <span class="stringliteral">'<='</span>) {</div>
+<div class="line"> $success = 1 <span class="keywordflow">if</span> $nrow < $maxrow;</div>
+<div class="line"></div>
+<div class="line"> } elsif ($logical_test eq <span class="charliteral">'>'</span> or $logical_test eq <span class="stringliteral">'>='</span>) {</div>
+<div class="line"> $success = 1 <span class="keywordflow">if</span> $nrow >= $maxrow;</div>
+<div class="line"></div>
+<div class="line"> } elsif ($logical_test eq <span class="stringliteral">'<>'</span> or $logical_test eq <span class="stringliteral">'!='</span>) {</div>
+<div class="line"> $success = 1 <span class="keywordflow">if</span> $nrow != $reference_size;</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> die <span class="stringliteral">"This should not happen. A logical test is not checked"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> warn $success ? <span class="stringliteral">"Success\n\n"</span> : <span class="stringliteral">"Failure\n\n"</span>;</div>
+<div class="line"> <span class="keywordflow">return</span> $success;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3d33b3c3256122e564dfffc8b745f5af"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::_validate_tests </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Checks that the tests are properly defined, and parses the "expected_size"</pre><pre> </pre><div id="codesection-_validate_tests" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_validate_tests-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_validate_tests-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_validate_tests-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a3d33b3c3256122e564dfffc8b745f5af">_validate_tests</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $test (@{$self->param(<span class="stringliteral">'tests'</span>)}) {</div>
+<div class="line"> die <span class="stringliteral">"The SQL query must be provided"</span> unless $test->{query};</div>
+<div class="line"> die <span class="stringliteral">"The description must be provided"</span> unless $test->{description};</div>
+<div class="line"> $test->{subst_query} = $self->param_substitute($test->{query});</div>
+<div class="line"> my $expected_size = $self->param_substitute($test->{expected_size} || <span class="stringliteral">''</span>);</div>
+<div class="line"> unless ($expected_size =~ /^\s*(=|==|>|>=|<|<=|<>|!=|)\s*(\d*)\s*$/) {</div>
+<div class="line"> die <span class="stringliteral">"Cannot interpret the 'expected_size' parameter: '$expected_size'"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> $test->{logical_test} = $1 || <span class="charliteral">'='</span>;</div>
+<div class="line"> $test->{reference_size} = $2 || <span class="charliteral">'0'</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="acabf587c254445072170ed6c7858cbe3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#acabf587c254445072170ed6c7858cbe3">fetch_input()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to read in parameters and load data.</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#acabf587c254445072170ed6c7858cbe3">fetch_input</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $self->param(<span class="stringliteral">'inputquery'</span>) && warn <span class="stringliteral">"'inputquery' is deprecated in SqlHealthcheck. Use 'query' instead\n"</span>;</div>
+<div class="line"> </div>
+<div class="line"> my $test = {</div>
+<div class="line"> description => $self->param(<span class="stringliteral">'description'</span>),</div>
+<div class="line"> query => $self->param(<span class="stringliteral">'inputquery'</span>) || $self->param_required(<span class="stringliteral">'query'</span>),</div>
+<div class="line"> expected_size => $self->param(<span class="stringliteral">'expected_size'</span>),</div>
+<div class="line"> };</div>
+<div class="line"></div>
+<div class="line"> $self->param(<span class="stringliteral">'tests'</span>, [$test]);</div>
+<div class="line"> $self->_validate_tests;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a454164834bbb0e68d7cd321a4416a506"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::param_defaults </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-param_defaults" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-param_defaults-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-param_defaults-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-param_defaults-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a454164834bbb0e68d7cd321a4416a506">param_defaults</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> description => <span class="stringliteral">'/no description/'</span>,</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7a00da78d95fdd5a586770e0c6ec1d6b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a7a00da78d95fdd5a586770e0c6ec1d6b">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a>
+ Iterate through the tests and run them all. Report the failed tests at the end</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a7a00da78d95fdd5a586770e0c6ec1d6b">run</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my @failures = ();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $test (@{$self->param(<span class="stringliteral">'tests'</span>)}) {</div>
+<div class="line"> push @failures, $test unless $self->_run_test($test);</div>
+<div class="line"> }</div>
+<div class="line"> die <span class="stringliteral">"The following tests have failed:\n"</span>.join(<span class="stringliteral">''</span>, map {sprintf(<span class="stringliteral">" - %s\n > %s\n"</span>, $_->{description}, $_->{subst_query})} @failures) <span class="keywordflow">if</span> @failures;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/<a class="el" href="_sql_healthcheck_8pm.html">SqlHealthcheck.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html">SqlHealthcheck</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck =
+[
+ [ "_run_test", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a1341a510369536f2cbcd09fdd2050bf2", null ],
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+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd Member List</div> </div>
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+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#ae29716145f0f87688b97e906c8247c5f">fetch_input</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a732af3c6c5e3c3eb4f272d0135c073be">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a4768c0e4d52965b3dc1a34aef202d368">strict_hash_format</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td><td class="entry"></td></tr>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#ab6378c2a90b17bc95ad26d994f63914b">write_output</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a></td><td class="entry"></td></tr>
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::RunnableDB::SystemCmd:</div>
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::RunnableDB::SystemCmd:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a4768c0e4d52965b3dc1a34aef202d368"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a4768c0e4d52965b3dc1a34aef202d368">strict_hash_format</a> ()</td></tr>
+<tr class="separator:a4768c0e4d52965b3dc1a34aef202d368"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ae29716145f0f87688b97e906c8247c5f"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a732af3c6c5e3c3eb4f272d0135c073be"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a732af3c6c5e3c3eb4f272d0135c073be">run</a> ()</td></tr>
+<tr class="separator:a732af3c6c5e3c3eb4f272d0135c073be"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:ab6378c2a90b17bc95ad26d994f63914b"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a></td></tr>
+<tr class="memitem:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a> ()</td></tr>
+<tr class="separator:ae2f3da1c5a538fc990739595101bbfc5 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">life_cycle</a> ()</td></tr>
+<tr class="separator:a1c6fcf03a764b66577f4e33477525401 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2344d158b5ca1a21fa9975fd424a3e6b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">enter_status</a> ()</td></tr>
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+<tr class="memitem:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">strict_hash_format</a> ()</td></tr>
+<tr class="separator:ab6663081a21ccab06ee06c3d3d920846 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">param_defaults</a> ()</td></tr>
+<tr class="separator:ab30a44eca469388da3db6df134ea1559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">fetch_input</a> ()</td></tr>
+<tr class="separator:acdd4d38526457335f615330593ab9329 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">run</a> ()</td></tr>
+<tr class="separator:a346410a6c7d0e5f2541bc304048efdb9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">write_output</a> ()</td></tr>
+<tr class="separator:a1c9525d489a6ef446c834ef3c08927a3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">worker</a> ()</td></tr>
+<tr class="separator:a9d01ac47d41d31f30aca69b0220e0d9d inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Boolean </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">execute_writes</a> ()</td></tr>
+<tr class="separator:a2172d0e9d3014f2ef8f117176904fde3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">db</a> ()</td></tr>
+<tr class="separator:a8ca200c10405c13d535353f2646b49a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">dbc</a> ()</td></tr>
+<tr class="separator:afb5ddec979f7e2ed1f2dc375e26c4456 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+Bio::EnsEMBL::DBSQL::DBConnection </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">data_dbc</a> ()</td></tr>
+<tr class="separator:afe4af3210589a3123a939ceaf83c0462 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a21e51ec58fe708d8875617da6912ca46 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">analysis</a> ()</td></tr>
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+<tr class="memitem:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public <br class="typebreak"/>
+<a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">Bio::EnsEMBL::Hive::AnalysisJob</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">input_job</a> ()</td></tr>
+<tr class="separator:abaf96e66f6740ec51a294e4164363166 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> ()</td></tr>
+<tr class="separator:aaa5d456135299916bbb43f4c8300a404 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">param</a> ()</td></tr>
+<tr class="separator:a6217efee02c3fc309ae8705356e5d8dd inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac4d8269232076e9956fbf09e32680c48 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">param_required</a> ()</td></tr>
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+<tr class="memitem:a472fd524e446e292b836f7f73af250e9 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">param_is_defined</a> ()</td></tr>
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+<tr class="memitem:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">param_substitute</a> ()</td></tr>
+<tr class="separator:a43ada6306f2f629c9d727ea5a0146f89 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5fef0ffecdd8b254a622f83baa8e03e3 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">warning</a> ()</td></tr>
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+<tr class="memitem:a3fd5b992716a3aa9a5810da1f007aa5b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">dataflow_output_id</a> ()</td></tr>
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+<tr class="memitem:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">debug</a> ()</td></tr>
+<tr class="separator:a4c9739f352e4eea538b17bb88de70285 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a3ee5bd7ae4938b858a48b3812814a0a1 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">worker_temp_directory_name</a> ()</td></tr>
+<tr class="separator:ab007327305a8dc5294ff757cb3d50559 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">cleanup_worker_temp_directory</a> ()</td></tr>
+<tr class="separator:a35dbbcb04656e835a31cbc927b2c8584 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">standaloneJob.pl <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a> --cmd <span class="stringliteral">'ls -1 ${ENSEMBL_CVS_ROOT_DIR}/ensembl-hive/modules/Bio/EnsEMBL/Hive/RunnableDB/*.pm >building_blocks.list'</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This RunnableDB module acts as a wrapper for shell-level command lines. If you behave you may also use parameter substitution.
+
+ The command can be given using two different syntaxes:
+
+ 1) Command line is stored in the input_id() or parameters() as the value corresponding to the 'cmd' key.
+ THIS IS THE RECOMMENDED WAY as it allows to pass in other parameters and use the parameter substitution mechanism in its full glory.
+
+ 2) Command line is stored in the 'input_id' field of the job table.
+ (only works with command lines shorter than 255 bytes).
+ This is a legacy syntax. Most people tend to use it not realizing there are other possiblities.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ae29716145f0f87688b97e906c8247c5f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::SystemCmd::fetch_input </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#ae29716145f0f87688b97e906c8247c5f">fetch_input()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to read in parameters and load data.
+ Here it deals with finding the command line, doing parameter substitution and storing the result in a predefined place.</pre><pre> param('cmd'): The recommended way of passing in the command line.</pre><pre> param('*'): Any other parameters can be freely used for parameter substitution.</pre><pre> </pre><div id="codesection-fetch_input" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch_input-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch_input-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch_input-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#ae29716145f0f87688b97e906c8247c5f">fetch_input</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # First, FIND the command line</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span> my $cmd = ($self->input_id()!~/^\{.*\}$/)</div>
+<div class="line"> ? $self->input_id() # assume the command line is given in <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a></div>
+<div class="line"> : $self->param(<span class="stringliteral">'cmd'</span>) # or defined as a hash value (in <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id</a> or parameters)</div>
+<div class="line"> or die <span class="stringliteral">"Could not find the command defined in param('cmd') or input_id()"</span>;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Store the value with parameter substitutions for the actual execution:</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span> $self->param(<span class="stringliteral">'cmd'</span>, $cmd);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a732af3c6c5e3c3eb4f272d0135c073be"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::SystemCmd::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a732af3c6c5e3c3eb4f272d0135c073be">run()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to perform the main bulk of the job (minus input and output).
+ Here it actually runs the command line.</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a732af3c6c5e3c3eb4f272d0135c073be">run</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> </div>
+<div class="line"> my $cmd = $self->param(<span class="stringliteral">'cmd'</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->debug()) {</div>
+<div class="line"> warn qq{cmd = <span class="stringliteral">"$cmd"</span>\n};</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->dbc and $self->dbc->disconnect_when_inactive(1); # release <span class="keyword">this</span> connection <span class="keywordflow">for</span> the duration of system() call</div>
+<div class="line"></div>
+<div class="line"> if(my $return_value = system($cmd)) {</div>
+<div class="line"> $return_value >>= 8;</div>
+<div class="line"> die <span class="stringliteral">"system( $cmd ) failed: $return_value"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->dbc and $self->dbc->disconnect_when_inactive(0); # allow the worker to keep the connection open again</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4768c0e4d52965b3dc1a34aef202d368"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::SystemCmd::strict_hash_format </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a4768c0e4d52965b3dc1a34aef202d368">strict_hash_format()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to set the strictness level of the parameters' parser.
+ Here we return 0 in order to indicate that neither <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">input_id()</a> nor parameters() is required to contain a hash.</pre><pre> </pre><div id="codesection-strict_hash_format" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-strict_hash_format-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-strict_hash_format-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-strict_hash_format-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a4768c0e4d52965b3dc1a34aef202d368">strict_hash_format</a> {</div>
+<div class="line"> <span class="keywordflow">return</span> 0;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab6378c2a90b17bc95ad26d994f63914b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::RunnableDB::SystemCmd::write_output </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#ab6378c2a90b17bc95ad26d994f63914b">write_output()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Bio::EnsEMBL::Hive::Process</a> that is used to deal with job's output after the execution.
+ Here we have nothing to do, as the wrapper is very generic.</pre><pre> </pre><div id="codesection-write_output" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-write_output-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-write_output-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-write_output-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#ab6378c2a90b17bc95ad26d994f63914b">write_output</a> {</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/RunnableDB/<a class="el" href="_system_cmd_8pm.html">SystemCmd.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">RunnableDB</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html">SystemCmd</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#a65f7b429d0ffbda238faeda2451350a8">schedule_workers_resync_if_necessary</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html">Bio::EnsEMBL::Hive::Scheduler</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler-members.html">List of all members</a> </div>
+ <div class="headertitle">
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+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a65f7b429d0ffbda238faeda2451350a8"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#a65f7b429d0ffbda238faeda2451350a8">schedule_workers_resync_if_necessary</a> ()</td></tr>
+<tr class="separator:a65f7b429d0ffbda238faeda2451350a8"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab56e0d78a8774c93dc262a5c63812891"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ab56e0d78a8774c93dc262a5c63812891">suggest_analysis_to_specialize_by_rc_id_meadow_type</a> ()</td></tr>
+<tr class="separator:ab56e0d78a8774c93dc262a5c63812891"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad37b01e88608cec39e5f883d95c8ea42"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ad37b01e88608cec39e5f883d95c8ea42">schedule_workers</a> ()</td></tr>
+<tr class="separator:ad37b01e88608cec39e5f883d95c8ea42"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Scheduler starts with the numbers of required workers for unblocked analyses,
+ then goes through several kinds of restrictions (submit_limit, meadow_limits, hive_capacity, etc)
+ that act as limiters and may cap the original numbers in several ways.
+ The capped numbers are then grouped by meadow_type and rc_name and returned in a two-level hash.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ad37b01e88608cec39e5f883d95c8ea42"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Scheduler::schedule_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-schedule_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-schedule_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-schedule_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-schedule_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ad37b01e88608cec39e5f883d95c8ea42">schedule_workers</a> {</div>
+<div class="line"> my ($queen, $submit_capacity, $default_meadow_type, $filter_rc_id, $filter_meadow_type, $filter_analysis, $meadow_capacity_limiter_hashed_by_type, $analysis_id2rc_name) = @_;</div>
+<div class="line"></div>
+<div class="line"> my @suitable_analyses = $filter_analysis</div>
+<div class="line"> ? ( $filter_analysis->stats )</div>
+<div class="line"> : @{ $queen->db->get_AnalysisStatsAdaptor->fetch_all_by_suitability_rc_id_meadow_type($filter_rc_id, $filter_meadow_type) };</div>
+<div class="line"></div>
+<div class="line"> unless(@suitable_analyses) {</div>
+<div class="line"> <span class="keywordflow">return</span> $analysis_id2rc_name ? ({}, 0, <span class="stringliteral">"Scheduler could not find any suitable analyses to start with\n"</span>) : undef; # FIXME: returns data in different format in <span class="stringliteral">"suggest analysis"</span> mode</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # the pre-pending-adjusted outcome will be stored here:</span></div>
+<div class="line"><span class="preprocessor"></span> my %workers_to_submit_by_meadow_type_rc_name = ();</div>
+<div class="line"> my $total_workers_required = 0;</div>
+<div class="line"> my $log_buffer = <span class="stringliteral">''</span>;</div>
+<div class="line"></div>
+<div class="line"> my $submit_capacity_limiter = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a89203ff40a85e13c7ef840a46dcf4487">new</a>( <span class="stringliteral">'Max number of Workers scheduled this time'</span>, $submit_capacity );</div>
+<div class="line"> my $queen_capacity_limiter = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a89203ff40a85e13c7ef840a46dcf4487">new</a>( <span class="stringliteral">'Total reciprocal capacity of the Hive'</span>, 1.0 - $queen->get_hive_current_load() );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $analysis_stats (@suitable_analyses) {</div>
+<div class="line"> last <span class="keywordflow">if</span>( $submit_capacity_limiter->reached );</div>
+<div class="line"></div>
+<div class="line"> my $analysis = $analysis_stats->get_analysis; # FIXME: <span class="keywordflow">if</span> it proves too expensive we may need to consider caching</div>
+<div class="line"> my $this_meadow_type = $analysis->meadow_type || $default_meadow_type;</div>
+<div class="line"></div>
+<div class="line"> next <span class="keywordflow">if</span>( $meadow_capacity_limiter_hashed_by_type && $meadow_capacity_limiter_hashed_by_type->{$this_meadow_type}->reached );</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> #digging deeper under the surface so need to sync:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>( $analysis_stats->status =~ /^(LOADING|ALL_CLAIMED|BLOCKED|SYNCHING)$/ ) {</div>
+<div class="line"> $queen->safe_synchronize_AnalysisStats($analysis_stats);</div>
+<div class="line"> }</div>
+<div class="line"> next <span class="keywordflow">if</span>( $analysis_stats->status =~ /^(BLOCKED|SYNCHING)$/ );</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # getting the initial worker requirement for this analysis (may be stale if not sync'ed recently)</span></div>
+<div class="line"><span class="preprocessor"></span> my $extra_workers_this_analysis = $analysis_stats->num_required_workers;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # if this analysis doesn't require any extra workers - just skip it:</span></div>
+<div class="line"><span class="preprocessor"></span> next <span class="keywordflow">if</span> ($extra_workers_this_analysis <= 0);</div>
+<div class="line"></div>
+<div class="line"> $total_workers_required += $extra_workers_this_analysis; # also keep the total number required so far (<span class="keywordflow">if</span> nothing required we may need a resync later)</div>
+<div class="line"></div>
+<div class="line"> <span class="preprocessor"># setting up all negotiating limiters:</span></div>
+<div class="line"><span class="preprocessor"></span> $queen_capacity_limiter->multiplier( $analysis_stats->hive_capacity );</div>
+<div class="line"> my @limiters = (</div>
+<div class="line"> $submit_capacity_limiter,</div>
+<div class="line"> $queen_capacity_limiter,</div>
+<div class="line"> $meadow_capacity_limiter_hashed_by_type</div>
+<div class="line"> ? $meadow_capacity_limiter_hashed_by_type->{$this_meadow_type}</div>
+<div class="line"> : (),</div>
+<div class="line"> defined($analysis->analysis_capacity)</div>
+<div class="line"> ? <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a89203ff40a85e13c7ef840a46dcf4487">new</a>( <span class="stringliteral">"Number of Workers working at '"</span>.$analysis->logic_name.<span class="stringliteral">"' analysis"</span>,</div>
+<div class="line"> $analysis->analysis_capacity - $analysis_stats->num_running_workers )</div>
+<div class="line"> : (),</div>
+<div class="line"> );</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # negotiations:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">foreach</span> my $limiter (@limiters) {</div>
+<div class="line"> $extra_workers_this_analysis = $limiter->preliminary_offer( $extra_workers_this_analysis );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # do not continue with this analysis if limiters haven't agreed on a positive number:</span></div>
+<div class="line"><span class="preprocessor"></span> next <span class="keywordflow">if</span> ($extra_workers_this_analysis <= 0);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # let all parties know the final decision of negotiations:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">foreach</span> my $limiter (@limiters) {</div>
+<div class="line"> $limiter->final_decision( $extra_workers_this_analysis );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($analysis_id2rc_name) {</div>
+<div class="line"> my $this_rc_name = $analysis_id2rc_name->{ $analysis_stats->analysis_id };</div>
+<div class="line"> $workers_to_submit_by_meadow_type_rc_name{ $this_meadow_type }{ $this_rc_name } += $extra_workers_this_analysis;</div>
+<div class="line"> $log_buffer .= $analysis_stats->toString . <span class="stringliteral">"\n"</span>;</div>
+<div class="line"> $log_buffer .= sprintf(<span class="stringliteral">"Before checking the Valley for pending jobs, Scheduler allocated $extra_workers_this_analysis x $this_meadow_type:$this_rc_name extra workers for '%s' [%.4f hive_load remaining]\n"</span>,</div>
+<div class="line"> $analysis->logic_name,</div>
+<div class="line"> $queen_capacity_limiter->available_capacity,</div>
+<div class="line"> );</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> <span class="keywordflow">return</span> $analysis_stats; # FIXME: returns data in different format in <span class="stringliteral">"suggest analysis"</span> mode</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> (\%workers_to_submit_by_meadow_type_rc_name, $total_workers_required, $log_buffer);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a65f7b429d0ffbda238faeda2451350a8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Scheduler::schedule_workers_resync_if_necessary </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-schedule_workers_resync_if_necessary" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-schedule_workers_resync_if_necessary-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-schedule_workers_resync_if_necessary-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-schedule_workers_resync_if_necessary-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#a65f7b429d0ffbda238faeda2451350a8">schedule_workers_resync_if_necessary</a> {</div>
+<div class="line"> my ($queen, $valley, $filter_analysis) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $submit_capacity = $valley->config_get(<span class="stringliteral">'SubmitWorkersMax'</span>);</div>
+<div class="line"> my $default_meadow_type = $valley->get_default_meadow()->type;</div>
+<div class="line"> my $meadow_capacity_limiter_hashed_by_type = $valley->get_meadow_capacity_hash_by_meadow_type();</div>
+<div class="line"></div>
+<div class="line"> my $analysis_id2rc_id = $queen->db->get_AnalysisAdaptor->fetch_HASHED_FROM_analysis_id_TO_resource_class_id();</div>
+<div class="line"> my $rc_id2name = $queen->db->get_ResourceClassAdaptor->fetch_HASHED_FROM_resource_class_id_TO_name();</div>
+<div class="line"><span class="preprocessor"> # combined mapping:</span></div>
+<div class="line"><span class="preprocessor"></span> my $analysis_id2rc_name = { map { $_ => $rc_id2name->{ $analysis_id2rc_id->{ $_ }} } keys %$analysis_id2rc_id };</div>
+<div class="line"></div>
+<div class="line"> my ($workers_to_submit_by_meadow_type_rc_name, $total_workers_required, $log_buffer)</div>
+<div class="line"> = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ad37b01e88608cec39e5f883d95c8ea42">schedule_workers</a>($queen, $submit_capacity, $default_meadow_type, undef, undef, $filter_analysis, $meadow_capacity_limiter_hashed_by_type, $analysis_id2rc_name);</div>
+<div class="line"> print $log_buffer;</div>
+<div class="line"></div>
+<div class="line"> unless( $total_workers_required ) {</div>
+<div class="line"> print <span class="stringliteral">"\nScheduler: according to analysis_stats no workers are required... let's see if resync can fix it.\n"</span> ;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # FIXME: here is an (optimistic) assumption all Workers the Queen can see are reachable from the Valley:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>( $queen->count_running_workers() != $valley->count_running_workers ) {</div>
+<div class="line"> print <span class="stringliteral">"Scheduler: mismatch between Queen's workers and Valley's workers detected, checking for dead workers...\n"</span>;</div>
+<div class="line"> $queen->check_for_dead_workers($valley, 1);</div>
+<div class="line"> }</div>
+<div class="line"> print <span class="stringliteral">"Scheduler: re-balancing of semaphore_counts...\n"</span>;</div>
+<div class="line"> $queen->db->get_AnalysisJobAdaptor->balance_semaphores($filter_analysis && $filter_analysis->dbID);</div>
+<div class="line"> print <span class="stringliteral">"Scheduler: re-synchronizing the Hive...\n"</span>;</div>
+<div class="line"> $queen->synchronize_hive($filter_analysis);</div>
+<div class="line"></div>
+<div class="line"> ($workers_to_submit_by_meadow_type_rc_name, $total_workers_required, $log_buffer)</div>
+<div class="line"> = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ad37b01e88608cec39e5f883d95c8ea42">schedule_workers</a>($queen, $submit_capacity, $default_meadow_type, undef, undef, $filter_analysis, $meadow_capacity_limiter_hashed_by_type, $analysis_id2rc_name);</div>
+<div class="line"> print $log_buffer;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # adjustment for pending workers:</span></div>
+<div class="line"><span class="preprocessor"></span> my ($pending_worker_counts_by_meadow_type_rc_name, $total_pending_all_meadows) = $valley->get_pending_worker_counts_by_meadow_type_rc_name();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>( my ($this_meadow_type, $partial_workers_to_submit_by_rc_name) = each %$workers_to_submit_by_meadow_type_rc_name) {</div>
+<div class="line"> <span class="keywordflow">while</span>( my ($this_rc_name, $workers_to_submit_this_group) = each %$partial_workers_to_submit_by_rc_name) {</div>
+<div class="line"> <span class="keywordflow">if</span>(my $pending_this_group = $pending_worker_counts_by_meadow_type_rc_name->{ $this_meadow_type }{ $this_rc_name }) {</div>
+<div class="line"></div>
+<div class="line"> print <span class="stringliteral">"Scheduler was thinking of submitting $workers_to_submit_this_group x $this_meadow_type:$this_rc_name workers when it detected $pending_this_group pending in this group, "</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $workers_to_submit_this_group > $pending_this_group) {</div>
+<div class="line"> $workers_to_submit_by_meadow_type_rc_name->{$this_meadow_type}{$this_rc_name} -= $pending_this_group; # adjust the hashed value</div>
+<div class="line"> print <span class="stringliteral">"so is going to submit only "</span>.$workers_to_submit_by_meadow_type_rc_name->{$this_meadow_type}{$this_rc_name}.<span class="stringliteral">" extra\n"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> <span class="keyword">delete</span> $workers_to_submit_by_meadow_type_rc_name->{$this_meadow_type}{$this_rc_name}; # avoid leaving an empty group in the hash</div>
+<div class="line"> print <span class="stringliteral">"so is not going to submit any extra\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> print <span class="stringliteral">"Scheduler is going to submit $workers_to_submit_this_group x $this_meadow_type:$this_rc_name workers\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> unless(keys %{ $workers_to_submit_by_meadow_type_rc_name->{$this_meadow_type} }) { # <span class="keywordflow">if</span> nothing has been scheduled <span class="keywordflow">for</span> a meadow,</div>
+<div class="line"> <span class="keyword">delete</span> $workers_to_submit_by_meadow_type_rc_name->{$this_meadow_type}; # <span class="keywordflow">do</span> not mention the meadow in the hash</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $workers_to_submit_by_meadow_type_rc_name;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab56e0d78a8774c93dc262a5c63812891"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Scheduler::suggest_analysis_to_specialize_by_rc_id_meadow_type </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-suggest_analysis_to_specialize_by_rc_id_meadow_type" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-suggest_analysis_to_specialize_by_rc_id_meadow_type-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-suggest_analysis_to_specialize_by_rc_id_meadow_type-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-suggest_analysis_to_specialize_by_rc_id_meadow_type-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ab56e0d78a8774c93dc262a5c63812891">suggest_analysis_to_specialize_by_rc_id_meadow_type</a> {</div>
+<div class="line"> my ($queen, $filter_rc_id, $filter_meadow_type) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ad37b01e88608cec39e5f883d95c8ea42">schedule_workers</a>($queen, 1, $filter_meadow_type, $filter_rc_id, $filter_meadow_type);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_scheduler_8pm.html">Scheduler.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html">Scheduler</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.js b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.js
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+[
+ [ "schedule_workers", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ad37b01e88608cec39e5f883d95c8ea42", null ],
+ [ "schedule_workers_resync_if_necessary", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#a65f7b429d0ffbda238faeda2451350a8", null ],
+ [ "suggest_analysis_to_specialize_by_rc_id_meadow_type", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ab56e0d78a8774c93dc262a5c63812891", null ]
+];
\ No newline at end of file
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+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
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+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
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+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
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+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::URLFactory Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a1cdc4eafa4fb5abf83942dfe21e3a7ff">create_cached_dba</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#acf08a2e7774e3dcc8643f8703d068c6a">DESTROY</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">fetch</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#ab067dc5c5216255309138355ecb085ee">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
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+ <li class="footer">Generated by
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diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html
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+  <span id="projectnumber">1.9</span>
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+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::URLFactory Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:ab067dc5c5216255309138355ecb085ee"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#ab067dc5c5216255309138355ecb085ee">new</a> ()</td></tr>
+<tr class="separator:ab067dc5c5216255309138355ecb085ee"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:acf08a2e7774e3dcc8643f8703d068c6a"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#acf08a2e7774e3dcc8643f8703d068c6a">DESTROY</a> ()</td></tr>
+<tr class="separator:acf08a2e7774e3dcc8643f8703d068c6a"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9b61c3f379811a6695c8bf57510fe293"><td class="memItemLeft" align="right" valign="top">public Blessed </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">fetch</a> ()</td></tr>
+<tr class="separator:a9b61c3f379811a6695c8bf57510fe293"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1cdc4eafa4fb5abf83942dfe21e3a7ff"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a1cdc4eafa4fb5abf83942dfe21e3a7ff">create_cached_dba</a> ()</td></tr>
+<tr class="separator:a1cdc4eafa4fb5abf83942dfe21e3a7ff"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">$url_string1 = <span class="stringliteral">'mysql://ensadmin:<pass>@ecs2:3362/compara_hive_23c'</span>; # type=hive by <span class="keywordflow">default</span></div>
+<div class="line">$url_string2 = <span class="stringliteral">'mysql://ensadmin:<pass>@ecs2:3362/ensembl_compara_22_1;type=compara'</span></div>
+<div class="line">$url_string3 = <span class="stringliteral">'mysql://ensadmin:<pass>@ecs2:3362/ensembl_core_homo_sapiens_22_34;type=core'</span></div>
+<div class="line"></div>
+<div class="line">$hive_dba = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">fetch</a>($url_string1);</div>
+<div class="line">$compara_dba = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">fetch</a>($url_string2);</div>
+<div class="line">$core_dba = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">fetch</a>($url_string3);</div>
+</div><!-- fragment --> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a1cdc4eafa4fb5abf83942dfe21e3a7ff"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::URLFactory::create_cached_dba </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-create_cached_dba" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-create_cached_dba-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-create_cached_dba-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-create_cached_dba-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a1cdc4eafa4fb5abf83942dfe21e3a7ff">create_cached_dba</a> {</div>
+<div class="line"> my ($class, $driver, $user, $pass, $host, $port, $dbname, $conn_params) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($driver eq <span class="stringliteral">'mysql'</span>) {</div>
+<div class="line"> $user ||= <span class="stringliteral">'ensro'</span>;</div>
+<div class="line"> $pass ||= <span class="stringliteral">''</span>;</div>
+<div class="line"> $host ||= <span class="stringliteral">''</span>;</div>
+<div class="line"> $port ||= 3306;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $type = $conn_params->{<span class="stringliteral">'type'</span>};</div>
+<div class="line"> my $discon = $conn_params->{<span class="stringliteral">'discon'</span>};</div>
+<div class="line"> my $nosqlvc = $conn_params->{<span class="stringliteral">'nosqlvc'</span>};</div>
+<div class="line"></div>
+<div class="line"> my $connectionKey = <span class="stringliteral">"$driver://$user:$pass\@$host:$port/$dbname;$type"</span>;</div>
+<div class="line"> my $dba = $_URLFactory_global_instance->{$connectionKey};</div>
+<div class="line"></div>
+<div class="line"> unless($dba) {</div>
+<div class="line"></div>
+<div class="line"> my $module = {</div>
+<div class="line"> <span class="stringliteral">'hive'</span> => <span class="stringliteral">'Bio::EnsEMBL::Hive::DBSQL::DBAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'compara'</span> => <span class="stringliteral">'Bio::EnsEMBL::Compara::DBSQL::DBAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'core'</span> => <span class="stringliteral">'Bio::EnsEMBL::DBSQL::DBAdaptor'</span>,</div>
+<div class="line"> <span class="stringliteral">'pipeline'</span> => <span class="stringliteral">'Bio::EnsEMBL::Pipeline::DBSQL::DBAdaptor'</span>,</div>
+<div class="line"> }->{$type};</div>
+<div class="line"></div>
+<div class="line"> eval <span class="stringliteral">"require $module"</span>;</div>
+<div class="line"></div>
+<div class="line"> $_URLFactory_global_instance->{$connectionKey} = $dba = $module->new (</div>
+<div class="line"> -driver => $driver,</div>
+<div class="line"> -host => $host,</div>
+<div class="line"> -port => $port,</div>
+<div class="line"> -user => $user,</div>
+<div class="line"> -pass => $pass,</div>
+<div class="line"> -dbname => $dbname,</div>
+<div class="line"> -species => $dbname,</div>
+<div class="line"> -disconnect_when_inactive => $discon,</div>
+<div class="line"> -no_sql_schema_version_check => $nosqlvc,</div>
+<div class="line"> );</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $dba;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="acf08a2e7774e3dcc8643f8703d068c6a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::URLFactory::DESTROY </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-DESTROY" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-DESTROY-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-DESTROY-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-DESTROY-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#acf08a2e7774e3dcc8643f8703d068c6a">DESTROY</a> {</div>
+<div class="line"> my ($obj) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $key (keys(%$_URLFactory_global_instance)) {</div>
+<div class="line"> $_URLFactory_global_instance->{$key} = undef;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a9b61c3f379811a6695c8bf57510fe293"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Blessed Bio::EnsEMBL::Hive::URLFactory::fetch </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg[1] : string $url
+ Example :</pre><div class="fragment"><div class="line">$url = <span class="stringliteral">'mysql://user:pass@host:3306/dbname/table_name?tparam_name=tparam_value;type=compara;discon=1'</span></div>
+<div class="line"> my $object = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">fetch</a>($url);</div>
+</div><!-- fragment --> <pre> Description: parses the URL, connects to appropriate DBAdaptor,
+ determines appropriate object_adaptor, fetches the object
+ Returntype : blessed instance of the object refered to or a DBAdaptor if simple URL
+ Exceptions : none
+ Caller : ?</pre><pre> </pre><div id="codesection-fetch" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-fetch-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-fetch-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-fetch-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">fetch</a> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"> my $url = shift @_ or <span class="keywordflow">return</span>;</div>
+<div class="line"> my $default_dba = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">Bio::EnsEMBL::Hive::URLFactory</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#ab067dc5c5216255309138355ecb085ee">new</a>(); # make sure global instance is created</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $parsed_url = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l.html#ac80cc911eba215fb0ed17104861fe5f7">Bio::EnsEMBL::Hive::Utils::URL::parse</a>( $url )) {</div>
+<div class="line"></div>
+<div class="line"> my $dba = ($parsed_url->{<span class="stringliteral">'dbconn_part'</span>} =~ m{^\w*:</div>
+<div class="line"> ? $default_dba</div>
+<div class="line"> : $class->create_cached_dba( @$parsed_url{qw(driver user pass host port dbname conn_params)} );</div>
+<div class="line"></div>
+<div class="line"> my $table_name = $parsed_url->{<span class="stringliteral">'table_name'</span>};</div>
+<div class="line"> my $tparam_name = $parsed_url->{<span class="stringliteral">'tparam_name'</span>};</div>
+<div class="line"> my $tparam_value = $parsed_url->{<span class="stringliteral">'tparam_value'</span>};</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(not $table_name) {</div>
+<div class="line"> </div>
+<div class="line"> <span class="keywordflow">return</span> $dba;</div>
+<div class="line"></div>
+<div class="line"> } elsif($table_name eq <span class="stringliteral">'analysis'</span>) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $dba->get_AnalysisAdaptor->fetch_by_url_query($tparam_name, $tparam_value);</div>
+<div class="line"></div>
+<div class="line"> } elsif($table_name eq <span class="stringliteral">'job'</span>) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $dba->get_AnalysisJobAdaptor->fetch_by_url_query($tparam_name, $tparam_value);</div>
+<div class="line"></div>
+<div class="line"> } elsif($table_name eq <span class="stringliteral">'accu'</span>) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html">Bio::EnsEMBL::Hive::Accumulator</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#ac035312016653df35c35398474835764">new</a>(</div>
+<div class="line"> -adaptor => $dba->get_AccumulatorAdaptor,</div>
+<div class="line"> -struct_name => $tparam_name,</div>
+<div class="line"> -signature_template => $tparam_value,</div>
+<div class="line"> );</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html">Bio::EnsEMBL::Hive::NakedTable</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a86e40bedaa4255b62bb61b92e1b663c8">new</a>(</div>
+<div class="line"> -adaptor => $dba->get_NakedTableAdaptor,</div>
+<div class="line"> -table_name => $table_name,</div>
+<div class="line"> $tparam_value ? (-insertion_method => $tparam_value) : ()</div>
+<div class="line"> );</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab067dc5c5216255309138355ecb085ee"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::URLFactory::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> unless($_URLFactory_global_instance) {</div>
+<div class="line"> $_URLFactory_global_instance = bless {}, $class;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $_URLFactory_global_instance;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_u_r_l_factory_8pm.html">URLFactory.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
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+<tr class="memitem:ad8abe58a987444c45b366ef5dba4e218"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad8abe58a987444c45b366ef5dba4e218">script_usage</a> ()</td></tr>
+<tr class="separator:ad8abe58a987444c45b366ef5dba4e218"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:af7e04ac99c85db0534b11541b99c96da"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#af7e04ac99c85db0534b11541b99c96da">url2dbconn_hash</a> ()</td></tr>
+<tr class="separator:af7e04ac99c85db0534b11541b99c96da"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aa1cbcb45d800cf3c5b47079e0b27e237"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#aa1cbcb45d800cf3c5b47079e0b27e237">go_figure_dbc</a> ()</td></tr>
+<tr class="separator:aa1cbcb45d800cf3c5b47079e0b27e237"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae4891d2eb87c70172c9d37b374647144"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ae4891d2eb87c70172c9d37b374647144">report_versions</a> ()</td></tr>
+<tr class="separator:ae4891d2eb87c70172c9d37b374647144"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line"><span class="preprocessor"> # Example of an import:</span></div>
+<div class="line"><span class="preprocessor"></span>use <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html">Bio::EnsEMBL::Hive::Utils</a> <span class="stringliteral">'stringify'</span>;</div>
+<div class="line">my $input_id_string = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a38ef61e77ea6ba6bb1e08c35228cb7c3">stringify</a>($input_id_hash);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Example of inheritance:</span></div>
+<div class="line"><span class="preprocessor"></span>use base (<span class="stringliteral">'Bio::EnsEMBL::Hive::Utils'</span>, ...);</div>
+<div class="line">my $input_id_string = $self->stringify($input_id_hash);</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # Example of a direct call:</span></div>
+<div class="line"><span class="preprocessor"></span>use Bio::EnsEMBL::Hive::Utils;</div>
+<div class="line">my $input_id_string = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a38ef61e77ea6ba6bb1e08c35228cb7c3">Bio::EnsEMBL::Hive::Utils::stringify</a>($input_id_hash);</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This module provides general utility functions that can be used in different contexts through three different calling mechanisms:
+
+ import: another module/script can selectively import methods from this module into its namespace
+
+ inheritance: another module can inherit from this one and so implicitly acquire the methods into its namespace
+
+ direct call to a module's method: another module/script can directly call a method from this module prefixed with this module's name
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ac3350cd70c4187290ded88a59533e62d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::destringify </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: This function takes in a string that may or may not contain a stingified Perl structure.
+ If it seems to contain a hash/array/quoted_string, the contents is evaluated, otherwise it is returned "as is".
+ This function is mainly used to read values from 'meta' table that may represent Perl structures, but generally don't have to.</pre><pre> Callers : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a> # destringification of general 'meta' params
+ <a class="el" href="beekeeper_8pl.html">beekeeper.pl</a> script # destringification of the 'pipeline_name' meta param</pre><pre> </pre><div id="codesection-destringify" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-destringify-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-destringify-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-destringify-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ac3350cd70c4187290ded88a59533e62d">destringify</a> {</div>
+<div class="line"> my $value = pop @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($value) {</div>
+<div class="line"> <span class="keywordflow">if</span>($value=~/^<span class="stringliteral">'.*'</span>$/</div>
+<div class="line"> or $value=~/^<span class="stringliteral">".*"</span>$/</div>
+<div class="line"> or $value=~/^{.*}$/</div>
+<div class="line"> or $value=~/^\[.*\]$/</div>
+<div class="line"> or $value eq <span class="stringliteral">'undef'</span>) {</div>
+<div class="line"></div>
+<div class="line"> $value = eval($value);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $value;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a8c682e65730f8bb07e2d6274958b640d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::dir_revhash </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: This function takes in a string (which is usually a numeric id) and turns its reverse into a multilevel directory hash.
+ Please note that no directory is created at this step - it is purely a string conversion function.</pre><pre> Callers : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a> # hashing of the worker output directories
+ <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a> # hashing of an arbitrary id</pre><pre> </pre><div id="codesection-dir_revhash" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dir_revhash-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dir_revhash-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dir_revhash-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a8c682e65730f8bb07e2d6274958b640d">dir_revhash</a> {</div>
+<div class="line"> my $id = pop @_;</div>
+<div class="line"></div>
+<div class="line"> my @dirs = reverse(split(<span class="comment">//, $id));</span></div>
+<div class="line"> pop @dirs; # <span class="keywordflow">do</span> not use the first digit <span class="keywordflow">for</span> hashing</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> join(<span class="charliteral">'/'</span>, @dirs);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a487b583d13e668734c35bcff7e427d9b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::find_submodules </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: This function takes one argument ("prefix" of a module name),
+ transforms it into a directory name from the filesystem's point of view
+ and finds all module names in these "directories".
+ Each module_name found is reported only once,
+ even if there are multiple matching files in different directories.</pre><pre> Callers : scripts</pre><pre> </pre><div id="codesection-find_submodules" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-find_submodules-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-find_submodules-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-find_submodules-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a487b583d13e668734c35bcff7e427d9b">find_submodules</a> {</div>
+<div class="line"> my $prefix = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $prefix=~s{::}{/}g;</div>
+<div class="line"></div>
+<div class="line"> my %seen_module_name = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $inc (@INC) {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $full_module_path (<$inc/$prefix<span class="comment">/*.pm>) {</span></div>
+<div class="line"><span class="comment"> my $module_name = substr($full_module_path, length($inc)+1, -3); # remove leading "$inc/" and trailing '.pm'</span></div>
+<div class="line"><span class="comment"> $module_name=~s{/}{::}g; # transform back to module_name space</span></div>
+<div class="line"><span class="comment"></span></div>
+<div class="line"><span class="comment"> $seen_module_name{$module_name}++;</span></div>
+<div class="line"><span class="comment"> }</span></div>
+<div class="line"><span class="comment"> }</span></div>
+<div class="line"><span class="comment"> return [ keys %seen_module_name ];</span></div>
+<div class="line"><span class="comment">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa1cbcb45d800cf3c5b47079e0b27e237"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::go_figure_dbc </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-go_figure_dbc" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-go_figure_dbc-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-go_figure_dbc-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-go_figure_dbc-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#aa1cbcb45d800cf3c5b47079e0b27e237">go_figure_dbc</a> {</div>
+<div class="line"> my ($foo, $schema_type) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(UNIVERSAL::isa($foo, <span class="stringliteral">'Bio::EnsEMBL::DBSQL::DBConnection'</span>)) { # already a DBConnection, <span class="keywordflow">return</span> it:</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $foo;</div>
+<div class="line"></div>
+<div class="line"> } elsif(UNIVERSAL::can($foo, <span class="stringliteral">'dbc'</span>) and UNIVERSAL::isa($foo->dbc, <span class="stringliteral">'Bio::EnsEMBL::DBSQL::DBConnection'</span>)) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $foo->dbc;</div>
+<div class="line"></div>
+<div class="line"> } elsif(UNIVERSAL::can($foo, <span class="stringliteral">'db'</span>) and UNIVERSAL::can($foo->db, <span class="stringliteral">'dbc'</span>) and UNIVERSAL::isa($foo->db->dbc, <span class="stringliteral">'Bio::EnsEMBL::DBSQL::DBConnection'</span>)) { # another data adaptor or Runnable:</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $foo->db->dbc;</div>
+<div class="line"></div>
+<div class="line"> } elsif(my $db_conn = (ref($foo) eq <span class="stringliteral">'HASH'</span>) ? $foo : <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#af7e04ac99c85db0534b11541b99c96da">url2dbconn_hash</a>( $foo ) ) { # either a hash or a URL that translates into a hash</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a>->new( %$db_conn );</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> unless(ref($foo)) { # maybe it is simply a registry key?</div>
+<div class="line"> my $dba;</div>
+<div class="line"> eval {</div>
+<div class="line"> $schema_type ||= <span class="stringliteral">'hive'</span>;</div>
+<div class="line"> $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($foo, $schema_type);</div>
+<div class="line"> };</div>
+<div class="line"> <span class="keywordflow">if</span>(UNIVERSAL::can($dba, <span class="stringliteral">'dbc'</span>)) {</div>
+<div class="line"> <span class="keywordflow">return</span> $dba->dbc;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> die <span class="stringliteral">"Sorry, could not figure out how to make a DBConnection object out of '$foo'"</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1956b39203f4df86e8d7aac981462ee5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::load_file_or_module </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: This function takes one argument, tries to determine whether it is a module name ('::'-separated)
+ or a path to the module ('/'-separated), finds the module_name and dynamically loads it.</pre><pre> Callers : scripts</pre><pre> </pre><div id="codesection-load_file_or_module" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-load_file_or_module-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-load_file_or_module-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-load_file_or_module-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a1956b39203f4df86e8d7aac981462ee5">load_file_or_module</a> {</div>
+<div class="line"> my $file_or_module = pop @_;</div>
+<div class="line"></div>
+<div class="line"> my $module_name;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $file_or_module=~/^(\w|::)+$/ ) {</div>
+<div class="line"></div>
+<div class="line"> $module_name = $file_or_module;</div>
+<div class="line"></div>
+<div class="line"> } elsif(-r $file_or_module) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $package_line = `grep ^package $file_or_module`) {</div>
+<div class="line"> <span class="keywordflow">if</span>($package_line=~/^\s*package\s+((?:\w|::)+)\s*;/) {</div>
+<div class="line"></div>
+<div class="line"> $module_name = $1;</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"Package line format unrecognized:\n$package_line\n"</span>;</div>
+<div class="line"> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad8abe58a987444c45b366ef5dba4e218">script_usage</a>(1);</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"Could not find the package definition line in '$file_or_module'\n"</span>;</div>
+<div class="line"> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad8abe58a987444c45b366ef5dba4e218">script_usage</a>(1);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"The parameter '$file_or_module' neither seems to be a valid module nor a valid readable file\n"</span>;</div>
+<div class="line"> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad8abe58a987444c45b366ef5dba4e218">script_usage</a>(1);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> eval <span class="stringliteral">"require $module_name;"</span>;</div>
+<div class="line"> die $@ <span class="keywordflow">if</span> ($@);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $module_name;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad08ca8e7270cfe9c94e0865e3cf75862"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::parse_cmdline_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: This function reads all options from command line into a key-value hash
+ (keys must be prefixed with a single or double dash, the following term becomes the value).
+ The rest of the terms go into the list.
+ Command line options are not removed from , so the same or another parser can be run again if needed.</pre><pre> Callers : scripts</pre><pre> </pre><div id="codesection-parse_cmdline_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-parse_cmdline_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-parse_cmdline_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-parse_cmdline_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad08ca8e7270cfe9c94e0865e3cf75862">parse_cmdline_options</a> {</div>
+<div class="line"> my %pairs = ();</div>
+<div class="line"> my @list = ();</div>
+<div class="line"></div>
+<div class="line"> my $temp_key;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $arg (@ARGV) {</div>
+<div class="line"> <span class="keywordflow">if</span>($temp_key) { # only the value, <span class="keyword">get</span> the key from buffer</div>
+<div class="line"> $pairs{$temp_key} = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ac3350cd70c4187290ded88a59533e62d">destringify</a>($arg);</div>
+<div class="line"> $temp_key = <span class="stringliteral">''</span>;</div>
+<div class="line"> } elsif($arg=~/^--?(\w+)=(.+)$/) { # both the key and the value</div>
+<div class="line"> $pairs{$1} = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ac3350cd70c4187290ded88a59533e62d">destringify</a>($2);</div>
+<div class="line"> } elsif($arg=~/^--?(\w+)$/) { # only the key, buffer it and expect the value on the next round</div>
+<div class="line"> $temp_key = $1;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> push @list, $arg;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> (\%pairs, \@list);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae4891d2eb87c70172c9d37b374647144"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::report_versions </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-report_versions" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-report_versions-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-report_versions-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-report_versions-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ae4891d2eb87c70172c9d37b374647144">report_versions</a> {</div>
+<div class="line"> print <span class="stringliteral">"CodeVersion\t"</span>.Bio::EnsEMBL::Hive::Version->get_code_version().<span class="stringliteral">"\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"CompatibleHiveDatabaseSchemaVersion\t"</span>.Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor->get_code_sql_schema_version().<span class="stringliteral">"\n"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad8abe58a987444c45b366ef5dba4e218"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::script_usage </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: This function takes one argument (return value).
+ It attempts to run perldoc on the current script, and if perldoc is not present, emulates its behaviour.
+ Then it exits with the return value given.</pre><pre> Callers : scripts</pre><pre> </pre><div id="codesection-script_usage" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-script_usage-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-script_usage-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-script_usage-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad8abe58a987444c45b366ef5dba4e218">script_usage</a> {</div>
+<div class="line"> my $retvalue = pop @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(`which perldoc`) {</div>
+<div class="line"> system(<span class="stringliteral">'perldoc'</span>, $0);</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $line (<main::DATA>) {</div>
+<div class="line"> <span class="keywordflow">if</span>($line!~s/\=\w+\s?<span class="comment">//) {</span></div>
+<div class="line"> $line = <span class="stringliteral">"\t$line"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> print $line;</div>
+<div class="line"> }</div>
+<div class="line"> <main::DATA>; # <span class="keyword">this</span> is just to stop the <span class="stringliteral">'used once'</span> warnings</div>
+<div class="line"> }</div>
+<div class="line"> exit($retvalue);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a38ef61e77ea6ba6bb1e08c35228cb7c3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::stringify </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description: This function takes in a Perl data structure and stringifies it using specific configuration
+ that allows us to store/recreate this data structure according to our specific storage/communication requirements.</pre><pre> Callers : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a> # stringification of input_id() hash
+ <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> # stringification of parameters() hash</pre><pre> </pre><div id="codesection-stringify" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-stringify-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-stringify-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-stringify-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a38ef61e77ea6ba6bb1e08c35228cb7c3">stringify</a> {</div>
+<div class="line"> my $structure = pop @_;</div>
+<div class="line"></div>
+<div class="line"> local $Data::Dumper::Indent = 0; # we want everything on one line</div>
+<div class="line"> local $Data::Dumper::Terse = 1; # and we want it without dummy variable names</div>
+<div class="line"> local $Data::Dumper::Sortkeys = 1; # make stringification more deterministic</div>
+<div class="line"> local $Data::Dumper::Quotekeys = 1; # conserve some space</div>
+<div class="line"> local $Data::Dumper::Useqq = 1; # escape the \n and \t correctly</div>
+<div class="line"> local $Data::Dumper::Pair = <span class="stringliteral">' => '</span>; # make sure we always produce Perl-parsable structures, no matter what is set externally</div>
+<div class="line"> local $Data::Dumper::Maxdepth = undef; # make sure nobody can mess up stringification by setting a lower Maxdepth</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> Dumper($structure);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af7e04ac99c85db0534b11541b99c96da"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::url2dbconn_hash </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-url2dbconn_hash" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-url2dbconn_hash-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-url2dbconn_hash-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-url2dbconn_hash-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#af7e04ac99c85db0534b11541b99c96da">url2dbconn_hash</a> {</div>
+<div class="line"> my $url = pop @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( my ($driver, $user, $pass, $host, $port, $dbname) =</div>
+<div class="line"> $url =~ m{^(\w*):<span class="comment">//(?:(\w+)(?:\:([^/\@]*))?\@)?(?:([\w\-\.]+)(?:\:(\d+))?)?/(\w*)} ) {</span></div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> <span class="stringliteral">'-driver'</span> => $driver || <span class="stringliteral">'mysql'</span>,</div>
+<div class="line"> <span class="stringliteral">'-host'</span> => $host || <span class="stringliteral">'localhost'</span>,</div>
+<div class="line"> <span class="stringliteral">'-port'</span> => $port || 3306,</div>
+<div class="line"> <span class="stringliteral">'-user'</span> => $user || <span class="stringliteral">''</span>,</div>
+<div class="line"> <span class="stringliteral">'-pass'</span> => $pass || <span class="stringliteral">''</span>,</div>
+<div class="line"> <span class="stringliteral">'-dbname'</span> => $dbname,</div>
+<div class="line"> };</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> <span class="keywordflow">return</span> 0;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_utils_8pm.html">Utils.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html">Utils</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+ [ "load_file_or_module", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a1956b39203f4df86e8d7aac981462ee5", null ],
+ [ "parse_cmdline_options", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad08ca8e7270cfe9c94e0865e3cf75862", null ],
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+ [ "script_usage", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad8abe58a987444c45b366ef5dba4e218", null ],
+ [ "stringify", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a38ef61e77ea6ba6bb1e08c35228cb7c3", null ],
+ [ "url2dbconn_hash", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#af7e04ac99c85db0534b11541b99c96da", null ]
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
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+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
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+ </tr>
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+<!-- end header part -->
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+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
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+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
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+<!-- window showing the filter options -->
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+ name="MSearchResults" id="MSearchResults">
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+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Utils::Config Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Bio::EnsEMBL::Hive::Utils::Config</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#ab0ede51b2658eddc43a8f6e9fbf34509">config_hash</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Bio::EnsEMBL::Hive::Utils::Config</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a2bd177535ba7ff4f0d8990a6c50a1241">default_config_files</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Bio::EnsEMBL::Hive::Utils::Config</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a61b3f0cfb4fb961204ed1be500a6443e">get</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Bio::EnsEMBL::Hive::Utils::Config</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a4d561e831fd88920ca38ba78582a7f93">load_from_json</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Bio::EnsEMBL::Hive::Utils::Config</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a74bd20559c70a83d01236591fc606691">merge</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Bio::EnsEMBL::Hive::Utils::Config</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#ae74fdb113363f2f412a30ce66d1651e3">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Bio::EnsEMBL::Hive::Utils::Config</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a97a169fff464c4653386c08b7df40496">set</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Bio::EnsEMBL::Hive::Utils::Config</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+  <span id="projectnumber">1.9</span>
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+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Utils::Config Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a2bd177535ba7ff4f0d8990a6c50a1241"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a2bd177535ba7ff4f0d8990a6c50a1241">default_config_files</a> ()</td></tr>
+<tr class="separator:a2bd177535ba7ff4f0d8990a6c50a1241"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae74fdb113363f2f412a30ce66d1651e3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#ae74fdb113363f2f412a30ce66d1651e3">new</a> ()</td></tr>
+<tr class="separator:ae74fdb113363f2f412a30ce66d1651e3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab0ede51b2658eddc43a8f6e9fbf34509"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#ab0ede51b2658eddc43a8f6e9fbf34509">config_hash</a> ()</td></tr>
+<tr class="separator:ab0ede51b2658eddc43a8f6e9fbf34509"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4d561e831fd88920ca38ba78582a7f93"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a4d561e831fd88920ca38ba78582a7f93">load_from_json</a> ()</td></tr>
+<tr class="separator:a4d561e831fd88920ca38ba78582a7f93"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a74bd20559c70a83d01236591fc606691"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a74bd20559c70a83d01236591fc606691">merge</a> ()</td></tr>
+<tr class="separator:a74bd20559c70a83d01236591fc606691"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a61b3f0cfb4fb961204ed1be500a6443e"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a61b3f0cfb4fb961204ed1be500a6443e">get</a> ()</td></tr>
+<tr class="separator:a61b3f0cfb4fb961204ed1be500a6443e"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a97a169fff464c4653386c08b7df40496"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a97a169fff464c4653386c08b7df40496">set</a> ()</td></tr>
+<tr class="separator:a97a169fff464c4653386c08b7df40496"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A parser for JSON-based configuration files mainly used in scheduling and graph generation.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ab0ede51b2658eddc43a8f6e9fbf34509"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Config::config_hash </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-config_hash" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-config_hash-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-config_hash-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-config_hash-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#ab0ede51b2658eddc43a8f6e9fbf34509">config_hash</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{_config_hash} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_config_hash};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2bd177535ba7ff4f0d8990a6c50a1241"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Config::default_config_files </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-default_config_files" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_config_files-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_config_files-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_config_files-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a2bd177535ba7ff4f0d8990a6c50a1241">default_config_files</a> { # a <span class="keyword">class </span>method, returns a list</div>
+<div class="line"></div>
+<div class="line"> my $system_config = $ENV{<span class="stringliteral">'EHIVE_ROOT_DIR'</span>}.<span class="stringliteral">'/hive_config.json'</span>;</div>
+<div class="line"> my $user_config = $ENV{<span class="stringliteral">'HOME'</span>}.<span class="stringliteral">'/.hive_config.json'</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ($system_config, (-r $user_config) ? ($user_config) : ());</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a61b3f0cfb4fb961204ed1be500a6443e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Config::get </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">get</span> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $option_name = pop @_;</div>
+<div class="line"></div>
+<div class="line"> my $hash_ptr = $self->config_hash;</div>
+<div class="line"> my $option_value = $hash_ptr->{$option_name}; # not necessatily defined</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $context_syll (@_) {</div>
+<div class="line"> $hash_ptr = $hash_ptr->{$context_syll};</div>
+<div class="line"> <span class="keywordflow">if</span>(exists $hash_ptr->{$option_name}) {</div>
+<div class="line"> $option_value = $hash_ptr->{$option_name};</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $option_value;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4d561e831fd88920ca38ba78582a7f93"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Config::load_from_json </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-load_from_json" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-load_from_json-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-load_from_json-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-load_from_json-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a4d561e831fd88920ca38ba78582a7f93">load_from_json</a> {</div>
+<div class="line"> my ($self, $filename) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(-r $filename) {</div>
+<div class="line"> my $json_text = `cat $filename`;</div>
+<div class="line"> my $json_parser = JSON->new->relaxed;</div>
+<div class="line"> my $perl_hash = $json_parser->decode($json_text);</div>
+<div class="line"> </div>
+<div class="line"> <span class="keywordflow">return</span> $perl_hash;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn <span class="stringliteral">"Can't read from '$filename'"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> undef;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a74bd20559c70a83d01236591fc606691"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Config::merge </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-merge" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-merge-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-merge-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-merge-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a74bd20559c70a83d01236591fc606691">merge</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $from = shift @_;</div>
+<div class="line"> my $to = shift @_ || $self->config_hash; # only defined in subsequent recursion steps</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>(my ($key,$value) = each %$from) {</div>
+<div class="line"> <span class="keywordflow">if</span>(exists $to->{$key} and ref($to->{$key})) {</div>
+<div class="line"> $self->merge($from->{$key}, $to->{$key});</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $to->{$key} = $from->{$key};</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae74fdb113363f2f412a30ce66d1651e3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Config::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = bless {}, $class;</div>
+<div class="line"> $self->config_hash( {} );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $cfg_file ( scalar(@_) ? @_ : $self->default_config_files ) {</div>
+<div class="line"> <span class="keywordflow">if</span>(my $cfg_hash = $self->load_from_json($cfg_file)) {</div>
+<div class="line"> $self->merge($cfg_hash);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a97a169fff464c4653386c08b7df40496"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Config::set </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-set" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-set-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-set-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-set-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub set {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> my $value = pop @_;</div>
+<div class="line"> my $key = pop @_;</div>
+<div class="line"></div>
+<div class="line"> my $hash_ptr = $self->config_hash;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $context_syll (@_) {</div>
+<div class="line"> unless(exists $hash_ptr->{$context_syll}) {</div>
+<div class="line"> $hash_ptr->{$context_syll} = {};</div>
+<div class="line"> }</div>
+<div class="line"> $hash_ptr = $hash_ptr->{$context_syll};</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(ref($hash_ptr->{$key}) ne ref($value)) {</div>
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+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Utils::Graph Class Reference</div> </div>
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+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::Utils::Graph:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_inherit__map" alt="Inheritance graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_inherit__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_inherit__map">
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::Utils::Graph:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_coll__map" alt="Collaboration graph"/></div>
+<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_coll__map">
+<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html" title="Bio::EnsEMBL::Hive\l::Configurable" alt="" coords="5,6,147,47"/></map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a0452e8098246f27173059b14600f190c"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html">Graph</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a0452e8098246f27173059b14600f190c">new</a> ()</td></tr>
+<tr class="separator:a0452e8098246f27173059b14600f190c"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5f9efde876681aea12fc343faae97dab"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">GraphViz</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f9efde876681aea12fc343faae97dab">graph</a> ()</td></tr>
+<tr class="separator:a5f9efde876681aea12fc343faae97dab"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aae6bcf902b62b4a4b698c2ad04165cbe"><td class="memItemLeft" align="right" valign="top">public DBAdaptor </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#aae6bcf902b62b4a4b698c2ad04165cbe">dba</a> ()</td></tr>
+<tr class="separator:aae6bcf902b62b4a4b698c2ad04165cbe"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab6415312e311c5a6fe8d7aa89ba3684a"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a> ()</td></tr>
+<tr class="separator:ab6415312e311c5a6fe8d7aa89ba3684a"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:af860b66fd159323a7c507fa27b2f3794"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#af860b66fd159323a7c507fa27b2f3794">_table_node_name</a> ()</td></tr>
+<tr class="separator:af860b66fd159323a7c507fa27b2f3794"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a546d1e3d214a8c2ba2c25a8d94ac0813"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a546d1e3d214a8c2ba2c25a8d94ac0813">_midpoint_name</a> ()</td></tr>
+<tr class="separator:a546d1e3d214a8c2ba2c25a8d94ac0813"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad7fad3a0d313ae9d07c6b6e636876109"><td class="memItemLeft" align="right" valign="top">public The </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ad7fad3a0d313ae9d07c6b6e636876109">build</a> ()</td></tr>
+<tr class="separator:ad7fad3a0d313ae9d07c6b6e636876109"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a56fbf0b2d2c70f562cb8aaa6c430ee64"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a56fbf0b2d2c70f562cb8aaa6c430ee64">_allocate_to_subgraph</a> ()</td></tr>
+<tr class="separator:a56fbf0b2d2c70f562cb8aaa6c430ee64"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad0284a21114d9ea4bc9569b28b86b3ac"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ad0284a21114d9ea4bc9569b28b86b3ac">_add_hive_details</a> ()</td></tr>
+<tr class="separator:ad0284a21114d9ea4bc9569b28b86b3ac"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a15c083cbf55912f540a1a62c63f36ccd"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a15c083cbf55912f540a1a62c63f36ccd">_add_analysis_node</a> ()</td></tr>
+<tr class="separator:a15c083cbf55912f540a1a62c63f36ccd"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0a4df43f72b40dfdbbd100f957a430c3"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a0a4df43f72b40dfdbbd100f957a430c3">_control_rules</a> ()</td></tr>
+<tr class="separator:a0a4df43f72b40dfdbbd100f957a430c3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:af6624dc439ed366dc32f51716c1de48f"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#af6624dc439ed366dc32f51716c1de48f">_dataflow_rules</a> ()</td></tr>
+<tr class="separator:af6624dc439ed366dc32f51716c1de48f"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a5f15e355d2750a68a1a219ef2decc55a"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f15e355d2750a68a1a219ef2decc55a">_add_table_node</a> ()</td></tr>
+<tr class="separator:a5f15e355d2750a68a1a219ef2decc55a"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td></tr>
+<tr class="memitem:a38c57142acfd31f32e87a94717620baf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">config</a> ()</td></tr>
+<tr class="separator:a38c57142acfd31f32e87a94717620baf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a419025891535ecd7b2f05183cf2ce8e4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">context</a> ()</td></tr>
+<tr class="separator:a419025891535ecd7b2f05183cf2ce8e4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeed405377caddb6a1aa3cb605ed6304f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">config_get</a> ()</td></tr>
+<tr class="separator:aeed405377caddb6a1aa3cb605ed6304f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3e556c76396430193c3f613c6f3e4079 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">config_set</a> ()</td></tr>
+<tr class="separator:a3e556c76396430193c3f613c6f3e4079 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">my $dba = get_hive_dba();</div>
+<div class="line">my $g = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html">Bio::EnsEMBL::Hive::Utils::Graph</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a0452e8098246f27173059b14600f190c">new</a>(-DBA => $dba);</div>
+<div class="line">my $graphviz = $g-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ad7fad3a0d313ae9d07c6b6e636876109">build</a>();</div>
+<div class="line">$graphviz->as_png(<span class="stringliteral">'location.png'</span>);</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is a module for converting a hive database's flow of analyses, control
+ rules and dataflows into the GraphViz model language. This information can
+ then be converted to an image or to the dot language for further manipulation
+ in GraphViz.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a15c083cbf55912f540a1a62c63f36ccd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Utils::Graph::_add_analysis_node </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_add_analysis_node" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_add_analysis_node-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_add_analysis_node-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_add_analysis_node-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a15c083cbf55912f540a1a62c63f36ccd">_add_analysis_node</a> {</div>
+<div class="line"> my ($self, $analysis) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $analysis_stats = $analysis->stats();</div>
+<div class="line"></div>
+<div class="line"> my ($breakout_label, $total_job_count, $count_hash) = $analysis_stats->job_count_breakout();</div>
+<div class="line"> my $analysis_status = $analysis_stats->status;</div>
+<div class="line"> my $analysis_status_colour = $self->config_get(<span class="stringliteral">'Node'</span>, <span class="stringliteral">'AnalysisStatus'</span>, $analysis_status, <span class="stringliteral">'Colour'</span>);</div>
+<div class="line"> my $style = $analysis->can_be_empty() ? <span class="stringliteral">'dashed, filled'</span> : <span class="stringliteral">'filled'</span> ;</div>
+<div class="line"> my $node_fontname = $self->config_get(<span class="stringliteral">'Node'</span>, <span class="stringliteral">'AnalysisStatus'</span>, $analysis_status, <span class="stringliteral">'Font'</span>);</div>
+<div class="line"> my $display_stats = $self->config_get(<span class="stringliteral">'DisplayStats'</span>);</div>
+<div class="line"></div>
+<div class="line"> my $colspan = 0;</div>
+<div class="line"> my $bar_chart = <span class="stringliteral">''</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $display_stats eq <span class="stringliteral">'barchart'</span> ) {</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $count_method (qw(SEMAPHORED READY INPROGRESS DONE FAILED)) {</div>
+<div class="line"> <span class="keywordflow">if</span>(my $count=$count_hash->{lc($count_method).<span class="stringliteral">'_job_count'</span>}) {</div>
+<div class="line"> $bar_chart .= <span class="stringliteral">'<td bgcolor="'</span>.$self->config_get(<span class="stringliteral">'Node'</span>, <span class="stringliteral">'JobStatus'</span>, $count_method, <span class="stringliteral">'Colour'</span>).<span class="stringliteral">'" width="'</span>.int(100*$count/$total_job_count).<span class="stringliteral">'%">'</span>.$count.lc(substr($count_method,0,1)).<span class="stringliteral">'</td>'</span>;</div>
+<div class="line"> ++$colspan;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">if</span>($colspan != 1) {</div>
+<div class="line"> $bar_chart .= <span class="stringliteral">'<td>='</span>.$total_job_count.<span class="stringliteral">'</td>'</span>;</div>
+<div class="line"> ++$colspan;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $colspan ||= 1;</div>
+<div class="line"> my $analysis_label = <span class="stringliteral">'<<table border="0" cellborder="0" cellspacing="0" cellpadding="1"><tr><td colspan="'</span>.$colspan.<span class="stringliteral">'">'</span>.$analysis->logic_name().<span class="stringliteral">' ('</span>.$analysis->dbID().<span class="stringliteral">')</td></tr>'</span>;</div>
+<div class="line"> <span class="keywordflow">if</span>( $display_stats ) {</div>
+<div class="line"> $analysis_label .= qq{<tr><td colspan=<span class="stringliteral">"$colspan"</span>> </td></tr>};</div>
+<div class="line"> <span class="keywordflow">if</span>( $display_stats eq <span class="stringliteral">'barchart'</span>) {</div>
+<div class="line"> $analysis_label .= qq{<tr>$bar_chart</tr>};</div>
+<div class="line"> } elsif( $display_stats eq <span class="stringliteral">'text'</span>) {</div>
+<div class="line"> $analysis_label .= qq{<tr><td colspan=<span class="stringliteral">"$colspan"</span>>$breakout_label</td></tr>};</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( my $job_limit = $self->config_get(<span class="stringliteral">'DisplayJobs'</span>) ) {</div>
+<div class="line"> my $adaptor = $self->dba->get_AnalysisJobAdaptor();</div>
+<div class="line"> my @jobs = sort {$a->dbID <=> $b->dbID} @{ $adaptor->fetch_some_by_analysis_id_limit( $analysis->dbID, $job_limit+1 )};</div>
+<div class="line"></div>
+<div class="line"> my $hit_limit;</div>
+<div class="line"> <span class="keywordflow">if</span>(scalar(@jobs)>$job_limit) {</div>
+<div class="line"> pop @jobs;</div>
+<div class="line"> $hit_limit = 1;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $analysis_label .= <span class="stringliteral">'<tr><td colspan="'</span>.$colspan.<span class="stringliteral">'"> </td></tr>'</span>;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $job (@jobs) {</div>
+<div class="line"> my $input_id = $job->input_id;</div>
+<div class="line"> my $status = $job->status;</div>
+<div class="line"> my $job_id = $job->dbID;</div>
+<div class="line"> $input_id=~s/\>/&gt;/g;</div>
+<div class="line"> $input_id=~s/\</&lt;/g;</div>
+<div class="line"> $input_id=~s/\{|\}<span class="comment">//g;</span></div>
+<div class="line"> $analysis_label .= qq{<tr><td colspan=<span class="stringliteral">"$colspan"</span> bgcolor=<span class="stringliteral">"}.$self->config_get('Node', 'JobStatus', $status, 'Colour').qq{"</span>>$job_id [$status]: $input_id</td></tr>};</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($hit_limit) {</div>
+<div class="line"> $analysis_label .= qq{<tr><td colspan=<span class="stringliteral">"$colspan"</span>>[ and }.($total_job_count-$job_limit).qq{ more ]</td></tr>};</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> $analysis_label .= <span class="stringliteral">'</table>>'</span>;</div>
+<div class="line"> </div>
+<div class="line"> $self->graph->add_node( <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a>( $analysis->dbID() ), </div>
+<div class="line"> label => $analysis_label,</div>
+<div class="line"> shape => <span class="stringliteral">'record'</span>,</div>
+<div class="line"> fontname => $node_fontname,</div>
+<div class="line"> style => $style,</div>
+<div class="line"> fillcolor => $analysis_status_colour,</div>
+<div class="line"> );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad0284a21114d9ea4bc9569b28b86b3ac"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Utils::Graph::_add_hive_details </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_add_hive_details" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_add_hive_details-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_add_hive_details-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_add_hive_details-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ad0284a21114d9ea4bc9569b28b86b3ac">_add_hive_details</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $node_fontname = $self->config_get(<span class="stringliteral">'Node'</span>, <span class="stringliteral">'Details'</span>, <span class="stringliteral">'Font'</span>);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $self->config_get(<span class="stringliteral">'DisplayDetails'</span>) ) {</div>
+<div class="line"> my $dbc = $self->dba()->dbc();</div>
+<div class="line"> my $label = sprintf(<span class="stringliteral">'%s@%s'</span>, $dbc->dbname, $dbc->host || <span class="charliteral">'-'</span>);</div>
+<div class="line"> $self->graph()->add_node( <span class="stringliteral">'Details'</span>,</div>
+<div class="line"> label => $label,</div>
+<div class="line"> fontname => $node_fontname,</div>
+<div class="line"> shape => <span class="stringliteral">'plaintext'</span>,</div>
+<div class="line"> );</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a5f15e355d2750a68a1a219ef2decc55a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Utils::Graph::_add_table_node </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_add_table_node" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_add_table_node-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_add_table_node-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_add_table_node-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f15e355d2750a68a1a219ef2decc55a">_add_table_node</a> {</div>
+<div class="line"> my ($self, $table_node, $table_name) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $node_fontname = $self->config_get(<span class="stringliteral">'Node'</span>, <span class="stringliteral">'Table'</span>, <span class="stringliteral">'Font'</span>);</div>
+<div class="line"> my (@column_names, $columns, $table_data, $data_limit, $hit_limit);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $data_limit = $self->config_get(<span class="stringliteral">'DisplayData'</span>) ) {</div>
+<div class="line"> my $adaptor = $self->dba->get_NakedTableAdaptor();</div>
+<div class="line"> $adaptor->table_name( $table_name );</div>
+<div class="line"></div>
+<div class="line"> @column_names = sort keys %{$adaptor->column_set};</div>
+<div class="line"> $columns = scalar(@column_names);</div>
+<div class="line"> $table_data = $adaptor->fetch_all( <span class="stringliteral">'LIMIT '</span>.($data_limit+1) );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(scalar(@$table_data)>$data_limit) {</div>
+<div class="line"> pop @$table_data;</div>
+<div class="line"> $hit_limit = 1;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $table_label = <span class="stringliteral">'<<table border="0" cellborder="0" cellspacing="0" cellpadding="1"><tr><td colspan="'</span>.($columns||1).<span class="stringliteral">'">'</span>.$table_name.<span class="stringliteral">'</td></tr>'</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $self->config_get(<span class="stringliteral">'DisplayData'</span>) ) {</div>
+<div class="line"> $table_label .= <span class="stringliteral">'<tr><td colspan="'</span>.$columns.<span class="stringliteral">'"> </td></tr>'</span>;</div>
+<div class="line"> $table_label .= <span class="stringliteral">'<tr>'</span>.join(<span class="stringliteral">''</span>, map { qq{<td bgcolor=<span class="stringliteral">"lightblue"</span> border=<span class="stringliteral">"1"</span>>$_</td>} } @column_names).<span class="stringliteral">'</tr>'</span>;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $row (@$table_data) {</div>
+<div class="line"> $table_label .= <span class="stringliteral">'<tr>'</span>.join(<span class="stringliteral">''</span>, map { qq{<td>$_</td>} } @{$row}{@column_names}).<span class="stringliteral">'</tr>'</span>;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">if</span>($hit_limit) {</div>
+<div class="line"> $table_label .= qq{<tr><td colspan=<span class="stringliteral">"$columns"</span>>[ more data ]</td></tr>};</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> $table_label .= <span class="stringliteral">'</table>>'</span>;</div>
+<div class="line"></div>
+<div class="line"> $self->graph()->add_node( $table_node, </div>
+<div class="line"> label => $table_label,</div>
+<div class="line"> shape => <span class="stringliteral">'record'</span>,</div>
+<div class="line"> fontname => $node_fontname,</div>
+<div class="line"> color => $self->config_get(<span class="stringliteral">'Node'</span>, <span class="stringliteral">'Table'</span>, <span class="stringliteral">'Colour'</span>),</div>
+<div class="line"> );</div>
+<div class="line">}</div>
+<div class="line"></div>
+<div class="line">1;</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a56fbf0b2d2c70f562cb8aaa6c430ee64"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Utils::Graph::_allocate_to_subgraph </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_allocate_to_subgraph" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_allocate_to_subgraph-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_allocate_to_subgraph-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_allocate_to_subgraph-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a56fbf0b2d2c70f562cb8aaa6c430ee64">_allocate_to_subgraph</a> {</div>
+<div class="line"> my ($self, $outflow_rules, $dfr_flows_into_node, $source_analysis_node_name, $subgraph_allocation ) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $source_analysis_allocation = $subgraph_allocation->{ $source_analysis_node_name }; # <span class="keywordflow">for</span> some analyses it will be undef</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $rule ( @{ $outflow_rules->{$source_analysis_node_name} } ) {</div>
+<div class="line"> my $target_object = $rule->to_analysis();</div>
+<div class="line"> my $target_node_name;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(UNIVERSAL::isa($target_object, <span class="stringliteral">'Bio::EnsEMBL::Hive::Analysis'</span>)) {</div>
+<div class="line"> $target_node_name = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a>( $rule->to_analysis->dbID() );</div>
+<div class="line"> } elsif(UNIVERSAL::isa($target_object, <span class="stringliteral">'Bio::EnsEMBL::Hive::NakedTable'</span>)) {</div>
+<div class="line"> $target_node_name = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#af860b66fd159323a7c507fa27b2f3794">_table_node_name</a>($target_object->table_name()) . <span class="charliteral">'_'</span> .</div>
+<div class="line"> ($self->config_get(<span class="stringliteral">'DuplicateTables'</span>) ? $rule->from_analysis_id() : ($source_analysis_allocation||<span class="stringliteral">''</span>));</div>
+<div class="line"> } elsif(UNIVERSAL::isa($target_object, <span class="stringliteral">'Bio::EnsEMBL::Hive::Accumulator'</span>)) {</div>
+<div class="line"> next;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn(<span class="stringliteral">'Do not know how to handle the type '</span>.ref($target_object));</div>
+<div class="line"> next;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $proposed_allocation; # will depend on whether we start a <span class="keyword">new</span> semaphore</div>
+<div class="line"> my $funnel_dataflow_rule_id = $rule->funnel_dataflow_rule_id();</div>
+<div class="line"> <span class="keywordflow">if</span>( $funnel_dataflow_rule_id ) {</div>
+<div class="line"> $proposed_allocation =</div>
+<div class="line"><span class="preprocessor"># $dfr_flows_into_node->{$funnel_dataflow_rule_id}; # if we do start a new semaphore, report to the new funnel (based on common funnel's analysis name)</span></div>
+<div class="line"><span class="preprocessor"></span> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a546d1e3d214a8c2ba2c25a8d94ac0813">_midpoint_name</a>( $funnel_dataflow_rule_id ); # <span class="keywordflow">if</span> we <span class="keywordflow">do</span> start a <span class="keyword">new</span> semaphore, report to the <span class="keyword">new</span> funnel (based on common funnel rule<span class="stringliteral">'s midpoint)</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $fan_midpoint_name = _midpoint_name( $rule->dbID() );</span></div>
+<div class="line"><span class="stringliteral"> $subgraph_allocation->{ $fan_midpoint_name } = $proposed_allocation;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $funnel_midpoint_name = _midpoint_name( $funnel_dataflow_rule_id );</span></div>
+<div class="line"><span class="stringliteral"> $subgraph_allocation->{ $funnel_midpoint_name } = $source_analysis_allocation; # draw the funnel'</span>s midpoint outside of the box</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $proposed_allocation = $source_analysis_allocation; # <span class="keywordflow">if</span> we don<span class="stringliteral">'t start a new semaphore, inherit the allocation of the source</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> # we allocate on first-come basis at the moment:</span></div>
+<div class="line"><span class="stringliteral"> if( exists $subgraph_allocation->{ $target_node_name } ) { # already allocated?</span></div>
+<div class="line"><span class="stringliteral"> my $known_allocation = $subgraph_allocation->{ $target_node_name } || '</span><span class="stringliteral">';</span></div>
+<div class="line"><span class="stringliteral"> $proposed_allocation ||= '</span><span class="stringliteral">';</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if( $known_allocation eq $proposed_allocation) {</span></div>
+<div class="line"><span class="stringliteral"> # warn "analysis '</span>$target_node_name<span class="stringliteral">' has already been allocated to the same '</span>$known_allocation<span class="stringliteral">' by another branch";</span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> # warn "analysis '</span>$target_node_name<span class="stringliteral">' has already been allocated to '</span>$known_allocation<span class="stringliteral">' however this branch would allocate it to '</span>$proposed_allocation<span class="stringliteral">'";</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($funnel_dataflow_rule_id) { # correction for multiple entries into the same box (probably needs re-thinking)</span></div>
+<div class="line"><span class="stringliteral"> my $fan_midpoint_name = _midpoint_name( $rule->dbID() );</span></div>
+<div class="line"><span class="stringliteral"> $subgraph_allocation->{ $fan_midpoint_name } = $subgraph_allocation->{ $target_node_name };</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> } else {</span></div>
+<div class="line"><span class="stringliteral"> # warn "allocating analysis '</span>$target_node_name<span class="stringliteral">' to '</span>$proposed_allocation<span class="stringliteral">'";</span></div>
+<div class="line"><span class="stringliteral"> $subgraph_allocation->{ $target_node_name } = $proposed_allocation;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $self->_allocate_to_subgraph( $outflow_rules, $dfr_flows_into_node, $target_node_name, $subgraph_allocation );</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab6415312e311c5a6fe8d7aa89ba3684a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Utils::Graph::_analysis_node_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_analysis_node_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_analysis_node_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_analysis_node_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_analysis_node_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a> {</div>
+<div class="line"> my $analysis_id = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'analysis_'</span> . $analysis_id;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0a4df43f72b40dfdbbd100f957a430c3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Utils::Graph::_control_rules </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_control_rules" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_control_rules-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_control_rules-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_control_rules-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a0a4df43f72b40dfdbbd100f957a430c3">_control_rules</a> {</div>
+<div class="line"> my ($self, $all_ctrl_rules) = @_;</div>
+<div class="line"> </div>
+<div class="line"> my $control_colour = $self->config_get(<span class="stringliteral">'Edge'</span>, <span class="stringliteral">'Control'</span>, <span class="stringliteral">'Colour'</span>);</div>
+<div class="line"> my $graph = $self->graph();</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> #The control rules are always from and to an analysis so no need to search for odd cases here</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">foreach</span> my $rule ( @$all_ctrl_rules ) {</div>
+<div class="line"> my ($from, $to) = ( <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a>( $rule->condition_analysis()->dbID() ), <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a>( $rule->ctrled_analysis()->dbID() ) );</div>
+<div class="line"> $graph->add_edge( $from => $to, </div>
+<div class="line"> color => $control_colour,</div>
+<div class="line"> arrowhead => <span class="stringliteral">'tee'</span>,</div>
+<div class="line"> );</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af6624dc439ed366dc32f51716c1de48f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Utils::Graph::_dataflow_rules </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_dataflow_rules" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_dataflow_rules-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_dataflow_rules-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_dataflow_rules-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#af6624dc439ed366dc32f51716c1de48f">_dataflow_rules</a> {</div>
+<div class="line"> my ($self, $all_dataflow_rules, $subgraph_allocation) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $graph = $self->graph();</div>
+<div class="line"> my $dataflow_colour = $self->config_get(<span class="stringliteral">'Edge'</span>, <span class="stringliteral">'Data'</span>, <span class="stringliteral">'Colour'</span>);</div>
+<div class="line"> my $semablock_colour = $self->config_get(<span class="stringliteral">'Edge'</span>, <span class="stringliteral">'Semablock'</span>, <span class="stringliteral">'Colour'</span>);</div>
+<div class="line"> my $accu_colour = $self->config_get(<span class="stringliteral">'Edge'</span>, <span class="stringliteral">'Accu'</span>, <span class="stringliteral">'Colour'</span>);</div>
+<div class="line"> my $df_edge_fontname = $self->config_get(<span class="stringliteral">'Edge'</span>, <span class="stringliteral">'Data'</span>, <span class="stringliteral">'Font'</span>);</div>
+<div class="line"></div>
+<div class="line"> my %needs_a_midpoint = ();</div>
+<div class="line"> my %aid2aid_nonsem = (); # simply a directed <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f9efde876681aea12fc343faae97dab">graph</a> between numerical analysis_ids, except <span class="keywordflow">for</span> semaphored rules</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $rule ( @$all_dataflow_rules ) {</div>
+<div class="line"> <span class="keywordflow">if</span>(my $to_id = $rule->to_analysis->can(<span class="stringliteral">'dbID'</span>) && $rule->to_analysis->dbID()) {</div>
+<div class="line"> unless( $rule->funnel_dataflow_rule_id ) {</div>
+<div class="line"> $aid2aid_nonsem{$rule->from_analysis_id()}{$to_id}++;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">if</span>(my $funnel_dataflow_rule_id = $rule->funnel_dataflow_rule_id()) {</div>
+<div class="line"> $needs_a_midpoint{$rule->dbID()}++;</div>
+<div class="line"> $needs_a_midpoint{$funnel_dataflow_rule_id}++;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $rule ( @$all_dataflow_rules ) {</div>
+<div class="line"> </div>
+<div class="line"> my ($rule_id, $from_analysis_id, $branch_code, $funnel_dataflow_rule_id, $to) =</div>
+<div class="line"> ($rule->dbID(), $rule->from_analysis_id(), $rule->branch_code(), $rule->funnel_dataflow_rule_id(), $rule->to_analysis());</div>
+<div class="line"> my ($from_node, $to_id, $to_node) = ( <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a>($from_analysis_id) );</div>
+<div class="line"> </div>
+<div class="line"><span class="preprocessor"> # Different treatment for analyses and tables:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>(UNIVERSAL::isa($to, <span class="stringliteral">'Bio::EnsEMBL::Hive::Analysis'</span>)) {</div>
+<div class="line"> $to_id = $to->dbID();</div>
+<div class="line"> $to_node = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a>($to_id);</div>
+<div class="line"> } elsif(UNIVERSAL::isa($to, <span class="stringliteral">'Bio::EnsEMBL::Hive::NakedTable'</span>)) {</div>
+<div class="line"></div>
+<div class="line"> $to_node = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#af860b66fd159323a7c507fa27b2f3794">_table_node_name</a>($to->table_name) . <span class="charliteral">'_'</span> .</div>
+<div class="line"> ( $self->config_get(<span class="stringliteral">'DuplicateTables'</span>) ? $rule->from_analysis_id() : ($subgraph_allocation->{$from_node}||<span class="stringliteral">''</span>));</div>
+<div class="line"></div>
+<div class="line"> $self->_add_table_node($to_node, $to->table_name);</div>
+<div class="line"> } elsif(UNIVERSAL::isa($to, <span class="stringliteral">'Bio::EnsEMBL::Hive::Accumulator'</span>)) {</div>
+<div class="line"> $to_node = $subgraph_allocation->{$from_node};</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> warn(<span class="stringliteral">'Do not know how to handle the type '</span>.ref($to));</div>
+<div class="line"> next;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($needs_a_midpoint{$rule_id}) {</div>
+<div class="line"> my $midpoint_name = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a546d1e3d214a8c2ba2c25a8d94ac0813">_midpoint_name</a>($rule_id);</div>
+<div class="line"></div>
+<div class="line"> $graph->add_node( $midpoint_name, # midpoint itself</div>
+<div class="line"> color => $dataflow_colour,</div>
+<div class="line"> label => <span class="stringliteral">''</span>,</div>
+<div class="line"> shape => <span class="stringliteral">'point'</span>,</div>
+<div class="line"> fixedsize => 1,</div>
+<div class="line"> width => 0.01,</div>
+<div class="line"> height => 0.01,</div>
+<div class="line"> );</div>
+<div class="line"> $graph->add_edge( $from_node => $midpoint_name, # first half of the two-part arrow</div>
+<div class="line"> color => $dataflow_colour,</div>
+<div class="line"> arrowhead => <span class="stringliteral">'none'</span>,</div>
+<div class="line"> fontname => $df_edge_fontname,</div>
+<div class="line"> fontcolor => $dataflow_colour,</div>
+<div class="line"> label => <span class="charliteral">'#'</span>.$branch_code,</div>
+<div class="line"> );</div>
+<div class="line"> $graph->add_edge( $midpoint_name => $to_node, # second half of the two-part arrow</div>
+<div class="line"> color => $dataflow_colour,</div>
+<div class="line"> );</div>
+<div class="line"> <span class="keywordflow">if</span>($funnel_dataflow_rule_id) {</div>
+<div class="line"> $graph->add_edge( $midpoint_name => <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a546d1e3d214a8c2ba2c25a8d94ac0813">_midpoint_name</a>($funnel_dataflow_rule_id), # semaphore inter-rule link</div>
+<div class="line"> color => $semablock_colour,</div>
+<div class="line"> style => <span class="stringliteral">'dashed'</span>,</div>
+<div class="line"> arrowhead => <span class="stringliteral">'tee'</span>,</div>
+<div class="line"> dir => <span class="stringliteral">'both'</span>,</div>
+<div class="line"> arrowtail => <span class="stringliteral">'crow'</span>,</div>
+<div class="line"> );</div>
+<div class="line"> }</div>
+<div class="line"> } elsif(UNIVERSAL::isa($to, <span class="stringliteral">'Bio::EnsEMBL::Hive::Accumulator'</span>)) {</div>
+<div class="line"><span class="preprocessor"> # one-part dashed arrow:</span></div>
+<div class="line"><span class="preprocessor"></span> $graph->add_edge( $from_node => $to_node,</div>
+<div class="line"> color => $accu_colour,</div>
+<div class="line"> style => <span class="stringliteral">'dashed'</span>,</div>
+<div class="line"> label => $to->struct_name().<span class="charliteral">'#'</span>.$branch_code,</div>
+<div class="line"> fontname => $df_edge_fontname,</div>
+<div class="line"> fontcolor => $accu_colour,</div>
+<div class="line"> dir => <span class="stringliteral">'both'</span>,</div>
+<div class="line"> arrowtail => <span class="stringliteral">'crow'</span>,</div>
+<div class="line"> );</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"><span class="preprocessor"> # one-part solid arrow:</span></div>
+<div class="line"><span class="preprocessor"></span> $graph->add_edge( $from_node => $to_node, </div>
+<div class="line"> color => $dataflow_colour,</div>
+<div class="line"> fontname => $df_edge_fontname,</div>
+<div class="line"> fontcolor => $dataflow_colour,</div>
+<div class="line"> label => <span class="charliteral">'#'</span>.$branch_code,</div>
+<div class="line"> );</div>
+<div class="line"> } # /<span class="keywordflow">if</span>($needs_a_midpoint{$rule_id})</div>
+<div class="line"> } # /<span class="keywordflow">foreach</span> my $rule (@$all_dataflow_rules)</div>
+<div class="line"></div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a546d1e3d214a8c2ba2c25a8d94ac0813"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Utils::Graph::_midpoint_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_midpoint_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_midpoint_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_midpoint_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_midpoint_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a546d1e3d214a8c2ba2c25a8d94ac0813">_midpoint_name</a> {</div>
+<div class="line"> my $rule_id = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'dfr_'</span>.$rule_id.<span class="stringliteral">'_mp'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af860b66fd159323a7c507fa27b2f3794"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Utils::Graph::_table_node_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_table_node_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_table_node_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_table_node_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_table_node_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#af860b66fd159323a7c507fa27b2f3794">_table_node_name</a> {</div>
+<div class="line"> my $table_name = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'table_'</span> . $table_name;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad7fad3a0d313ae9d07c6b6e636876109"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public The Bio::EnsEMBL::Hive::Utils::Graph::build </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Returntype : The <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">GraphViz</a> object built & populated
+ Exceptions : Raised if there are issues with accessing the database
+ Description : Builds the graph object and returns it.
+ Status : Beta</pre><pre> </pre><div id="codesection-build" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-build-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-build-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-build-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ad7fad3a0d313ae9d07c6b6e636876109">build</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $all_analyses = $self->dba()->get_AnalysisAdaptor()->fetch_all();</div>
+<div class="line"> my $all_ctrl_rules = $self->dba()->get_AnalysisCtrlRuleAdaptor()->fetch_all();</div>
+<div class="line"> my $all_dataflow_rules = $self->dba()->get_DataflowRuleAdaptor()->fetch_all();</div>
+<div class="line"></div>
+<div class="line"> my %inflow_count = (); # used to detect sources (nodes with zero inflow)</div>
+<div class="line"> my %outflow_rules = (); # maps from anlaysis_node_name to a list of all dataflow rules that flow out of it</div>
+<div class="line"> my %dfr_flows_into_node = (); # maps from dfr_id to target analysis_node_name</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $rule ( @$all_dataflow_rules ) {</div>
+<div class="line"> my $target_object = $rule->to_analysis;</div>
+<div class="line"> <span class="keywordflow">if</span>(my $to_id = $target_object->can(<span class="stringliteral">'dbID'</span>) && $target_object->dbID()) {</div>
+<div class="line"> my $to_node_name = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a>( $to_id );</div>
+<div class="line"> $inflow_count{$to_node_name}++;</div>
+<div class="line"> $dfr_flows_into_node{$rule->dbID()} = $to_node_name;</div>
+<div class="line"> }</div>
+<div class="line"> push @{$outflow_rules{ <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a>($rule->from_analysis_id()) }}, $rule;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my %subgraph_allocation = ();</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # NB: this is a very approximate algorithm with rough edges!</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # It will not find all start nodes in cyclic components!</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">foreach</span> my $source_analysis_node_name ( map { <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a>( $_->dbID ) } @$all_analyses ) {</div>
+<div class="line"> unless($inflow_count{$source_analysis_node_name}) { # <span class="keywordflow">if</span> there is no dataflow into <span class="keyword">this</span> analysis</div>
+<div class="line"> $self->_allocate_to_subgraph(\%outflow_rules, \%dfr_flows_into_node, $source_analysis_node_name, \%subgraph_allocation ); # run the recursion in each component that has a non-cyclic start</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->_add_hive_details();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $a (@$all_analyses) {</div>
+<div class="line"> $self->_add_analysis_node($a);</div>
+<div class="line"> }</div>
+<div class="line"> $self->_control_rules( $all_ctrl_rules );</div>
+<div class="line"> $self->_dataflow_rules( $all_dataflow_rules, \%subgraph_allocation );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->config_get(<span class="stringliteral">'DisplayStretched'</span>) ) {</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # The invisible edges will be linked to the destination analysis instead of the midpoint</span></div>
+<div class="line"><span class="preprocessor"></span> my $id_to_rule = {map { $_->dbID => $_ } @$all_dataflow_rules};</div>
+<div class="line"> my @all_fdr_id = grep {$_} (map {$_->funnel_dataflow_rule_id} @$all_dataflow_rules);</div>
+<div class="line"> my $midpoint_to_analysis = {map { <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a546d1e3d214a8c2ba2c25a8d94ac0813">_midpoint_name</a>( $_ ) => <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">_analysis_node_name</a>( $id_to_rule->{$_}->to_analysis->dbID ) } @all_fdr_id};</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>( my($from, $to) = each %subgraph_allocation) {</div>
+<div class="line"> <span class="keywordflow">if</span>($to && $from=~/^analysis/) {</div>
+<div class="line"> $self->graph->add_edge( $from => $to,</div>
+<div class="line"> color => <span class="stringliteral">'black'</span>,</div>
+<div class="line"> style => <span class="stringliteral">'invis'</span>, # toggle visibility by changing <span class="stringliteral">'invis'</span> to <span class="stringliteral">'dashed'</span></div>
+<div class="line"> );</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->config_get(<span class="stringliteral">'DisplaySemaphoreBoxes'</span>) ) {</div>
+<div class="line"> $self->graph->subgraphs( \%subgraph_allocation );</div>
+<div class="line"> $self->graph->colour_scheme( $self->config_get(<span class="stringliteral">'Box'</span>, <span class="stringliteral">'ColourScheme'</span>) );</div>
+<div class="line"> $self->graph->colour_offset( $self->config_get(<span class="stringliteral">'Box'</span>, <span class="stringliteral">'ColourOffset'</span>) );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->graph();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aae6bcf902b62b4a4b698c2ad04165cbe"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public DBAdaptor Bio::EnsEMBL::Hive::Utils::Graph::dba </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : The DBAdaptor instance
+ Returntype : DBAdaptor
+ Exceptions : If the given object is not a hive DBAdaptor
+ Status : Beta</pre><pre> </pre><div id="codesection-dba" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dba-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dba-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dba-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub dba {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{dba} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{dba};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a5f9efde876681aea12fc343faae97dab"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">GraphViz</a> Bio::EnsEMBL::Hive::Utils::Graph::graph </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : The <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">GraphViz</a> instance created by this module
+ Returntype : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">GraphViz</a>
+ Exceptions : None
+ Status : Beta</pre><pre> </pre><div id="codesection-graph" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-graph-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-graph-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-graph-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f9efde876681aea12fc343faae97dab">graph</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(! exists $self->{<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f9efde876681aea12fc343faae97dab">graph</a>}) {</div>
+<div class="line"> my $padding = $self->config_get(<span class="stringliteral">'Pad'</span>) || 0;</div>
+<div class="line"> $self->{<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f9efde876681aea12fc343faae97dab">graph</a>} = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">Bio::EnsEMBL::Hive::Utils::GraphViz</a>->new( name => <span class="stringliteral">'AnalysisWorkflow'</span>, ratio => qq{compress<span class="stringliteral">"; pad = "</span>$padding} ); # injection hack!</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f9efde876681aea12fc343faae97dab">graph</a>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0452e8098246f27173059b14600f190c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html">Graph</a> Bio::EnsEMBL::Hive::Utils::Graph::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a> $dba;
+ The adaptor to get information from
+ Arg [2] : (optional) string $config_file_name;
+ A JSON file name to initialize the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Config</a> object with.
+ If one is not given then we don't pass anything into <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Config</a>'s constructor,
+ which results in loading configuration from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Config</a>'s standard locations.
+ Returntype : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html">Graph</a> object
+ Exceptions : If the parameters are not as required
+ Status : Beta</pre><pre> </pre><div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my ($class, $dba, $config_file_name) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = bless({}, ref($class) || $class);</div>
+<div class="line"></div>
+<div class="line"> $self->dba($dba);</div>
+<div class="line"> my $config = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Bio::EnsEMBL::Hive::Utils::Config</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#ae74fdb113363f2f412a30ce66d1651e3">new</a>( $config_file_name ? $config_file_name : () );</div>
+<div class="line"> $self->config($config);</div>
+<div class="line"> $self->context( [ <span class="stringliteral">'Graph'</span> ] );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/Utils/<a class="el" href="_graph_8pm.html">Graph.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
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+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
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+ <tbody>
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+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+<div class="title">Bio::EnsEMBL::Hive::Utils::GraphViz Member List</div> </div>
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+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">Bio::EnsEMBL::Hive::Utils::GraphViz</a>, including all inherited members.</p>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a7b1487d4809792cc1322687655f2d984">colour_offset</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">Bio::EnsEMBL::Hive::Utils::GraphViz</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#afe6a7243b9051c98db319ecbcf89d212">colour_scheme</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">Bio::EnsEMBL::Hive::Utils::GraphViz</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#af99b2f612b6d9e52dbbf721c0993c746">display_subgraph</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">Bio::EnsEMBL::Hive::Utils::GraphViz</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a20c82c55eba3cfa7120208fe131a94d1">get_nodes_that_point_at</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">Bio::EnsEMBL::Hive::Utils::GraphViz</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#ac3527fe831ae9d80d246ce20072eb10e">get_top_clusters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">Bio::EnsEMBL::Hive::Utils::GraphViz</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a3b6578d1cc8a3a1922fd92177690e904">subgraphs</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">Bio::EnsEMBL::Hive::Utils::GraphViz</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
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diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html
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+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Utils::GraphViz Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a3b6578d1cc8a3a1922fd92177690e904"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a3b6578d1cc8a3a1922fd92177690e904">subgraphs</a> ()</td></tr>
+<tr class="separator:a3b6578d1cc8a3a1922fd92177690e904"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:afe6a7243b9051c98db319ecbcf89d212"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#afe6a7243b9051c98db319ecbcf89d212">colour_scheme</a> ()</td></tr>
+<tr class="separator:afe6a7243b9051c98db319ecbcf89d212"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7b1487d4809792cc1322687655f2d984"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a7b1487d4809792cc1322687655f2d984">colour_offset</a> ()</td></tr>
+<tr class="separator:a7b1487d4809792cc1322687655f2d984"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac3527fe831ae9d80d246ce20072eb10e"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#ac3527fe831ae9d80d246ce20072eb10e">get_top_clusters</a> ()</td></tr>
+<tr class="separator:ac3527fe831ae9d80d246ce20072eb10e"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a20c82c55eba3cfa7120208fe131a94d1"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a20c82c55eba3cfa7120208fe131a94d1">get_nodes_that_point_at</a> ()</td></tr>
+<tr class="separator:a20c82c55eba3cfa7120208fe131a94d1"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:af99b2f612b6d9e52dbbf721c0993c746"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#af99b2f612b6d9e52dbbf721c0993c746">display_subgraph</a> ()</td></tr>
+<tr class="separator:af99b2f612b6d9e52dbbf721c0993c746"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a65653a19ade3aa317b9a40dac5af679b"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a65653a19ade3aa317b9a40dac5af679b">_as_debug</a> ()</td></tr>
+<tr class="separator:a65653a19ade3aa317b9a40dac5af679b"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ An extension of GraphViz that supports nested clusters
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a65653a19ade3aa317b9a40dac5af679b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Utils::GraphViz::_as_debug </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_as_debug" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_as_debug-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_as_debug-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_as_debug-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a65653a19ade3aa317b9a40dac5af679b">_as_debug</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $text = $self->SUPER::_as_debug;</div>
+<div class="line"></div>
+<div class="line"> $text=~s/^}$<span class="comment">//m;</span></div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $node_name ( @{ $self->get_top_clusters() } ) {</div>
+<div class="line"> $text .= $self->display_subgraph( $node_name, 1);</div>
+<div class="line"> }</div>
+<div class="line"> $text .= <span class="stringliteral">"}\n"</span>;</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7b1487d4809792cc1322687655f2d984"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::GraphViz::colour_offset </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-colour_offset" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-colour_offset-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-colour_offset-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-colour_offset-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a7b1487d4809792cc1322687655f2d984">colour_offset</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{_colour_offset} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_colour_offset};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="afe6a7243b9051c98db319ecbcf89d212"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::GraphViz::colour_scheme </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-colour_scheme" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-colour_scheme-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-colour_scheme-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-colour_scheme-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#afe6a7243b9051c98db319ecbcf89d212">colour_scheme</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{_colour_scheme} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_colour_scheme};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af99b2f612b6d9e52dbbf721c0993c746"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::GraphViz::display_subgraph </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-display_subgraph" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-display_subgraph-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-display_subgraph-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-display_subgraph-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#af99b2f612b6d9e52dbbf721c0993c746">display_subgraph</a> {</div>
+<div class="line"> my ($self, $cluster_name, $depth) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $colour_scheme = $self->colour_scheme();</div>
+<div class="line"> my $colour_offset = $self->colour_offset();</div>
+<div class="line"></div>
+<div class="line"> my $prefix = <span class="stringliteral">"\t"</span> x $depth;</div>
+<div class="line"></div>
+<div class="line"> my $text = <span class="stringliteral">''</span>;</div>
+<div class="line"></div>
+<div class="line"> $text .= $prefix . <span class="stringliteral">"subgraph cluster_${cluster_name} {\n"</span>;</div>
+<div class="line"><span class="preprocessor"># $text .= $prefix . "\tlabel=\"$cluster_name\";\n";</span></div>
+<div class="line"><span class="preprocessor"></span> $text .= $prefix . <span class="stringliteral">"\tcolorscheme=$colour_scheme;\n"</span>;</div>
+<div class="line"> $text .= $prefix . <span class="stringliteral">"\tstyle=filled;\n"</span>;</div>
+<div class="line"> $text .= $prefix . <span class="stringliteral">"\tcolor="</span>.($depth+$colour_offset).<span class="stringliteral">";\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $node_name ( @{ $self->get_nodes_that_point_at( $cluster_name ) } ) {</div>
+<div class="line"></div>
+<div class="line"> $text .= $prefix . <span class="stringliteral">"\t${node_name};\n"</span>;</div>
+<div class="line"> <span class="keywordflow">if</span>( @{ $self->get_nodes_that_point_at( $node_name ) } ) {</div>
+<div class="line"> $text .= $self->display_subgraph( $node_name, $depth+1 );</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> $text .= $prefix . <span class="stringliteral">"}\n"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $text;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a20c82c55eba3cfa7120208fe131a94d1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::GraphViz::get_nodes_that_point_at </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_nodes_that_point_at" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_nodes_that_point_at-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_nodes_that_point_at-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_nodes_that_point_at-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a20c82c55eba3cfa7120208fe131a94d1">get_nodes_that_point_at</a> {</div>
+<div class="line"> my ($self, $node) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $subgraphs = $self->subgraphs();</div>
+<div class="line"> my %set = ();</div>
+<div class="line"> <span class="keywordflow">while</span>( my ($key,$value) = each %$subgraphs) {</div>
+<div class="line"> <span class="keywordflow">if</span>($value and ($value eq $node)) {</div>
+<div class="line"> $set{$key}++;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> [ keys %set ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac3527fe831ae9d80d246ce20072eb10e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::GraphViz::get_top_clusters </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_top_clusters" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_top_clusters-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_top_clusters-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_top_clusters-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#ac3527fe831ae9d80d246ce20072eb10e">get_top_clusters</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $subgraphs = $self->subgraphs();</div>
+<div class="line"></div>
+<div class="line"> my %set = ();</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $potential_top_cluster (values %$subgraphs) {</div>
+<div class="line"> <span class="keywordflow">if</span>( $potential_top_cluster and !$subgraphs->{ $potential_top_cluster } ) { # <span class="keywordflow">if</span> it<span class="stringliteral">'s a valid node not mentioned in the keys, it is a top cluster</span></div>
+<div class="line"><span class="stringliteral"> $set{$potential_top_cluster}++;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> return [ keys %set ];</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3b6578d1cc8a3a1922fd92177690e904"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::GraphViz::subgraphs </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-subgraphs" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-subgraphs-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-subgraphs-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-subgraphs-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a3b6578d1cc8a3a1922fd92177690e904">subgraphs</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{_subgraphs} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_subgraphs};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/Utils/<a class="el" href="_graph_viz_8pm.html">GraphViz.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
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+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
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+var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz =
+[
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+ [ "colour_scheme", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#afe6a7243b9051c98db319ecbcf89d212", null ],
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+ [ "get_nodes_that_point_at", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a20c82c55eba3cfa7120208fe131a94d1", null ],
+ [ "get_top_clusters", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#ac3527fe831ae9d80d246ce20072eb10e", null ],
+ [ "subgraphs", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a3b6578d1cc8a3a1922fd92177690e904", null ]
+];
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+<title>ensembl-hive: Member List</title>
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+<div class="title">Bio::EnsEMBL::Hive::Utils::RedirectStack Member List</div> </div>
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+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html
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+ <td style="padding-left: 0.5em;">
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+  <span id="projectnumber">1.9</span>
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+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Utils::RedirectStack Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a11b71d1d7802b7c52d23f49b8dab377c"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#a11b71d1d7802b7c52d23f49b8dab377c">new</a> ()</td></tr>
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+<tr class="separator:a1f475d12cf96160a963d47c370618856"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Sometimes there is a need to intercept STDOUT/STDERR and log it in multiple files,
+ depending on which of the nested objects is "in control" at the moment.
+
+ In Hive when a Worker is running a job it logs into a job's file, but between jobs it logs into its own file.
+ This class implements a convenient stack of proxy file descriptors that lets you log STDOUT or STDERR in various files.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a11b71d1d7802b7c52d23f49b8dab377c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::RedirectStack::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my ($class, $fh) = @_;</div>
+<div class="line"></div>
+<div class="line"> die <span class="stringliteral">"Please supply filehandle to be redirected as the only argument"</span> unless $fh;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> bless {</div>
+<div class="line"> <span class="stringliteral">'_fh'</span> => $fh,</div>
+<div class="line"> <span class="stringliteral">'_sp'</span> => 0,</div>
+<div class="line"> <span class="stringliteral">'_handle_stack'</span> => [],</div>
+<div class="line"> }, $class;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1f475d12cf96160a963d47c370618856"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::RedirectStack::pop </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-pop" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pop-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pop-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pop-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#a1f475d12cf96160a963d47c370618856">pop</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->{_handle_stack}[$self->{_sp}]) {</div>
+<div class="line"> close $self->{_handle_stack}[$self->{_sp}];</div>
+<div class="line"> <span class="keyword">delete</span> $self->{_handle_stack}[$self->{_sp}];</div>
+<div class="line"> }</div>
+<div class="line"> close $self->{_fh};</div>
+<div class="line"> open $self->{_fh}, <span class="stringliteral">'>&'</span>, $self->{_handle_stack}[--$self->{_sp}];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af152aba8ac48eb58a0a7e1901eb8d94b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::RedirectStack::push </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-push" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-push-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-push-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-push-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#af152aba8ac48eb58a0a7e1901eb8d94b">push</a> {</div>
+<div class="line"> my ($self, $filename) = @_;</div>
+<div class="line"></div>
+<div class="line"> die <span class="stringliteral">"Please supply filename to be redirected into as the only argument"</span> unless $filename;</div>
+<div class="line"></div>
+<div class="line"> unless($self->{_handle_stack}[$self->{_sp}]) {</div>
+<div class="line"> open $self->{_handle_stack}[$self->{_sp}], <span class="stringliteral">'>&'</span>, $self->{_fh};</div>
+<div class="line"> }</div>
+<div class="line"> close $self->{_fh};</div>
+<div class="line"> open $self->{_fh}, <span class="charliteral">'>'</span>, $filename;</div>
+<div class="line"> ++$self->{_sp};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/Utils/<a class="el" href="_redirect_stack_8pm.html">RedirectStack.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html">Utils</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html">RedirectStack</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+ [ "new", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#a11b71d1d7802b7c52d23f49b8dab377c", null ],
+ [ "pop", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#a1f475d12cf96160a963d47c370618856", null ],
+ [ "push", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#af152aba8ac48eb58a0a7e1901eb8d94b", null ]
+];
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
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+ </tr>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
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+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+<div class="title">Bio::EnsEMBL::Hive::Utils::Stopwatch Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a278a474770becadc0c47562beb111e4f">_unit</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a243a5222c2176291094dd9d83b51b7c3">accumulated</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#ad91a33ccd3234b64b19bc3083e9367f0">continue</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#ad933938ea83c78477a8580d500fdec94">get_elapsed</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a27af7e8ae932532af50bfee75b08d2f3">is_counting</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a1cbc5b3e6c40f0a5862e55e228dc34a3">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a17462e9ef3668063b549484e293c7f24">pause</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a233743ce015c7df93ad06562fe3b35dd">restart</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
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+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
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+ <li class="footer">Generated by
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+  <span id="projectnumber">1.9</span>
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+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Utils::Stopwatch Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a1cbc5b3e6c40f0a5862e55e228dc34a3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a1cbc5b3e6c40f0a5862e55e228dc34a3">new</a> ()</td></tr>
+<tr class="separator:a1cbc5b3e6c40f0a5862e55e228dc34a3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a278a474770becadc0c47562beb111e4f"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a278a474770becadc0c47562beb111e4f">_unit</a> ()</td></tr>
+<tr class="separator:a278a474770becadc0c47562beb111e4f"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a27af7e8ae932532af50bfee75b08d2f3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a27af7e8ae932532af50bfee75b08d2f3">is_counting</a> ()</td></tr>
+<tr class="separator:a27af7e8ae932532af50bfee75b08d2f3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a243a5222c2176291094dd9d83b51b7c3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a243a5222c2176291094dd9d83b51b7c3">accumulated</a> ()</td></tr>
+<tr class="separator:a243a5222c2176291094dd9d83b51b7c3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad91a33ccd3234b64b19bc3083e9367f0"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#ad91a33ccd3234b64b19bc3083e9367f0">continue</a> ()</td></tr>
+<tr class="separator:ad91a33ccd3234b64b19bc3083e9367f0"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a233743ce015c7df93ad06562fe3b35dd"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a233743ce015c7df93ad06562fe3b35dd">restart</a> ()</td></tr>
+<tr class="separator:a233743ce015c7df93ad06562fe3b35dd"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ad933938ea83c78477a8580d500fdec94"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#ad933938ea83c78477a8580d500fdec94">get_elapsed</a> ()</td></tr>
+<tr class="separator:ad933938ea83c78477a8580d500fdec94"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a17462e9ef3668063b549484e293c7f24"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a17462e9ef3668063b549484e293c7f24">pause</a> ()</td></tr>
+<tr class="separator:a17462e9ef3668063b549484e293c7f24"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">my $total_stopwatch = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a1cbc5b3e6c40f0a5862e55e228dc34a3">new</a>()->restart;</div>
+<div class="line">my $fetching_stopwatch = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a1cbc5b3e6c40f0a5862e55e228dc34a3">new</a>();</div>
+<div class="line">my $running_stopwatch = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a1cbc5b3e6c40f0a5862e55e228dc34a3">new</a>();</div>
+<div class="line"></div>
+<div class="line">$fetching_stopwatch->continue();</div>
+<div class="line">$runnable->fetch_input();</div>
+<div class="line">$fetching_stopwatch->pause();</div>
+<div class="line"></div>
+<div class="line">$running_stopwatch->continue();</div>
+<div class="line">$runnable->run();</div>
+<div class="line">$running_stopwatch->pause();</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"># ...</span></div>
+<div class="line"><span class="preprocessor"></span></div>
+<div class="line">my $only_fetches = $fetching_stopwatch->get_elapsed; # probably stopped</div>
+<div class="line">my $total_time_elapsed = $total_stopwatch->get_elapsed; # running through</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is a standalone object used to time various events in the Hive.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a278a474770becadc0c47562beb111e4f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Bio::EnsEMBL::Hive::Utils::Stopwatch::_unit </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_unit" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_unit-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_unit-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_unit-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a278a474770becadc0c47562beb111e4f">_unit</a> { # only set it once <span class="keywordflow">for each</span> timer to avoid messing everything up</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_unit'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_unit'</span>} || $default_unit;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a243a5222c2176291094dd9d83b51b7c3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Stopwatch::accumulated </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-accumulated" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-accumulated-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-accumulated-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-accumulated-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a243a5222c2176291094dd9d83b51b7c3">accumulated</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_accumulated'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_accumulated'</span>} || 0;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad91a33ccd3234b64b19bc3083e9367f0"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Stopwatch::continue </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-continue" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-continue-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-continue-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-continue-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keywordflow">continue</span> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> unless($self->is_counting) { # ignore <span class="keywordflow">if</span> it was already running</div>
+<div class="line"> $self->is_counting(1);</div>
+<div class="line"> $self->{<span class="stringliteral">'_start'</span>} = time() * $self->_unit</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ad933938ea83c78477a8580d500fdec94"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Stopwatch::get_elapsed </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_elapsed" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_elapsed-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_elapsed-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_elapsed-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#ad933938ea83c78477a8580d500fdec94">get_elapsed</a> { # peek without stopping (in <span class="keywordflow">case</span> it was running)</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ($self->accumulated + $self->is_counting * (time() * $self->_unit - $self->{<span class="stringliteral">'_start'</span>}));</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a27af7e8ae932532af50bfee75b08d2f3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Stopwatch::is_counting </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-is_counting" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-is_counting-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-is_counting-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-is_counting-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a27af7e8ae932532af50bfee75b08d2f3">is_counting</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_is_counting'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_is_counting'</span>} || 0;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1cbc5b3e6c40f0a5862e55e228dc34a3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Stopwatch::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = bless {}, $class;</div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a17462e9ef3668063b549484e293c7f24"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Stopwatch::pause </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-pause" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pause-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pause-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pause-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a17462e9ef3668063b549484e293c7f24">pause</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $self->accumulated( $self->get_elapsed );</div>
+<div class="line"> $self->is_counting(0);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a233743ce015c7df93ad06562fe3b35dd"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::Stopwatch::restart </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-restart" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-restart-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-restart-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-restart-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a233743ce015c7df93ad06562fe3b35dd">restart</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $self->accumulated(0);</div>
+<div class="line"> $self->continue;</div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/Utils/<a class="el" href="_stopwatch_8pm.html">Stopwatch.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html">Utils</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Stopwatch</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<div class="title">Bio::EnsEMBL::Hive::Utils::URL Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l.html">Bio::EnsEMBL::Hive::Utils::URL</a>, including all inherited members.</p>
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+
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+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Utils::URL Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:ac80cc911eba215fb0ed17104861fe5f7"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l.html#ac80cc911eba215fb0ed17104861fe5f7">parse</a> ()</td></tr>
+<tr class="separator:ac80cc911eba215fb0ed17104861fe5f7"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A Hive-specific URL parser.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ac80cc911eba215fb0ed17104861fe5f7"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Utils::URL::parse </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-parse" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-parse-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-parse-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-parse-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l.html#ac80cc911eba215fb0ed17104861fe5f7">parse</a> {</div>
+<div class="line"> my $url = shift @_ or <span class="keywordflow">return</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( my ($dbconn_part, $driver, $user, $pass, $host, $port, $dbname, $table_name, $tparam_name, $tparam_value, $conn_param_string) =</div>
+<div class="line"> $url =~ m{^((\w*):<span class="comment">//(?:(\w+)(?:\:([^/\@]*))?\@)?(?:([\w\-\.]+)(?:\:(\d*))?)?/([\w\-]*))(?:/(\w+)(?:\?(\w+)=([\w\[\]\{\}]+))?)?((?:;(\w+)=(\w+))*)$} ) {</span></div>
+<div class="line"></div>
+<div class="line"> my %conn_params = split(/[;=]/, <span class="stringliteral">'type=hive;discon=0'</span>.$conn_param_string );</div>
+<div class="line"></div>
+<div class="line"> my $parsed_url = {</div>
+<div class="line"> <span class="stringliteral">'dbconn_part'</span> => $dbconn_part,</div>
+<div class="line"> <span class="stringliteral">'driver'</span> => $driver,</div>
+<div class="line"> <span class="stringliteral">'user'</span> => $user,</div>
+<div class="line"> <span class="stringliteral">'pass'</span> => $pass,</div>
+<div class="line"> <span class="stringliteral">'host'</span> => $host,</div>
+<div class="line"> <span class="stringliteral">'port'</span> => $port,</div>
+<div class="line"> <span class="stringliteral">'dbname'</span> => $dbname,</div>
+<div class="line"> <span class="stringliteral">'table_name'</span> => $table_name,</div>
+<div class="line"> <span class="stringliteral">'tparam_name'</span> => $tparam_name,</div>
+<div class="line"> <span class="stringliteral">'tparam_value'</span> => $tparam_value,</div>
+<div class="line"> <span class="stringliteral">'conn_params'</span> => \%conn_params,</div>
+<div class="line"> };</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $parsed_url;</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span>;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/Utils/<a class="el" href="_u_r_l_8pm.html">URL.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html">Utils</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l.html">URL</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+<div class="title">Bio::EnsEMBL::Hive::Valley Member List</div> </div>
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+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html">Bio::EnsEMBL::Hive::Valley</a>, including all inherited members.</p>
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+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">config</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">config_get</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td><td class="entry"></td></tr>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#ae5d7a34a10c8f72107156a73d348b54f">find_available_meadow_responsible_for_worker</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html">Bio::EnsEMBL::Hive::Valley</a></td><td class="entry"></td></tr>
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+<div class="header">
+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Valley Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::Valley:</div>
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+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::Valley:</div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a63cab22c63e3c5aa31191ec02f0a6bf1"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a63cab22c63e3c5aa31191ec02f0a6bf1">meadow_class_path</a> ()</td></tr>
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+<tr class="separator:a51140e4714459dccef65cb34d97bfe13"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a3d03fc09525b8349ab06bff8e387686e"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a77f0a0b7a8de56d43c0271065bef6ebe"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a77f0a0b7a8de56d43c0271065bef6ebe">get_available_meadow_list</a> ()</td></tr>
+<tr class="separator:a77f0a0b7a8de56d43c0271065bef6ebe"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:af85407f558029e59470a282e82c4f8ad"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#af85407f558029e59470a282e82c4f8ad">set_default_meadow_type</a> ()</td></tr>
+<tr class="separator:af85407f558029e59470a282e82c4f8ad"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a80eeade51960beb35d31f35cf61f4c79"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a80eeade51960beb35d31f35cf61f4c79">get_default_meadow</a> ()</td></tr>
+<tr class="separator:a80eeade51960beb35d31f35cf61f4c79"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae5d7a34a10c8f72107156a73d348b54f"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#ae5d7a34a10c8f72107156a73d348b54f">find_available_meadow_responsible_for_worker</a> ()</td></tr>
+<tr class="separator:ae5d7a34a10c8f72107156a73d348b54f"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a626d8f4a721513ef5d4e6b2172226719"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a626d8f4a721513ef5d4e6b2172226719">whereami</a> ()</td></tr>
+<tr class="separator:a626d8f4a721513ef5d4e6b2172226719"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aee959b792ccd1f79a3edb5e0f53cd38b"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#aee959b792ccd1f79a3edb5e0f53cd38b">get_pending_worker_counts_by_meadow_type_rc_name</a> ()</td></tr>
+<tr class="separator:aee959b792ccd1f79a3edb5e0f53cd38b"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a04d1116b668a322e92ad5c916cffe4b9"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a04d1116b668a322e92ad5c916cffe4b9">get_meadow_capacity_hash_by_meadow_type</a> ()</td></tr>
+<tr class="separator:a04d1116b668a322e92ad5c916cffe4b9"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7e7eed865f3ba9395495adf304668843"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a7e7eed865f3ba9395495adf304668843">count_running_workers</a> ()</td></tr>
+<tr class="separator:a7e7eed865f3ba9395495adf304668843"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Bio::EnsEMBL::Hive::Configurable</a></td></tr>
+<tr class="memitem:a38c57142acfd31f32e87a94717620baf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">config</a> ()</td></tr>
+<tr class="separator:a38c57142acfd31f32e87a94717620baf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a419025891535ecd7b2f05183cf2ce8e4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">context</a> ()</td></tr>
+<tr class="separator:a419025891535ecd7b2f05183cf2ce8e4 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aeed405377caddb6a1aa3cb605ed6304f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">config_get</a> ()</td></tr>
+<tr class="separator:aeed405377caddb6a1aa3cb605ed6304f inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3e556c76396430193c3f613c6f3e4079 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">config_set</a> ()</td></tr>
+<tr class="separator:a3e556c76396430193c3f613c6f3e4079 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ A Valley represents a collection of available Meadows.
+
+ Certain methods fit better with the concept of Valley -
+ such as identifying all dead workers, or killing a particular one given worker_id.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a3d03fc09525b8349ab06bff8e387686e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Valley::available_meadow_hash </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-available_meadow_hash" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-available_meadow_hash-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-available_meadow_hash-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-available_meadow_hash-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a3d03fc09525b8349ab06bff8e387686e">available_meadow_hash</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{_available_meadow_hash} = shift @_;</div>
+<div class="line"> } </div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_available_meadow_hash};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7e7eed865f3ba9395495adf304668843"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Valley::count_running_workers </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-count_running_workers" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-count_running_workers-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-count_running_workers-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-count_running_workers-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a7e7eed865f3ba9395495adf304668843">count_running_workers</a> { # just an aggregator</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $valley_running_workers = 0;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $meadow (@{ $self->get_available_meadow_list }) {</div>
+<div class="line"> $valley_running_workers += $meadow->count_running_workers;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $valley_running_workers;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae5d7a34a10c8f72107156a73d348b54f"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Valley::find_available_meadow_responsible_for_worker </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-find_available_meadow_responsible_for_worker" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-find_available_meadow_responsible_for_worker-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-find_available_meadow_responsible_for_worker-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-find_available_meadow_responsible_for_worker-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#ae5d7a34a10c8f72107156a73d348b54f">find_available_meadow_responsible_for_worker</a> {</div>
+<div class="line"> my ($self, $worker) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( my $meadow = $self->available_meadow_hash->{$worker->meadow_type} ) {</div>
+<div class="line"> <span class="keywordflow">if</span>($meadow->name eq $worker->meadow_name) {</div>
+<div class="line"> <span class="keywordflow">return</span> $meadow;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> undef;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a77f0a0b7a8de56d43c0271065bef6ebe"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Valley::get_available_meadow_list </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_available_meadow_list" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_available_meadow_list-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_available_meadow_list-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_available_meadow_list-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a77f0a0b7a8de56d43c0271065bef6ebe">get_available_meadow_list</a> { # <span class="keyword">this</span> beautiful one-liner pushes $local to the bottom of the list</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $local = $self->meadow_class_path . <span class="stringliteral">'::LOCAL'</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> [ sort { (ref($a) eq $local) or -(ref($b) eq $local) } values %{ $self->available_meadow_hash } ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a80eeade51960beb35d31f35cf61f4c79"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Valley::get_default_meadow </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_default_meadow" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_default_meadow-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_default_meadow-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_default_meadow-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a80eeade51960beb35d31f35cf61f4c79">get_default_meadow</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_default_meadow};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a04d1116b668a322e92ad5c916cffe4b9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Valley::get_meadow_capacity_hash_by_meadow_type </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_meadow_capacity_hash_by_meadow_type" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_meadow_capacity_hash_by_meadow_type-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_meadow_capacity_hash_by_meadow_type-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_meadow_capacity_hash_by_meadow_type-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a04d1116b668a322e92ad5c916cffe4b9">get_meadow_capacity_hash_by_meadow_type</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my %meadow_capacity_hash = ();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $meadow (@{ $self->get_available_meadow_list }) {</div>
+<div class="line"></div>
+<div class="line"> my $available_worker_slots = defined($meadow->config_get(<span class="stringliteral">'TotalRunningWorkersMax'</span>))</div>
+<div class="line"> ? $meadow->config_get(<span class="stringliteral">'TotalRunningWorkersMax'</span>) - $meadow->count_running_workers</div>
+<div class="line"> : undef;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # so the hash will contain limiters for every meadow_type, but not all of them active:</span></div>
+<div class="line"><span class="preprocessor"></span> $meadow_capacity_hash{ $meadow->type } = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a89203ff40a85e13c7ef840a46dcf4487">new</a>( <span class="stringliteral">"Number of workers in '"</span>.$meadow->signature.<span class="stringliteral">"' meadow"</span>, $available_worker_slots );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> \%meadow_capacity_hash;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aee959b792ccd1f79a3edb5e0f53cd38b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Valley::get_pending_worker_counts_by_meadow_type_rc_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_pending_worker_counts_by_meadow_type_rc_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_pending_worker_counts_by_meadow_type_rc_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_pending_worker_counts_by_meadow_type_rc_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_pending_worker_counts_by_meadow_type_rc_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#aee959b792ccd1f79a3edb5e0f53cd38b">get_pending_worker_counts_by_meadow_type_rc_name</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my %pending_counts = ();</div>
+<div class="line"> my $total_pending_all_meadows = 0;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">foreach</span> my $meadow (@{ $self->get_available_meadow_list }) {</div>
+<div class="line"> my ($pending_this_meadow_by_rc_name, $total_pending_this_meadow) = ($meadow->count_pending_workers_by_rc_name());</div>
+<div class="line"> $pending_counts{ $meadow->type } = $pending_this_meadow_by_rc_name;</div>
+<div class="line"> $total_pending_all_meadows += $total_pending_this_meadow;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> (\%pending_counts, $total_pending_all_meadows);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a63cab22c63e3c5aa31191ec02f0a6bf1"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Valley::meadow_class_path </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-meadow_class_path" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-meadow_class_path-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-meadow_class_path-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-meadow_class_path-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a63cab22c63e3c5aa31191ec02f0a6bf1">meadow_class_path</a> {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">'Bio::EnsEMBL::Hive::Meadow'</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a51140e4714459dccef65cb34d97bfe13"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Valley::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my ($class, $config, $default_meadow_type, $pipeline_name) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = bless {}, $class;</div>
+<div class="line"></div>
+<div class="line"> $self->config( $config );</div>
+<div class="line"> $self->context( [ <span class="stringliteral">'Valley'</span> ] );</div>
+<div class="line"></div>
+<div class="line"> my $amh = $self->available_meadow_hash( {} );</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # make sure modules are loaded and available ones are checked prior to setting the current one</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">foreach</span> my $meadow_class (@{ find_submodules( $self->meadow_class_path ) }) {</div>
+<div class="line"> eval <span class="stringliteral">"require $meadow_class"</span>;</div>
+<div class="line"> <span class="keywordflow">if</span>($meadow_class->name) {</div>
+<div class="line"> my $meadow_object = $meadow_class->new( $config );</div>
+<div class="line"></div>
+<div class="line"> $meadow_object->pipeline_name( $pipeline_name ) <span class="keywordflow">if</span>($pipeline_name);</div>
+<div class="line"></div>
+<div class="line"> $amh->{$meadow_class->type} = $meadow_object;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->set_default_meadow_type($default_meadow_type); # run <span class="keyword">this</span> method even <span class="keywordflow">if</span> $default_meadow_type was not specified</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="af85407f558029e59470a282e82c4f8ad"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Valley::set_default_meadow_type </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-set_default_meadow_type" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-set_default_meadow_type-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-set_default_meadow_type-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-set_default_meadow_type-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#af85407f558029e59470a282e82c4f8ad">set_default_meadow_type</a> {</div>
+<div class="line"> my ($self, $default_meadow_type) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($default_meadow_type) {</div>
+<div class="line"> <span class="keywordflow">if</span>( my $default_meadow = $self->available_meadow_hash->{$default_meadow_type} ) { # store <span class="keywordflow">if</span> available</div>
+<div class="line"> $self->{_default_meadow} = $default_meadow;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> die <span class="stringliteral">"Meadow '$default_meadow_type' does not seem to be available on this machine, please investigate"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $self->{_default_meadow} = $self->get_available_meadow_list->[0]; # take the first from preference list</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a626d8f4a721513ef5d4e6b2172226719"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Valley::whereami </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-whereami" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-whereami-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-whereami-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-whereami-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a626d8f4a721513ef5d4e6b2172226719">whereami</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my ($meadow_type, $meadow_name, $pid);</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $meadow (@{ $self->get_available_meadow_list }) {</div>
+<div class="line"> eval {</div>
+<div class="line"> $pid = $meadow->get_current_worker_process_id();</div>
+<div class="line"> $meadow_type = $meadow->type();</div>
+<div class="line"> $meadow_name = $meadow->name();</div>
+<div class="line"> };</div>
+<div class="line"> unless($@) {</div>
+<div class="line"> last;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> unless($pid) {</div>
+<div class="line"> die <span class="stringliteral">"Could not determine the Meadow, please investigate"</span>;</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $exechost = hostname();</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> ($meadow_type, $meadow_name, $pid, $exechost);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_valley_8pm.html">Valley.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html">Valley</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+ [ "meadow_class_path", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a63cab22c63e3c5aa31191ec02f0a6bf1", null ],
+ [ "new", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a51140e4714459dccef65cb34d97bfe13", null ],
+ [ "set_default_meadow_type", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#af85407f558029e59470a282e82c4f8ad", null ],
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
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+<body>
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
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+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
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+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Version Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_version.html">Bio::EnsEMBL::Hive::Version</a>, including all inherited members.</p>
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+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
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diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_version.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_version.html
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+<title>ensembl-hive: Bio::EnsEMBL::Hive::Version Class Reference</title>
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+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_version-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Version Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a8ec4c346c160d25cab629a0c56af720b"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_version.html#a8ec4c346c160d25cab629a0c56af720b">get_code_version</a> ()</td></tr>
+<tr class="separator:a8ec4c346c160d25cab629a0c56af720b"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">use <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_version.html">Bio::EnsEMBL::Hive::Version</a> 2.0;</div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Version number of the Hive code.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a8ec4c346c160d25cab629a0c56af720b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Version::get_code_version </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_code_version" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_code_version-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_code_version-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_code_version-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_version.html#a8ec4c346c160d25cab629a0c56af720b">get_code_version</a> {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $VERSION;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_version_8pm.html">Version.pm</a></li>
+</ul>
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+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+<title>ensembl-hive: Member List</title>
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
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+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
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+ <li><a href="annotated.html"><span>Class List</span></a></li>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
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+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+<!-- iframe showing the search results (closed by default) -->
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+<div class="title">Bio::EnsEMBL::Hive::Worker Member List</div> </div>
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+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a>, including all inherited members.</p>
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+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a0904a2e1b64e956c6400d8344eb6fc71">born</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a0c047d0bd965ee20025093fa837ee897">can_respecialize</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3c525fb34ae49638bf9898949f995388">cause_of_death</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a274245e911fc8e5f0ef621993c96732a">debug</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abd46b21982209917b8fbace6d01ac0a5">died</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a13e1e3b2aa2905efe3f7dfef55019d2c">enter_status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#acc3848e02dd266ca7c193257ec036701">execute_writes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a6b49c7779e183bd1e314bc76354cd569">get_stderr_redirector</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aa4629bbbaa4103888c05c5936ae2823e">get_stdout_redirector</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3bf4200e3a8a6603db7ef6a544df3356">host</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a85d390e244fcd69c62f4544d8b384e44">init</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a83d25a571d54e205e8707f27f3277b2c">job_limiter</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a23a37f5e84b64bdeb435f726e20255fc">last_check_in</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a83d94917e06cca7e9f59aa999bec0c45">life_span</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#affdf64209cfb2b62895ced6e678206a9">life_span_limit_reached</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a529d571f05adaa243ced017ee4c51fd2">lifespan_stopwatch</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a2ddf6136f8b9cb3fca032b2ba6f152ff">log_dir</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a21077df2d82c57eda4845c9ea1d153d0">meadow_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abf98a83eafeb602f3109fb147f9a2c19">meadow_type</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a54f5f9c0d65d4e71c50fd1fdf3e702cc">more_work_done</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ac85bb24d028f6a102654f3fdbadf4c74">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a23b1369583a49f99f47d654993775113">perform_cleanup</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab71a53273f57e143655703eaee5bfdc5">prev_job_error</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a631e3067f5825bf38d981150fac0512d">process_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aec650e3731644a420c7a2be8597e0250">resource_class_id</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a03e3c2ca474c831a1700dbfdfb424fb6">retry_throwing_jobs</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab6456d819b72b807884df4b49ea30492">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a7fe639feb3731120a1a66663e8c2a2e8">run_one_batch</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a4bc0dde1eb43909e1e8f8a87fd0a3257">runnable_object</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab6470f448766be332f7e4d081e6d7cc2">special_batch</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ae432e7a7dbc6a8b0109353d4f6938d9c">specialize_and_compile_wrapper</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aac9ba54b8924088ef41717fab6240ef4">start_job_output_redirection</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a814f0afa7c9b155777e5267a4b4fa145">status</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#acb9fec0fad8f289eed242f5b1fe7e284">stop_job_output_redirection</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ac8931e351f68c7b4c927c9a400f595c3">toString</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ae34a70dcbfd02a12e20b1285adcbad1b">work_done</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a91724c25ce62bea58013fd483aad3abe">worker_say</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Bio::EnsEMBL::Hive::Worker</a></td><td class="entry"></td></tr>
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diff --git a/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html b/docs/doxygen/class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html
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+  <span id="projectnumber">1.9</span>
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+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Bio::EnsEMBL::Hive::Worker Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for Bio::EnsEMBL::Hive::Worker:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
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+</map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for Bio::EnsEMBL::Hive::Worker:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
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+</map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:ac85bb24d028f6a102654f3fdbadf4c74"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ac85bb24d028f6a102654f3fdbadf4c74">new</a> ()</td></tr>
+<tr class="separator:ac85bb24d028f6a102654f3fdbadf4c74"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a85d390e244fcd69c62f4544d8b384e44"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a85d390e244fcd69c62f4544d8b384e44">init</a> ()</td></tr>
+<tr class="separator:a85d390e244fcd69c62f4544d8b384e44"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aa7b8e54f437a9427f268c91ed61626e5"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aa7b8e54f437a9427f268c91ed61626e5">analysis_id</a> ()</td></tr>
+<tr class="separator:aa7b8e54f437a9427f268c91ed61626e5"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abf98a83eafeb602f3109fb147f9a2c19"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abf98a83eafeb602f3109fb147f9a2c19">meadow_type</a> ()</td></tr>
+<tr class="separator:abf98a83eafeb602f3109fb147f9a2c19"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a21077df2d82c57eda4845c9ea1d153d0"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3bf4200e3a8a6603db7ef6a544df3356"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3bf4200e3a8a6603db7ef6a544df3356">host</a> ()</td></tr>
+<tr class="separator:a3bf4200e3a8a6603db7ef6a544df3356"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a631e3067f5825bf38d981150fac0512d"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a631e3067f5825bf38d981150fac0512d">process_id</a> ()</td></tr>
+<tr class="separator:a631e3067f5825bf38d981150fac0512d"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aec650e3731644a420c7a2be8597e0250"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aec650e3731644a420c7a2be8597e0250">resource_class_id</a> ()</td></tr>
+<tr class="separator:aec650e3731644a420c7a2be8597e0250"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae34a70dcbfd02a12e20b1285adcbad1b"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ae34a70dcbfd02a12e20b1285adcbad1b">work_done</a> ()</td></tr>
+<tr class="separator:ae34a70dcbfd02a12e20b1285adcbad1b"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a814f0afa7c9b155777e5267a4b4fa145"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a814f0afa7c9b155777e5267a4b4fa145">status</a> ()</td></tr>
+<tr class="separator:a814f0afa7c9b155777e5267a4b4fa145"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0904a2e1b64e956c6400d8344eb6fc71"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a0904a2e1b64e956c6400d8344eb6fc71">born</a> ()</td></tr>
+<tr class="separator:a0904a2e1b64e956c6400d8344eb6fc71"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23a37f5e84b64bdeb435f726e20255fc"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a23a37f5e84b64bdeb435f726e20255fc">last_check_in</a> ()</td></tr>
+<tr class="separator:a23a37f5e84b64bdeb435f726e20255fc"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:abd46b21982209917b8fbace6d01ac0a5"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abd46b21982209917b8fbace6d01ac0a5">died</a> ()</td></tr>
+<tr class="separator:abd46b21982209917b8fbace6d01ac0a5"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3c525fb34ae49638bf9898949f995388"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3c525fb34ae49638bf9898949f995388">cause_of_death</a> ()</td></tr>
+<tr class="separator:a3c525fb34ae49638bf9898949f995388"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a2ddf6136f8b9cb3fca032b2ba6f152ff"><td class="memItemLeft" align="right" valign="top">public String </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a2ddf6136f8b9cb3fca032b2ba6f152ff">log_dir</a> ()</td></tr>
+<tr class="separator:a2ddf6136f8b9cb3fca032b2ba6f152ff"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a274245e911fc8e5f0ef621993c96732a"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a274245e911fc8e5f0ef621993c96732a">debug</a> ()</td></tr>
+<tr class="separator:a274245e911fc8e5f0ef621993c96732a"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:acc3848e02dd266ca7c193257ec036701"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#acc3848e02dd266ca7c193257ec036701">execute_writes</a> ()</td></tr>
+<tr class="separator:acc3848e02dd266ca7c193257ec036701"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab6470f448766be332f7e4d081e6d7cc2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab6470f448766be332f7e4d081e6d7cc2">special_batch</a> ()</td></tr>
+<tr class="separator:ab6470f448766be332f7e4d081e6d7cc2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a23b1369583a49f99f47d654993775113"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a23b1369583a49f99f47d654993775113">perform_cleanup</a> ()</td></tr>
+<tr class="separator:a23b1369583a49f99f47d654993775113"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a03e3c2ca474c831a1700dbfdfb424fb6"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a03e3c2ca474c831a1700dbfdfb424fb6">retry_throwing_jobs</a> ()</td></tr>
+<tr class="separator:a03e3c2ca474c831a1700dbfdfb424fb6"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a0c047d0bd965ee20025093fa837ee897"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a0c047d0bd965ee20025093fa837ee897">can_respecialize</a> ()</td></tr>
+<tr class="separator:a0c047d0bd965ee20025093fa837ee897"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a9447a3ac1aa3c45822c8d495c405785e"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a9447a3ac1aa3c45822c8d495c405785e">analysis</a> ()</td></tr>
+<tr class="separator:a9447a3ac1aa3c45822c8d495c405785e"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a83d94917e06cca7e9f59aa999bec0c45"><td class="memItemLeft" align="right" valign="top">public Int </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a83d94917e06cca7e9f59aa999bec0c45">life_span</a> ()</td></tr>
+<tr class="separator:a83d94917e06cca7e9f59aa999bec0c45"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a529d571f05adaa243ced017ee4c51fd2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a529d571f05adaa243ced017ee4c51fd2">lifespan_stopwatch</a> ()</td></tr>
+<tr class="separator:a529d571f05adaa243ced017ee4c51fd2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:affdf64209cfb2b62895ced6e678206a9"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#affdf64209cfb2b62895ced6e678206a9">life_span_limit_reached</a> ()</td></tr>
+<tr class="separator:affdf64209cfb2b62895ced6e678206a9"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a83d25a571d54e205e8707f27f3277b2c"><td class="memItemLeft" align="right" valign="top">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Hive::Limiter</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a83d25a571d54e205e8707f27f3277b2c">job_limiter</a> ()</td></tr>
+<tr class="separator:a83d25a571d54e205e8707f27f3277b2c"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a54f5f9c0d65d4e71c50fd1fdf3e702cc"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a54f5f9c0d65d4e71c50fd1fdf3e702cc">more_work_done</a> ()</td></tr>
+<tr class="separator:a54f5f9c0d65d4e71c50fd1fdf3e702cc"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab71a53273f57e143655703eaee5bfdc5"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab71a53273f57e143655703eaee5bfdc5">prev_job_error</a> ()</td></tr>
+<tr class="separator:ab71a53273f57e143655703eaee5bfdc5"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a4bc0dde1eb43909e1e8f8a87fd0a3257"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a4bc0dde1eb43909e1e8f8a87fd0a3257">runnable_object</a> ()</td></tr>
+<tr class="separator:a4bc0dde1eb43909e1e8f8a87fd0a3257"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aa4629bbbaa4103888c05c5936ae2823e"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aa4629bbbaa4103888c05c5936ae2823e">get_stdout_redirector</a> ()</td></tr>
+<tr class="separator:aa4629bbbaa4103888c05c5936ae2823e"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a6b49c7779e183bd1e314bc76354cd569"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a6b49c7779e183bd1e314bc76354cd569">get_stderr_redirector</a> ()</td></tr>
+<tr class="separator:a6b49c7779e183bd1e314bc76354cd569"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a91724c25ce62bea58013fd483aad3abe"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a91724c25ce62bea58013fd483aad3abe">worker_say</a> ()</td></tr>
+<tr class="separator:a91724c25ce62bea58013fd483aad3abe"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac8931e351f68c7b4c927c9a400f595c3"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ac8931e351f68c7b4c927c9a400f595c3">toString</a> ()</td></tr>
+<tr class="separator:ac8931e351f68c7b4c927c9a400f595c3"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab6456d819b72b807884df4b49ea30492"><td class="memItemLeft" align="right" valign="top">public void </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab6456d819b72b807884df4b49ea30492">run</a> ()</td></tr>
+<tr class="separator:ab6456d819b72b807884df4b49ea30492"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ae432e7a7dbc6a8b0109353d4f6938d9c"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ae432e7a7dbc6a8b0109353d4f6938d9c">specialize_and_compile_wrapper</a> ()</td></tr>
+<tr class="separator:ae432e7a7dbc6a8b0109353d4f6938d9c"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a7fe639feb3731120a1a66663e8c2a2e8"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a7fe639feb3731120a1a66663e8c2a2e8">run_one_batch</a> ()</td></tr>
+<tr class="separator:a7fe639feb3731120a1a66663e8c2a2e8"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a13e1e3b2aa2905efe3f7dfef55019d2c"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a13e1e3b2aa2905efe3f7dfef55019d2c">enter_status</a> ()</td></tr>
+<tr class="separator:a13e1e3b2aa2905efe3f7dfef55019d2c"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aac9ba54b8924088ef41717fab6240ef4"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aac9ba54b8924088ef41717fab6240ef4">start_job_output_redirection</a> ()</td></tr>
+<tr class="separator:aac9ba54b8924088ef41717fab6240ef4"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:acb9fec0fad8f289eed242f5b1fe7e284"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#acb9fec0fad8f289eed242f5b1fe7e284">stop_job_output_redirection</a> ()</td></tr>
+<tr class="separator:acb9fec0fad8f289eed242f5b1fe7e284"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ Object which encapsulates the details of how to find jobs, how to run those
+ jobs, and then check the rules to create the next jobs in the chain.
+ Essentially knows where to find data, how to process data, and where to
+ put it when it is done (put in next persons INBOX) so the next Worker
+ in the chain can find data to work on.
+
+ Hive based processing is a concept based on a more controlled version
+ of an autonomous agent type system. Each worker is not told what to do
+ (like a centralized control system - like the current pipeline system)
+ but rather queries a central database for jobs (give me jobs).
+
+ Each worker is linked to an analysis_id, registers its self on creation
+ into the Hive, creates a RunnableDB instance of the Analysis->module,
+ gets relevant configuration information from the database, does its
+ work, creates the next layer of job entries by interfacing to
+ the DataflowRuleAdaptor to determine the analyses it needs to pass its
+ output data to and creates jobs on the database of the next analysis.
+ It repeats this cycle until it has lived its lifetime or until there are no
+ more jobs left to process.
+ The lifetime limit is a safety limit to prevent these from 'infecting'
+ a system and sitting on a compute node for longer than is socially exceptable.
+ This is primarily needed on compute resources like an LSF system where jobs
+ are not preempted and run until they are done.
+
+ The Queens primary job is to create Workers to get the work down.
+ As part of this, she is also responsible for summarizing the status of the
+ analyses by querying the jobs, summarizing, and updating the
+ analysis_stats table. From this she is also responsible for monitoring and
+ 'unblocking' analyses via the analysis_ctrl_rules.
+ The Queen is also responsible for freeing up jobs that were claimed by Workers
+ that died unexpectantly so that other workers can take over the work.
+
+ The Beekeeper is in charge of interfacing between the Queen and a compute resource
+ or 'compute farm'. Its job is to query Queens if they need any workers and to
+ send the requested number of workers to open machines via the runWorker.pl script.
+ It is also responsible for interfacing with the Queen to identify workers which died
+ unexpectantly so that she can free the dead workers unfinished jobs.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a9447a3ac1aa3c45822c8d495c405785e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> Bio::EnsEMBL::Hive::Worker::analysis </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : (optional) <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> $value
+ Title : analysis
+ Usage : $analysis = $self->analysis;
+ $self->analysis($analysis);
+ Description: Get/Set analysis object of this <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Worker</a>
+ DefaultValue : undef
+ Returntype : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Bio::EnsEMBL::Hive::Analysis</a> object</pre><pre> </pre><div id="codesection-analysis" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-analysis-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-analysis-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-analysis-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a9447a3ac1aa3c45822c8d495c405785e">analysis</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) { # setter mode</div>
+<div class="line"> $self->{<span class="stringliteral">'_analysis'</span>} = shift @_;</div>
+<div class="line"> } elsif(! $self->{<span class="stringliteral">'_analysis'</span>} ) {</div>
+<div class="line"> <span class="keywordflow">if</span>(my $analysis_id = $self->analysis_id()) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_analysis'</span>} = $self->adaptor->db->get_AnalysisAdaptor->fetch_by_dbID( $analysis_id )</div>
+<div class="line"> or die <span class="stringliteral">"Could not fetch analysis for analysis_id=$analysis_id"</span>;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> die <span class="stringliteral">"analysis_id not defined, could not fetch Hive::Analysis object"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_analysis'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa7b8e54f437a9427f268c91ed61626e5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::analysis_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-analysis_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-analysis_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-analysis_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-analysis_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aa7b8e54f437a9427f268c91ed61626e5">analysis_id</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_analysis_id'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_analysis_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0904a2e1b64e956c6400d8344eb6fc71"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::born </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-born" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-born-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-born-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-born-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a0904a2e1b64e956c6400d8344eb6fc71">born</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_born'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_born'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a0c047d0bd965ee20025093fa837ee897"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::can_respecialize </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-can_respecialize" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-can_respecialize-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-can_respecialize-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-can_respecialize-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a0c047d0bd965ee20025093fa837ee897">can_respecialize</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_can_respecialize'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_can_respecialize'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3c525fb34ae49638bf9898949f995388"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::cause_of_death </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-cause_of_death" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-cause_of_death-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-cause_of_death-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-cause_of_death-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3c525fb34ae49638bf9898949f995388">cause_of_death</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_cause_of_death'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_cause_of_death'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a274245e911fc8e5f0ef621993c96732a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::debug </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-debug" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-debug-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-debug-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-debug-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a274245e911fc8e5f0ef621993c96732a">debug</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_debug'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_debug'</span>}=0 unless(defined($self->{<span class="stringliteral">'_debug'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_debug'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="abd46b21982209917b8fbace6d01ac0a5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::died </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-died" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-died-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-died-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-died-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abd46b21982209917b8fbace6d01ac0a5">died</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_died'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_died'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a13e1e3b2aa2905efe3f7dfef55019d2c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::enter_status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-enter_status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-enter_status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-enter_status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-enter_status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a13e1e3b2aa2905efe3f7dfef55019d2c">enter_status</a> {</div>
+<div class="line"> my ($self, $status, $msg) = @_;</div>
+<div class="line"></div>
+<div class="line"> $msg ||= <span class="stringliteral">": $status"</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->debug) {</div>
+<div class="line"> $self->worker_say( $msg );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> $self->status( $status );</div>
+<div class="line"> $self->adaptor->check_in_worker( $self );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="acc3848e02dd266ca7c193257ec036701"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::execute_writes </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-execute_writes" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-execute_writes-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-execute_writes-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-execute_writes-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#acc3848e02dd266ca7c193257ec036701">execute_writes</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_execute_writes'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_execute_writes'</span>}=1 unless(defined($self->{<span class="stringliteral">'_execute_writes'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_execute_writes'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a6b49c7779e183bd1e314bc76354cd569"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::get_stderr_redirector </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_stderr_redirector" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_stderr_redirector-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_stderr_redirector-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_stderr_redirector-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a6b49c7779e183bd1e314bc76354cd569">get_stderr_redirector</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_stderr_redirector} ||= <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html">Bio::EnsEMBL::Hive::Utils::RedirectStack</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#a11b71d1d7802b7c52d23f49b8dab377c">new</a>(\*STDERR);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aa4629bbbaa4103888c05c5936ae2823e"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::get_stdout_redirector </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-get_stdout_redirector" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-get_stdout_redirector-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-get_stdout_redirector-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-get_stdout_redirector-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aa4629bbbaa4103888c05c5936ae2823e">get_stdout_redirector</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self->{_stdout_redirector} ||= <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html">Bio::EnsEMBL::Hive::Utils::RedirectStack</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#a11b71d1d7802b7c52d23f49b8dab377c">new</a>(\*STDOUT);</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3bf4200e3a8a6603db7ef6a544df3356"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::host </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-host" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-host-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-host-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-host-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3bf4200e3a8a6603db7ef6a544df3356">host</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_host'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_host'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a85d390e244fcd69c62f4544d8b384e44"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::init </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-init" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-init-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-init-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-init-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a85d390e244fcd69c62f4544d8b384e44">init</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"></div>
+<div class="line"> my $lifespan_stopwatch = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a1cbc5b3e6c40f0a5862e55e228dc34a3">new</a>();</div>
+<div class="line"> $lifespan_stopwatch->_unit(1); # count in seconds (<span class="keywordflow">default</span> is milliseconds)</div>
+<div class="line"> $lifespan_stopwatch->restart;</div>
+<div class="line"> $self->lifespan_stopwatch( $lifespan_stopwatch );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a83d25a571d54e205e8707f27f3277b2c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Hive::Limiter</a> Bio::EnsEMBL::Hive::Worker::job_limiter </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : job_limiter
+ Arg [1] : (optional) integer $value
+ Usage : $limiter_obj = $self->job_limiter;
+ $self->job_limiter($new_value);
+ Description: The maximum number of jobs to be done by the <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Worker</a> can be limited by the given number.
+ A worker 'dies' when either the 'life_span' or 'job_limit' is exceeded.
+ DefaultValue : undef (relies on life_span to limit life of worker)
+ Returntype : <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Hive::Limiter</a> object</pre><pre> </pre><div id="codesection-job_limiter" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-job_limiter-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-job_limiter-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-job_limiter-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a83d25a571d54e205e8707f27f3277b2c">job_limiter</a> {</div>
+<div class="line"> my $self=shift;</div>
+<div class="line"> <span class="keywordflow">if</span>( scalar(@_) or !defined($self->{<span class="stringliteral">'_job_limiter'</span>}) ) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_job_limiter'</span>} = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Bio::EnsEMBL::Hive::Limiter</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a89203ff40a85e13c7ef840a46dcf4487">new</a>(<span class="stringliteral">"Total number of jobs this Worker is allowed to take"</span>, shift @_);</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_job_limiter'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a23a37f5e84b64bdeb435f726e20255fc"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::last_check_in </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-last_check_in" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-last_check_in-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-last_check_in-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-last_check_in-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a23a37f5e84b64bdeb435f726e20255fc">last_check_in</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_last_check_in'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_last_check_in'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a83d94917e06cca7e9f59aa999bec0c45"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Int Bio::EnsEMBL::Hive::Worker::life_span </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : (optional) integer $value (in seconds)
+ Title : life_span
+ Usage : $value = $self->life_span;
+ $self->life_span($new_value);
+ Description: Defines the maximum time a worker can live for. Workers are always
+ allowed to complete the jobs they get, but whether they can
+ do multiple rounds of work is limited by their life_span
+ DefaultValue : 3600 (60 minutes)
+ Returntype : integer scalar</pre><pre> </pre><div id="codesection-life_span" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-life_span-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-life_span-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-life_span-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a83d94917e06cca7e9f59aa999bec0c45">life_span</a> { # <span class="keywordflow">default</span> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a83d94917e06cca7e9f59aa999bec0c45">life_span</a> = 60minutes</div>
+<div class="line"> my ($self, $value) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(defined($value)) { # you can still set it to 0 and avoid having the limit on lifespan</div>
+<div class="line"> $self->{<span class="stringliteral">'_life_span'</span>} = $value;</div>
+<div class="line"> } elsif(!defined($self->{<span class="stringliteral">'_life_span'</span>})) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_life_span'</span>} = 60*60;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_life_span'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="affdf64209cfb2b62895ced6e678206a9"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::life_span_limit_reached </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-life_span_limit_reached" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-life_span_limit_reached-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-life_span_limit_reached-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-life_span_limit_reached-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#affdf64209cfb2b62895ced6e678206a9">life_span_limit_reached</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $self->life_span() ) {</div>
+<div class="line"> my $alive_for_secs = $self->lifespan_stopwatch->get_elapsed;</div>
+<div class="line"> <span class="keywordflow">if</span>($alive_for_secs > $self->life_span() ) {</div>
+<div class="line"> <span class="keywordflow">return</span> $alive_for_secs;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> 0;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a529d571f05adaa243ced017ee4c51fd2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::lifespan_stopwatch </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-lifespan_stopwatch" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-lifespan_stopwatch-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-lifespan_stopwatch-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-lifespan_stopwatch-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a529d571f05adaa243ced017ee4c51fd2">lifespan_stopwatch</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(@_) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_lifespan_stopwatch'</span>} = shift @_;</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_lifespan_stopwatch'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a2ddf6136f8b9cb3fca032b2ba6f152ff"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public String Bio::EnsEMBL::Hive::Worker::log_dir </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Arg [1] : (optional) string directory path
+ Title : log_dir
+ Usage : $worker_log_dir = $self->log_dir;
+ $self->log_dir($worker_log_dir);
+ Description: Storable getter/setter attribute for the directory where STDOUT and STRERR of the worker will be redirected to.
+ In this directory each job will have its own .out and .err files.
+ Returntype : string</pre><pre> </pre><div id="codesection-log_dir" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-log_dir-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-log_dir-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-log_dir-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a2ddf6136f8b9cb3fca032b2ba6f152ff">log_dir</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_log_dir'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_log_dir'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a21077df2d82c57eda4845c9ea1d153d0"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::meadow_name </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-meadow_name" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-meadow_name-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-meadow_name-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-meadow_name-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a21077df2d82c57eda4845c9ea1d153d0">meadow_name</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_meadow_name'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_meadow_name'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="abf98a83eafeb602f3109fb147f9a2c19"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::meadow_type </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-meadow_type" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-meadow_type-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-meadow_type-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-meadow_type-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abf98a83eafeb602f3109fb147f9a2c19">meadow_type</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_meadow_type'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_meadow_type'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a54f5f9c0d65d4e71c50fd1fdf3e702cc"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::more_work_done </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-more_work_done" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-more_work_done-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-more_work_done-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-more_work_done-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a54f5f9c0d65d4e71c50fd1fdf3e702cc">more_work_done</a> {</div>
+<div class="line"> my ($self, $job_partial_timing) = @_;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_work_done'</span>}++;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span>( my ($state, $partial_timing_in_state) = each %$job_partial_timing ) {</div>
+<div class="line"> $self->{<span class="stringliteral">'_interval_partial_timing'</span>}{$state} += $partial_timing_in_state;</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac85bb24d028f6a102654f3fdbadf4c74"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::new </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-new" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-new-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-new-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-new-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <span class="keyword">new</span> {</div>
+<div class="line"> my $class = shift @_;</div>
+<div class="line"></div>
+<div class="line"> my $self = $class->SUPER::new( @_ ); # deal with Storable stuff</div>
+<div class="line"></div>
+<div class="line"> my($analysis_id, $meadow_type, $meadow_name, $host, $process_id, $resource_class_id, $work_done, $status, $born, $last_check_in, $died, $cause_of_death, $log_dir) =</div>
+<div class="line"> rearrange([qw(<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aa7b8e54f437a9427f268c91ed61626e5">analysis_id</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abf98a83eafeb602f3109fb147f9a2c19">meadow_type</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a21077df2d82c57eda4845c9ea1d153d0">meadow_name</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3bf4200e3a8a6603db7ef6a544df3356">host</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a631e3067f5825bf38d981150fac0512d">process_id</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aec650e3731644a420c7a2be8597e0250">resource_class_id</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ae34a70dcbfd02a12e20b1285adcbad1b">work_done</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a814f0afa7c9b155777e5267a4b4fa145">status</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a0904a2e1b64e956c6400d8344eb6fc71">born</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a23a37f5e84b64bdeb435f726e20255fc">last_check_in</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abd46b21982209917b8fbace6d01ac0a5">died</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3c525fb34ae49638bf9898949f995388">cause_of_death</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a2ddf6136f8b9cb3fca032b2ba6f152ff">log_dir</a>) ], @_);</div>
+<div class="line"></div>
+<div class="line"> $self->analysis_id($analysis_id) <span class="keywordflow">if</span>(defined($analysis_id));</div>
+<div class="line"> $self->meadow_type($meadow_type) <span class="keywordflow">if</span>(defined($meadow_type));</div>
+<div class="line"> $self->meadow_name($meadow_name) <span class="keywordflow">if</span>(defined($meadow_name));</div>
+<div class="line"> $self->host($host) <span class="keywordflow">if</span>(defined($host));</div>
+<div class="line"> $self->process_id($process_id) <span class="keywordflow">if</span>(defined($process_id));</div>
+<div class="line"> $self->resource_class_id($resource_class_id) <span class="keywordflow">if</span>(defined($resource_class_id));</div>
+<div class="line"> $self->work_done($work_done) <span class="keywordflow">if</span>(defined($work_done));</div>
+<div class="line"> $self->status($status) <span class="keywordflow">if</span>(defined($status));</div>
+<div class="line"> $self->born($born) <span class="keywordflow">if</span>(defined($born));</div>
+<div class="line"> $self->last_check_in($last_check_in) <span class="keywordflow">if</span>(defined($last_check_in));</div>
+<div class="line"> $self->died($died) <span class="keywordflow">if</span>(defined($died));</div>
+<div class="line"> $self->cause_of_death($cause_of_death) <span class="keywordflow">if</span>(defined($cause_of_death));</div>
+<div class="line"> $self->log_dir($log_dir) <span class="keywordflow">if</span>(defined($log_dir));</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $self;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a23b1369583a49f99f47d654993775113"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::perform_cleanup </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-perform_cleanup" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-perform_cleanup-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-perform_cleanup-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-perform_cleanup-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a23b1369583a49f99f47d654993775113">perform_cleanup</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_perform_cleanup'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> $self->{<span class="stringliteral">'_perform_cleanup'</span>} = 1 unless(defined($self->{<span class="stringliteral">'_perform_cleanup'</span>}));</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_perform_cleanup'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab71a53273f57e143655703eaee5bfdc5"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::prev_job_error </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-prev_job_error" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-prev_job_error-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-prev_job_error-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-prev_job_error-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab71a53273f57e143655703eaee5bfdc5">prev_job_error</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_prev_job_error'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_prev_job_error'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a631e3067f5825bf38d981150fac0512d"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::process_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-process_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-process_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-process_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-process_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a631e3067f5825bf38d981150fac0512d">process_id</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_process_id'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_process_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aec650e3731644a420c7a2be8597e0250"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::resource_class_id </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-resource_class_id" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-resource_class_id-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-resource_class_id-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-resource_class_id-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aec650e3731644a420c7a2be8597e0250">resource_class_id</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_resource_class_id'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_resource_class_id'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a03e3c2ca474c831a1700dbfdfb424fb6"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::retry_throwing_jobs </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-retry_throwing_jobs" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-retry_throwing_jobs-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-retry_throwing_jobs-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-retry_throwing_jobs-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a03e3c2ca474c831a1700dbfdfb424fb6">retry_throwing_jobs</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_retry_throwing_jobs'</span>} = shift @_ <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> defined($self->{<span class="stringliteral">'_retry_throwing_jobs'</span>}) ? $self->{<span class="stringliteral">'_retry_throwing_jobs'</span>} : 1;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab6456d819b72b807884df4b49ea30492"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public void Bio::EnsEMBL::Hive::Worker::run </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Title : run
+ Usage : $worker->run;
+ Description:
+ This is a self looping autonomous function to process jobs.
+ First all STDOUT/STDERR is rediected, then looping commences.
+ Looping consists of
+ 1) claiming jobs,
+ 2) processing those jobs through an instance of the 'module class' of
+ the analysis asigned to this worker,
+ 3) updating the job, analysis_stats, and hive tables to track the
+ progress of the job, the analysis and this worker.
+ Looping stops when any one of these are met:
+ 1) there is no more jobs to process
+ 2) job_limit is reached
+ 3) life_span has been reached.
+ Returntype : none</pre><pre> </pre><div id="codesection-run" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab6456d819b72b807884df4b49ea30492">run</a> {</div>
+<div class="line"> my ($self, $specialization_arglist) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( my $worker_log_dir = $self->log_dir ) {</div>
+<div class="line"> $self->get_stdout_redirector->push( $worker_log_dir.<span class="stringliteral">'/worker.out'</span> );</div>
+<div class="line"> $self->get_stderr_redirector->push( $worker_log_dir.<span class="stringliteral">'/worker.err'</span> );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $min_batch_time = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ab1aa9f23e9feaec53f6e404dfe19f000">Bio::EnsEMBL::Hive::AnalysisStats::min_batch_time</a>();</div>
+<div class="line"> my $job_adaptor = $self->adaptor->db->get_AnalysisJobAdaptor;</div>
+<div class="line"></div>
+<div class="line"> print <span class="stringliteral">"\n"</span>; # to clear beekeeper<span class="stringliteral">'s prompt in case output is not logged</span></div>
+<div class="line"><span class="stringliteral"> $self->worker_say( $self->toString() );</span></div>
+<div class="line"><span class="stringliteral"> $self->specialize_and_compile_wrapper( $specialization_arglist );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> while (!$self->cause_of_death) { # Worker'</span>s lifespan loop (ends only when the worker dies <span class="keywordflow">for</span> any reason)</div>
+<div class="line"></div>
+<div class="line"> my $batches_stopwatch = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a1cbc5b3e6c40f0a5862e55e228dc34a3">new</a>()->restart();</div>
+<div class="line"> my $jobs_done_by_batches_loop = 0; # by all iterations of <span class="keyword">internal</span> loop</div>
+<div class="line"> $self->{<span class="stringliteral">'_interval_partial_timing'</span>} = {};</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( my $special_batch = $self->special_batch() ) {</div>
+<div class="line"> my $special_batch_length = scalar(@$special_batch); # has to be recorded because the list is gradually destroyed</div>
+<div class="line"> $jobs_done_by_batches_loop += $self->run_one_batch( $special_batch );</div>
+<div class="line"> $self->cause_of_death( $jobs_done_by_batches_loop == $special_batch_length ? <span class="stringliteral">'JOB_LIMIT'</span> : <span class="stringliteral">'CONTAMINATED'</span>);</div>
+<div class="line"> } <span class="keywordflow">else</span> { # a proper <span class="stringliteral">"BATCHES"</span> loop</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">while</span> (!$self->cause_of_death and $batches_stopwatch->get_elapsed < $min_batch_time) {</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( scalar(@{ $job_adaptor->fetch_all_incomplete_jobs_by_worker_id( $self->dbID ) }) ) {</div>
+<div class="line"> my $msg = <span class="stringliteral">"Lost control. Check your Runnable for loose 'next' statements that are not part of a loop"</span>;</div>
+<div class="line"> $self->worker_say( $msg );</div>
+<div class="line"> $self->cause_of_death(<span class="stringliteral">'CONTAMINATED'</span>);</div>
+<div class="line"> $job_adaptor->release_undone_jobs_from_worker($self, $msg);</div>
+<div class="line"></div>
+<div class="line"> } elsif( $self->job_limiter->reached()) {</div>
+<div class="line"> $self->worker_say( <span class="stringliteral">"job_limit reached ("</span>.$self->work_done.<span class="stringliteral">" jobs completed)"</span> );</div>
+<div class="line"> $self->cause_of_death(<span class="stringliteral">'JOB_LIMIT'</span>);</div>
+<div class="line"></div>
+<div class="line"> } elsif ( my $alive_for_secs = $self->life_span_limit_reached()) {</div>
+<div class="line"> $self->worker_say( <span class="stringliteral">"life_span limit reached (alive for $alive_for_secs secs)"</span> );</div>
+<div class="line"> $self->cause_of_death(<span class="stringliteral">'LIFESPAN'</span>);</div>
+<div class="line"></div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> my $desired_batch_size = $self->analysis->stats->get_or_estimate_batch_size();</div>
+<div class="line"> $desired_batch_size = $self->job_limiter->preliminary_offer( $desired_batch_size );</div>
+<div class="line"></div>
+<div class="line"> my $workers_rank = $self->adaptor->get_workers_rank( $self );</div>
+<div class="line"> my $actual_batch = $job_adaptor->grab_jobs_for_worker( $self, $desired_batch_size, $workers_rank );</div>
+<div class="line"> <span class="keywordflow">if</span>(scalar(@$actual_batch)) {</div>
+<div class="line"> my $jobs_done_by_this_batch = $self->run_one_batch( $actual_batch );</div>
+<div class="line"> $jobs_done_by_batches_loop += $jobs_done_by_this_batch;</div>
+<div class="line"> $self->job_limiter->final_decision( $jobs_done_by_this_batch );</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $self->cause_of_death(<span class="stringliteral">'NO_WORK'</span>);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # The following two database-updating operations are resource-expensive (all workers hammering the same database+tables),</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # so they are not allowed to happen too frequently (not before $min_batch_time of work has been done)</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>($jobs_done_by_batches_loop) {</div>
+<div class="line"></div>
+<div class="line"> $self->adaptor->db->get_AnalysisStatsAdaptor->interval_update_work_done(</div>
+<div class="line"> $self->analysis->dbID,</div>
+<div class="line"> $jobs_done_by_batches_loop,</div>
+<div class="line"> $batches_stopwatch->get_elapsed,</div>
+<div class="line"> $self->{<span class="stringliteral">'_interval_partial_timing'</span>}{<span class="stringliteral">'FETCH_INPUT'</span>} || 0,</div>
+<div class="line"> $self->{<span class="stringliteral">'_interval_partial_timing'</span>}{<span class="stringliteral">'RUN'</span>} || 0,</div>
+<div class="line"> $self->{<span class="stringliteral">'_interval_partial_timing'</span>}{<span class="stringliteral">'WRITE_OUTPUT'</span>} || 0,</div>
+<div class="line"> );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> # A mechanism whereby workers can be caused to exit even if they were doing fine:</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span> (!$self->cause_of_death) {</div>
+<div class="line"> my $stats = $self->analysis->stats; # make sure it is fresh from the DB</div>
+<div class="line"> <span class="keywordflow">if</span>( defined($stats->hive_capacity) && (0 <= $stats->hive_capacity) && ($self->adaptor->get_hive_current_load >= 1.1)</div>
+<div class="line"> or defined($self->analysis->analysis_capacity) && (0 <= $self->analysis->analysis_capacity) && ($self->analysis->analysis_capacity < $stats->num_running_workers)</div>
+<div class="line"> ) {</div>
+<div class="line"> $self->cause_of_death(<span class="stringliteral">'HIVE_OVERLOAD'</span>);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $self->cause_of_death() =~ /^(NO_WORK|HIVE_OVERLOAD)$/ ) {</div>
+<div class="line"> <span class="keywordflow">if</span>( $self->cause_of_death() eq <span class="stringliteral">'NO_WORK'</span>) {</div>
+<div class="line"> $self->adaptor->db->get_AnalysisStatsAdaptor->update_status($self->analysis_id, <span class="stringliteral">'ALL_CLAIMED'</span>);</div>
+<div class="line"> }</div>
+<div class="line"> </div>
+<div class="line"> <span class="keywordflow">if</span>( $self->can_respecialize and !$specialization_arglist ) {</div>
+<div class="line"> $self->cause_of_death(undef);</div>
+<div class="line"> $self->adaptor->db->get_AnalysisStatsAdaptor->decrease_running_workers($self->analysis->dbID); # FIXME: tidy up <span class="keyword">this</span> counting of active roles</div>
+<div class="line"> $self->specialize_and_compile_wrapper();</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> } # /Worker<span class="stringliteral">'s lifespan loop</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> # have runnable clean up any global/process files/data it may have created</span></div>
+<div class="line"><span class="stringliteral"> if($self->perform_cleanup) {</span></div>
+<div class="line"><span class="stringliteral"> if(my $runnable_object = $self->runnable_object()) { # the temp_directory is actually kept in the Process object:</span></div>
+<div class="line"><span class="stringliteral"> $runnable_object->cleanup_worker_temp_directory();</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $self->adaptor->register_worker_death($self, 1);</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($self->debug) {</span></div>
+<div class="line"><span class="stringliteral"> $self->worker_say( '</span>AnalysisStats : <span class="stringliteral">'.$self->analysis->stats->toString ) if($self->analysis_id());</span></div>
+<div class="line"><span class="stringliteral"> $self->worker_say( '</span>dbc <span class="stringliteral">'.$self->adaptor->db->dbc->disconnect_count. '</span> disconnect cycles<span class="stringliteral">' );</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $self->worker_say( "Having completed ".$self->work_done." jobs the Worker exits : ".$self->cause_of_death );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if( $self->log_dir ) {</span></div>
+<div class="line"><span class="stringliteral"> $self->get_stdout_redirector->pop();</span></div>
+<div class="line"><span class="stringliteral"> $self->get_stderr_redirector->pop();</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7fe639feb3731120a1a66663e8c2a2e8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::run_one_batch </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-run_one_batch" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-run_one_batch-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-run_one_batch-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-run_one_batch-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a7fe639feb3731120a1a66663e8c2a2e8">run_one_batch</a> {</div>
+<div class="line"> my ($self, $jobs) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $jobs_done_here = 0;</div>
+<div class="line"></div>
+<div class="line"> my $hive_use_param_stack = $self->adaptor->db->hive_use_param_stack();</div>
+<div class="line"> my $accu_adaptor = $self->adaptor->db->get_AccumulatorAdaptor;</div>
+<div class="line"> my $max_retry_count = $self->analysis->max_retry_count(); # a constant (as the Worker is already specialized by the Queen) needed later <span class="keywordflow">for</span> retrying jobs</div>
+<div class="line"></div>
+<div class="line"> $self->adaptor->check_in_worker( $self );</div>
+<div class="line"> $self->adaptor->safe_synchronize_AnalysisStats($self->analysis->stats);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->debug) {</div>
+<div class="line"> $self->worker_say( <span class="stringliteral">'AnalysisStats : '</span>.$self->analysis->stats->toString );</div>
+<div class="line"> $self->worker_say( <span class="stringliteral">'claimed '</span>.scalar(@{$jobs}).<span class="stringliteral">' jobs to process'</span> );</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $job_partial_timing;</div>
+<div class="line"></div>
+<div class="line"> ONE_BATCH: <span class="keywordflow">while</span>(my $job = shift @$jobs) { # to make sure jobs go out of scope without undue delay</div>
+<div class="line"></div>
+<div class="line"> my $job_id = $job->dbID();</div>
+<div class="line"> $self->worker_say( $job->toString ) <span class="keywordflow">if</span>($self->debug); </div>
+<div class="line"></div>
+<div class="line"> my $job_stopwatch = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a1cbc5b3e6c40f0a5862e55e228dc34a3">new</a>();</div>
+<div class="line"> $job_partial_timing = {};</div>
+<div class="line"></div>
+<div class="line"> $self->start_job_output_redirection($job); # <span class="keywordflow">switch</span> logging into job<span class="stringliteral">'s STDERR</span></div>
+<div class="line"><span class="stringliteral"> eval { # capture any throw/die</span></div>
+<div class="line"><span class="stringliteral"> $job->incomplete(1);</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $job->accu_hash( $accu_adaptor->fetch_structures_for_job_ids( $job_id )->{ $job_id } );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $runnable_object = $self->runnable_object();</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $self->adaptor->db->dbc->query_count(0);</span></div>
+<div class="line"><span class="stringliteral"> $job_stopwatch->restart();</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my @params_precedence = (</span></div>
+<div class="line"><span class="stringliteral"> $runnable_object->param_defaults(),</span></div>
+<div class="line"><span class="stringliteral"> $self->adaptor->db->get_MetaContainer->get_param_hash(),</span></div>
+<div class="line"><span class="stringliteral"> $self->analysis->parameters(),</span></div>
+<div class="line"><span class="stringliteral"> );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if( $hive_use_param_stack ) {</span></div>
+<div class="line"><span class="stringliteral"> my $input_ids_hash = $job->adaptor->fetch_input_ids_for_job_ids( $job->param_id_stack, 2, 0 ); # input_ids have lower precedence (FOR EACH ID)</span></div>
+<div class="line"><span class="stringliteral"> my $accu_hash = $accu_adaptor->fetch_structures_for_job_ids( $job->accu_id_stack, 2, 1 ); # accus have higher precedence (FOR EACH ID)</span></div>
+<div class="line"><span class="stringliteral"> my %input_id_accu_hash = ( %$input_ids_hash, %$accu_hash );</span></div>
+<div class="line"><span class="stringliteral"> push @params_precedence, @input_id_accu_hash{ sort { $a <=> $b } keys %input_id_accu_hash }; # take a slice. Mmm...</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> push @params_precedence, $job->input_id(), $job->accu_hash();</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $job->param_init( $runnable_object->strict_hash_format(), @params_precedence );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $self->worker_say( "Job $job_id unsubstituted_params= ".stringify($job->{'</span>_unsubstituted_param_hash<span class="stringliteral">'}) ) if($self->debug());</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $runnable_object->input_job( $job ); # "take" the job</span></div>
+<div class="line"><span class="stringliteral"> $job_partial_timing = $runnable_object->life_cycle();</span></div>
+<div class="line"><span class="stringliteral"> $runnable_object->input_job( undef ); # release an extra reference to the job</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $job->incomplete(0);</span></div>
+<div class="line"><span class="stringliteral"> };</span></div>
+<div class="line"><span class="stringliteral"> my $msg_thrown = $@;</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $job->runtime_msec( $job_stopwatch->get_elapsed ); # whether successful or not</span></div>
+<div class="line"><span class="stringliteral"> $job->query_count( $self->adaptor->db->dbc->query_count );</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> my $job_completion_line = "Job $job_id : complete";</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($msg_thrown) { # record the message - whether it was a success or failure:</span></div>
+<div class="line"><span class="stringliteral"> my $job_status_at_the_moment = $job->status();</span></div>
+<div class="line"><span class="stringliteral"> my $action = $job->incomplete ? '</span><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abd46b21982209917b8fbace6d01ac0a5">died</a><span class="stringliteral">' : '</span>exited<span class="stringliteral">';</span></div>
+<div class="line"><span class="stringliteral"> $job_completion_line = "Job $job_id : $action in status '</span>$job_status_at_the_moment<span class="stringliteral">' for the following reason: $msg_thrown";</span></div>
+<div class="line"><span class="stringliteral"> $self->adaptor->db->get_LogMessageAdaptor()->store_job_message($job_id, $msg_thrown, $job->incomplete );</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> print STDERR "\n$job_completion_line\n" if($self->log_dir and ($self->debug or $job->incomplete)); # one copy goes to the job'</span>s STDERR</div>
+<div class="line"> $self->stop_job_output_redirection($job); # and then we <span class="keywordflow">switch</span> back to worker<span class="stringliteral">'s STDERR</span></div>
+<div class="line"><span class="stringliteral"> $self->worker_say( $job_completion_line ); # one copy goes to the worker'</span>s STDERR</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($job->incomplete) {</div>
+<div class="line"><span class="preprocessor"> # If the job specifically said what to do next, respect that last wish.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # Otherwise follow the default behaviour set by the beekeeper in $worker:</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> #</span></div>
+<div class="line"><span class="preprocessor"></span> my $may_retry = defined($job->transient_error) ? $job->transient_error : $self->retry_throwing_jobs;</div>
+<div class="line"></div>
+<div class="line"> $job->adaptor->release_and_age_job( $job_id, $max_retry_count, $may_retry, $job->runtime_msec );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>( $self->prev_job_error # a bit of AI: <span class="keywordflow">if</span> the previous job failed as well, it is LIKELY that we have contamination</div>
+<div class="line"> or $job->lethal_for_worker ) { # trust the job<span class="stringliteral">'s expert knowledge</span></div>
+<div class="line"><span class="stringliteral"> my $reason = $self->prev_job_error ? '</span>two failed jobs in a row<span class="stringliteral">'</span></div>
+<div class="line"><span class="stringliteral"> : '</span>suggested by job itself<span class="stringliteral">';</span></div>
+<div class="line"><span class="stringliteral"> $self->worker_say( "Job'</span>s error has contaminated the Worker ($reason), so the Worker will now die<span class="stringliteral">" );</span></div>
+<div class="line"><span class="stringliteral"> $self->cause_of_death('CONTAMINATED');</span></div>
+<div class="line"><span class="stringliteral"> last ONE_BATCH;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> } else { # job successfully completed:</span></div>
+<div class="line"><span class="stringliteral"> $self->more_work_done( $job_partial_timing );</span></div>
+<div class="line"><span class="stringliteral"> $jobs_done_here++;</span></div>
+<div class="line"><span class="stringliteral"> $job->update_status('DONE');</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if(my $semaphored_job_id = $job->semaphored_job_id) {</span></div>
+<div class="line"><span class="stringliteral"> my $dbc = $self->adaptor->db->dbc;</span></div>
+<div class="line"><span class="stringliteral"> $dbc->do( "</span>SELECT 1 FROM job WHERE job_id=$semaphored_job_id FOR UPDATE<span class="stringliteral">" ) if($dbc->driver ne 'sqlite');</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $job->adaptor->decrease_semaphore_count_for_jobid( $semaphored_job_id ); # step-unblock the semaphore</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> if($job->lethal_for_worker) {</span></div>
+<div class="line"><span class="stringliteral"> $self->worker_say( "</span>The Job, although complete, wants the Worker to die<span class="stringliteral">" );</span></div>
+<div class="line"><span class="stringliteral"> $self->cause_of_death('CONTAMINATED');</span></div>
+<div class="line"><span class="stringliteral"> last ONE_BATCH;</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"> }</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> $self->prev_job_error( $job->incomplete );</span></div>
+<div class="line"><span class="stringliteral"> $self->enter_status('READY');</span></div>
+<div class="line"><span class="stringliteral"> } # /while(my $job = shift @$jobs)</span></div>
+<div class="line"><span class="stringliteral"></span></div>
+<div class="line"><span class="stringliteral"> return $jobs_done_here;</span></div>
+<div class="line"><span class="stringliteral">}</span></div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a4bc0dde1eb43909e1e8f8a87fd0a3257"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::runnable_object </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-runnable_object" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-runnable_object-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-runnable_object-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-runnable_object-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a4bc0dde1eb43909e1e8f8a87fd0a3257">runnable_object</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> $self->{<span class="stringliteral">'_runnable_object'</span>} = shift @_ <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_runnable_object'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab6470f448766be332f7e4d081e6d7cc2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::special_batch </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-special_batch" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-special_batch-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-special_batch-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-special_batch-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab6470f448766be332f7e4d081e6d7cc2">special_batch</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_special_batch'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_special_batch'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae432e7a7dbc6a8b0109353d4f6938d9c"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::specialize_and_compile_wrapper </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-specialize_and_compile_wrapper" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-specialize_and_compile_wrapper-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-specialize_and_compile_wrapper-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-specialize_and_compile_wrapper-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ae432e7a7dbc6a8b0109353d4f6938d9c">specialize_and_compile_wrapper</a> {</div>
+<div class="line"> my ($self, $specialization_arglist) = @_;</div>
+<div class="line"></div>
+<div class="line"> eval {</div>
+<div class="line"> $self->enter_status(<span class="stringliteral">'SPECIALIZATION'</span>);</div>
+<div class="line"> my $respecialization_from = $self->analysis_id && $self->analysis->logic_name.<span class="charliteral">'('</span>.$self->analysis_id.<span class="charliteral">')'</span>;</div>
+<div class="line"> $self->adaptor->specialize_new_worker( $self, $specialization_arglist ? @$specialization_arglist : () );</div>
+<div class="line"> my $specialization_to = $self->analysis->logic_name.<span class="charliteral">'('</span>.$self->analysis_id.<span class="charliteral">')'</span>;</div>
+<div class="line"> <span class="keywordflow">if</span>($respecialization_from) {</div>
+<div class="line"> my $msg = <span class="stringliteral">"respecializing from $respecialization_from to $specialization_to"</span>;</div>
+<div class="line"> $self->worker_say( $msg );</div>
+<div class="line"> $self->adaptor->db->get_LogMessageAdaptor()->store_worker_message($self->dbID, $msg, 0 );</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> $self->worker_say( <span class="stringliteral">"specializing to $specialization_to"</span> );</div>
+<div class="line"> }</div>
+<div class="line"> 1;</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aac9ba54b8924088ef41717fab6240ef4"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::start_job_output_redirection </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-start_job_output_redirection" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-start_job_output_redirection-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-start_job_output_redirection-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-start_job_output_redirection-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aac9ba54b8924088ef41717fab6240ef4">start_job_output_redirection</a> {</div>
+<div class="line"> my ($self, $job) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $worker_log_dir = $self->log_dir) {</div>
+<div class="line"> $self->get_stdout_redirector->push( $job->stdout_file( $worker_log_dir . <span class="stringliteral">'/job_id_'</span> . $job->dbID . <span class="charliteral">'_'</span> . $job->retry_count . <span class="stringliteral">'.out'</span> ) );</div>
+<div class="line"> $self->get_stderr_redirector->push( $job->stderr_file( $worker_log_dir . <span class="stringliteral">'/job_id_'</span> . $job->dbID . <span class="charliteral">'_'</span> . $job->retry_count . <span class="stringliteral">'.err'</span> ) );</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $job_adaptor = $job->adaptor) {</div>
+<div class="line"> $job_adaptor->store_out_files($job);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a814f0afa7c9b155777e5267a4b4fa145"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::status </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-status" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-status-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-status-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-status-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a814f0afa7c9b155777e5267a4b4fa145">status</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_status'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_status'</span>};</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="acb9fec0fad8f289eed242f5b1fe7e284"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::stop_job_output_redirection </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-stop_job_output_redirection" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-stop_job_output_redirection-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-stop_job_output_redirection-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-stop_job_output_redirection-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#acb9fec0fad8f289eed242f5b1fe7e284">stop_job_output_redirection</a> {</div>
+<div class="line"> my ($self, $job) = @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->log_dir) {</div>
+<div class="line"> $self->get_stdout_redirector->pop();</div>
+<div class="line"> $self->get_stderr_redirector->pop();</div>
+<div class="line"></div>
+<div class="line"> my $force_cleanup = !($self->debug || $job->incomplete);</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($force_cleanup or -z $job->stdout_file) {</div>
+<div class="line"> $self->worker_say( <span class="stringliteral">"Deleting '"</span>.$job->stdout_file.<span class="stringliteral">"' file"</span> );</div>
+<div class="line"> unlink $job->stdout_file;</div>
+<div class="line"> $job->stdout_file(undef);</div>
+<div class="line"> }</div>
+<div class="line"> <span class="keywordflow">if</span>($force_cleanup or -z $job->stderr_file) {</div>
+<div class="line"> $self->worker_say( <span class="stringliteral">"Deleting '"</span>.$job->stderr_file.<span class="stringliteral">"' file"</span> );</div>
+<div class="line"> unlink $job->stderr_file;</div>
+<div class="line"> $job->stderr_file(undef);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>(my $job_adaptor = $job->adaptor) {</div>
+<div class="line"> $job_adaptor->store_out_files($job);</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ac8931e351f68c7b4c927c9a400f595c3"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::toString </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-toString" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-toString-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-toString-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-toString-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ac8931e351f68c7b4c927c9a400f595c3">toString</a> {</div>
+<div class="line"> my $self = shift @_;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> join(<span class="stringliteral">', '</span>,</div>
+<div class="line"> <span class="stringliteral">'analysis='</span>.($self->analysis_id ? $self->analysis->logic_name.<span class="charliteral">'('</span>.$self->analysis_id.<span class="charliteral">')'</span> : <span class="stringliteral">'UNSPECIALIZED'</span>),</div>
+<div class="line"> <span class="stringliteral">'resource_class_id='</span>.($self->resource_class_id || <span class="stringliteral">'NULL'</span>),</div>
+<div class="line"> <span class="stringliteral">'meadow='</span>.$self->meadow_type.<span class="charliteral">'/'</span>.$self->meadow_name,</div>
+<div class="line"> <span class="stringliteral">'process='</span>.$self->process_id.<span class="charliteral">'@'</span>.$self->host,</div>
+<div class="line"> <span class="stringliteral">'last_check_in='</span>.$self->last_check_in,</div>
+<div class="line"> <span class="stringliteral">'batch_size='</span>.($self->analysis_id ? $self->analysis->stats->get_or_estimate_batch_size() : <span class="stringliteral">'UNSPECIALIZED'</span>),</div>
+<div class="line"> <span class="stringliteral">'job_limit='</span>.($self->job_limiter->available_capacity() || <span class="stringliteral">'NONE'</span>),</div>
+<div class="line"> <span class="stringliteral">'life_span='</span>.($self->life_span || <span class="stringliteral">'UNLIM'</span>),</div>
+<div class="line"> <span class="stringliteral">'worker_log_dir='</span>.($self->log_dir || <span class="stringliteral">'STDOUT/STDERR'</span>),</div>
+<div class="line"> );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ae34a70dcbfd02a12e20b1285adcbad1b"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::work_done </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-work_done" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-work_done-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-work_done-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-work_done-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ae34a70dcbfd02a12e20b1285adcbad1b">work_done</a> {</div>
+<div class="line"> my $self = shift;</div>
+<div class="line"> $self->{<span class="stringliteral">'_work_done'</span>} = shift <span class="keywordflow">if</span>(@_);</div>
+<div class="line"> <span class="keywordflow">return</span> $self->{<span class="stringliteral">'_work_done'</span>} || 0;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a91724c25ce62bea58013fd483aad3abe"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Bio::EnsEMBL::Hive::Worker::worker_say </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-worker_say" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-worker_say-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-worker_say-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-worker_say-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a91724c25ce62bea58013fd483aad3abe">worker_say</a> {</div>
+<div class="line"> my ($self, $msg) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $worker_id = $self->dbID();</div>
+<div class="line"> my $analysis_name = $self->analysis_id ? $self->analysis->logic_name.<span class="charliteral">'('</span>.$self->analysis_id.<span class="charliteral">')'</span> : <span class="stringliteral">''</span>;</div>
+<div class="line"> print <span class="stringliteral">"Worker $worker_id [ $analysis_name ] $msg\n"</span>;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>modules/Bio/EnsEMBL/Hive/<a class="el" href="_worker_8pm.html">Worker.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="namespace_bio.html">Bio</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Hive</a></li><li class="navelem"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Worker</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+  <span id="projectnumber">1.9</span>
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+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
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+<div class="title">MiniPecanMulti_conf Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_mini_pecan_multi__conf.html">MiniPecanMulti_conf</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_mini_pecan_multi__conf.html#a80b54e2491d5ea2289c81e3fc5e7745a">default_options</a>()</td><td class="entry"><a class="el" href="class_mini_pecan_multi__conf.html">MiniPecanMulti_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_mini_pecan_multi__conf.html#a3f50a960f6c073b41cf825a2057628cc">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_mini_pecan_multi__conf.html">MiniPecanMulti_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_mini_pecan_multi__conf-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">MiniPecanMulti_conf Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for MiniPecanMulti_conf:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-0-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_mini_pecan_multi__conf__inherit__graph.png" border="0" usemap="#_mini_pecan_multi__conf_inherit__map" alt="Inheritance graph"/></div>
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+<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html" title="Bio::EnsEMBL::Hive\l::PipeConfig::HiveGeneric_conf" alt="" coords="5,97,211,138"/><area shape="rect" id="node3" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html" title="Bio::EnsEMBL::Hive\l::DependentOptions" alt="" coords="37,6,179,47"/></map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<div id="dynsection-1" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for MiniPecanMulti_conf:</div>
+<div id="dynsection-1-summary" class="dynsummary" style="display:block;">
+</div>
+<div id="dynsection-1-content" class="dyncontent" style="display:none;">
+<div class="center"><img src="class_mini_pecan_multi__conf__coll__graph.png" border="0" usemap="#_mini_pecan_multi__conf_coll__map" alt="Collaboration graph"/></div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
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+<tr class="memitem:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_mini_pecan_multi__conf.html">MiniPecanMulti_conf</a> -password <your_password></div>
+<div class="line"></div>
+<div class="line">init_pipeline.pl <a class="code" href="class_mini_pecan_multi__conf.html">MiniPecanMulti_conf</a> -hive_driver sqlite -password <FOO></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is an example pipeline put together from basic building blocks:
+
+ Analysis_1: SystemCmd.pm is used to run Pecan on a set of files
+
+ the job is sent down the branch #1 into the second analysis
+
+ Analysis_2: SystemCmd.pm is used to run gerp_col on the resulting alignment
+
+ the job is sent down the branch #1 into the third analysis
+
+ Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a80b54e2491d5ea2289c81e3fc5e7745a"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public MiniPecanMulti_conf::default_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_mini_pecan_multi__conf.html#a80b54e2491d5ea2289c81e3fc5e7745a">default_options()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that is used to initialize default options.</pre><pre> </pre><div id="codesection-default_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_mini_pecan_multi__conf.html#a80b54e2491d5ea2289c81e3fc5e7745a">default_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{ $self->SUPER::default_options() }, # inherit other stuff from the base <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'pipeline_name'</span> => <span class="stringliteral">'mini_pecan_multi'</span>, # name used by the beekeeper to prefix job names on the farm</div>
+<div class="line"></div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3f50a960f6c073b41cf825a2057628cc"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public MiniPecanMulti_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_mini_pecan_multi__conf.html#a3f50a960f6c073b41cf825a2057628cc">pipeline_analyses()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that defines the structure of the pipeline: analyses, jobs, rules, etc.
+ Here it defines two analyses:</pre><pre> 'pecan' aligns sequences with Pecan
+ Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.</pre><pre> 'gerp_col' runs gerp_col on Pecan output
+ Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.</pre><pre> 'gerp_elem' runs gerp_elem on gerp_col output</pre><pre> </pre><div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_mini_pecan_multi__conf.html#a3f50a960f6c073b41cf825a2057628cc">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## First analysis: PECAN</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'pecan'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"><span class="preprocessor"> # The cmd parameter is required by the SystemCmd module. It defines the command line to be run.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # Note that some values are written between #hashes#. Those will be subtituted by the corresponding input values</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'java -cp /soft/pecan_v0.8/pecan_v0.8.jar bp.pecan.Pecan -E "#tree_string#" -F #input_files# -G #msa_file#'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> </div>
+<div class="line"> -hive_capacity => 200, # max. number of parallel jobs</div>
+<div class="line"></div>
+<div class="line"> -input_ids => [</div>
+<div class="line"><span class="preprocessor"> # Each input_id is a new job for this analysis. Here we are defining the input_files and the msa_file for</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # three different jobs.</span></div>
+<div class="line"><span class="preprocessor"></span> {</div>
+<div class="line"> <span class="stringliteral">'tree_string'</span> => <span class="stringliteral">'(((HUMAN,(MOUSE,RAT)),COW),OPOSSUM);'</span>,</div>
+<div class="line"> <span class="stringliteral">'input_files'</span> => <span class="stringliteral">'human.fa mouse.fa rat.fa cow.fa opossum.fa'</span>,</div>
+<div class="line"> <span class="stringliteral">'msa_file'</span> => <span class="stringliteral">"pecan_no_chicken.mfa"</span>,</div>
+<div class="line"> },</div>
+<div class="line"> {</div>
+<div class="line"> <span class="stringliteral">'tree_string'</span> => <span class="stringliteral">'((((HUMAN,MOUSE),COW),OPOSSUM),CHICKEN);'</span>,</div>
+<div class="line"> <span class="stringliteral">'input_files'</span> => <span class="stringliteral">'human.fa mouse.fa cow.fa opossum.fa chicken.fa'</span>,</div>
+<div class="line"> <span class="stringliteral">'msa_file'</span> => <span class="stringliteral">"pecan_no_rat.mfa"</span>,</div>
+<div class="line"> },</div>
+<div class="line"> {</div>
+<div class="line"> <span class="stringliteral">'tree_string'</span> => <span class="stringliteral">'(((HUMAN,COW),OPOSSUM),CHICKEN);'</span>,</div>
+<div class="line"> <span class="stringliteral">'input_files'</span> => <span class="stringliteral">'human.fa cow.fa opossum.fa chicken.fa'</span>,</div>
+<div class="line"> <span class="stringliteral">'msa_file'</span> => <span class="stringliteral">"pecan_no_rodents.mfa"</span>,</div>
+<div class="line"> },</div>
+<div class="line"> ],</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"><span class="preprocessor"> # dataflow rule. Once a 'pecan' job is done, it will create a new 'gerp_col' job.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # The input_id for the new job will be the same as for the previous job (this is</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # only true for branch 1. In this case, 'tree_string', 'input_files' and 'msa_file'</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # values are used to create a new 'gerp_col' job (only msa_file is actually required).</span></div>
+<div class="line"><span class="preprocessor"></span> 1 => [ <span class="stringliteral">'gerp_col'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## Second analysis: GERP_COL</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'gerp_col'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"><span class="preprocessor"> # In this case, #msa_file# comes from the parent 'pecan' job.</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'gerpcol -t tree.nw -f #msa_file# -a -e HUMAN'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> -hive_capacity => 20, # max. number of parallel jobs</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"><span class="preprocessor"> # dataflow rule, branch 1. The input_id for the new job will be the same as for the</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # previous job, i.e. 'tree_string', 'input_files' and 'msa_file' values are used to</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # create a new 'gerp_elem' job (only msa_file is actually required).</span></div>
+<div class="line"><span class="preprocessor"></span> 1 => [ <span class="stringliteral">'gerp_elem'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## Third analysis: GERP_ELEM</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'gerp_elem'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"><span class="preprocessor"> # In this case, #msa_file# comes from the parent 'gerp_col' job, which in turn comes from its parent 'pecan' job.</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'gerpelem -f #msa_file#.rates -c chr13 -s 32878016 -x .bed'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> -hive_capacity => 200, # max. number of parallel jobs</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>docs/presentations/HiveWorkshop_22Feb2013/<a class="el" href="_mini_pecan_multi__conf_8pm.html">MiniPecanMulti_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
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+ <li class="navelem"><a class="el" href="class_mini_pecan_multi__conf.html">MiniPecanMulti_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
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+ <li><a href="annotated.html"><span>Class List</span></a></li>
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+<div class="title">MiniPecanSingle2_conf Member List</div> </div>
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+
+<p>This is the complete list of members for <a class="el" href="class_mini_pecan_single2__conf.html">MiniPecanSingle2_conf</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_mini_pecan_single2__conf.html#ab1bb3850c9086897fc4f0cadf59b4cac">default_options</a>()</td><td class="entry"><a class="el" href="class_mini_pecan_single2__conf.html">MiniPecanSingle2_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_mini_pecan_single2__conf.html#a45e6c49458b9a332221b8f49217f8fac">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_mini_pecan_single2__conf.html">MiniPecanSingle2_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+<tr class="memitem:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a> ()</td></tr>
+<tr class="separator:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a> ()</td></tr>
+<tr class="separator:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> ()</td></tr>
+<tr class="separator:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_mini_pecan_single2__conf.html">MiniPecanSingle2_conf</a> -password <your_password></div>
+<div class="line"></div>
+<div class="line">init_pipeline.pl <a class="code" href="class_mini_pecan_single2__conf.html">MiniPecanSingle2_conf</a> -hive_driver sqlite -password <FOO></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is an example pipeline put together from basic building blocks:
+
+ Analysis_1: SystemCmd.pm is used to run Pecan on a set of files
+
+ the job is sent down the branch #1 into the second analysis
+
+ Analysis_2: SystemCmd.pm is used to run gerp_col on the resulting alignment
+
+ the job is sent down the branch #1 into the third analysis
+
+ Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ab1bb3850c9086897fc4f0cadf59b4cac"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public MiniPecanSingle2_conf::default_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_mini_pecan_single2__conf.html#ab1bb3850c9086897fc4f0cadf59b4cac">default_options()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that is used to initialize default options.
+ In addition to the standard things it defines three options:
+ o('capacity') defines how many files can be run in parallel</pre><pre> There are rules dependent on two options that do not have defaults (this makes them mandatory):
+ o('password') your read-write password for creation and maintenance of the hive database</pre><pre> </pre><div id="codesection-default_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_mini_pecan_single2__conf.html#ab1bb3850c9086897fc4f0cadf59b4cac">default_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{ $self->SUPER::default_options() }, # inherit other stuff from the base <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'pipeline_name'</span> => <span class="stringliteral">'mini_pecan_single2'</span>, # name used by the beekeeper to prefix job names on the farm</div>
+<div class="line"></div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a45e6c49458b9a332221b8f49217f8fac"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public MiniPecanSingle2_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_mini_pecan_single2__conf.html#a45e6c49458b9a332221b8f49217f8fac">pipeline_analyses()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that defines the structure of the pipeline: analyses, jobs, rules, etc.
+ Here it defines two analyses:</pre><pre> 'pecan' aligns sequences with Pecan
+ Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.</pre><pre> 'gerp_col' runs gerp_col on Pecan output
+ Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.</pre><pre> 'gerp_elem' runs gerp_elem on gerp_col output</pre><pre> </pre><div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_mini_pecan_single2__conf.html#a45e6c49458b9a332221b8f49217f8fac">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## First analysis: PECAN</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'pecan'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"><span class="preprocessor"> # The cmd parameter is required by the SystemCmd module. It defines the command line to be run.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # Note that some values are written between #hashes#. Those will be subtituted by the corresponding input values</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'java -cp /soft/pecan_v0.8/pecan_v0.8.jar bp.pecan.Pecan -E "#tree_string#" -F #input_files# -G #msa_file#'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> </div>
+<div class="line"> -input_ids => [</div>
+<div class="line"><span class="preprocessor"> # Each input_id is a new job for this analysis. Here we are defining the input_files and the msa_file for</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # the first and only job.</span></div>
+<div class="line"><span class="preprocessor"></span> {</div>
+<div class="line"> <span class="stringliteral">'tree_string'</span> => <span class="stringliteral">'((((HUMAN,(MOUSE,RAT)),COW),OPOSSUM),CHICKEN);'</span>,</div>
+<div class="line"> <span class="stringliteral">'input_files'</span> => <span class="stringliteral">'human.fa mouse.fa rat.fa cow.fa opossum.fa chicken.fa'</span>,</div>
+<div class="line"> <span class="stringliteral">'msa_file'</span> => <span class="stringliteral">"pecan2.mfa"</span>,</div>
+<div class="line"> },</div>
+<div class="line"> ],</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"><span class="preprocessor"> # dataflow rule. Once a 'pecan' job is done, it will create a new 'gerp_col' job.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # The input_id for the new job will be the same as for the previous job (this is</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # only true for branch 1. In this case, 'tree_string', 'input_files' and 'msa_file'</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # values are used to create a new 'gerp_col' job (only msa_file is actually required).</span></div>
+<div class="line"><span class="preprocessor"></span> 1 => { <span class="stringliteral">'gerp_col'</span> => {<span class="stringliteral">'input_file'</span> => <span class="stringliteral">'#msa_file#'</span>} },</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## Second analysis: GERP_COL</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'gerp_col'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"><span class="preprocessor"> # In this case, #msa_file# comes from the parent 'pecan' job.</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'gerpcol -t tree.nw -f #input_file# -a -e HUMAN'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"><span class="preprocessor"> # dataflow rule, branch 1. The input_id for the new job will be the same as for the</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # previous job, i.e. 'tree_string', 'input_files' and 'msa_file' values are used to</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # create a new 'gerp_elem' job (only msa_file is actually required).</span></div>
+<div class="line"><span class="preprocessor"></span> 1 => { <span class="stringliteral">'gerp_elem'</span> => {<span class="stringliteral">'input_file'</span> => <span class="stringliteral">'#input_file#.rates'</span>} },</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## Third analysis: GERP_ELEM</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'gerp_elem'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"><span class="preprocessor"> # In this case, #msa_file# comes from the parent 'gerp_col' job, which in turn comes from its parent 'pecan' job.</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'gerpelem -f #input_file# -c chr13 -s 32878016 -x .bed'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>docs/presentations/HiveWorkshop_22Feb2013/<a class="el" href="_mini_pecan_single2__conf_8pm.html">MiniPecanSingle2_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
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+ <ul>
+ <li class="navelem"><a class="el" href="class_mini_pecan_single2__conf.html">MiniPecanSingle2_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
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+  <span id="projectnumber">1.9</span>
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+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_mini_pecan_single3__conf.html#acfb2470be4a35c3a5d63df3fa4e96ad2">default_options</a>()</td><td class="entry"><a class="el" href="class_mini_pecan_single3__conf.html">MiniPecanSingle3_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_mini_pecan_single3__conf.html#a7740c91be5f2d349a94909a7c152a998">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_mini_pecan_single3__conf.html">MiniPecanSingle3_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+<a href="#pub-methods">Public Member Functions</a> |
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+<div class="title">MiniPecanSingle3_conf Class Reference</div> </div>
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+<div class="contents">
+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for MiniPecanSingle3_conf:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
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+<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html" title="Bio::EnsEMBL::Hive\l::PipeConfig::HiveGeneric_conf" alt="" coords="5,97,211,138"/><area shape="rect" id="node3" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html" title="Bio::EnsEMBL::Hive\l::DependentOptions" alt="" coords="37,6,179,47"/></map>
+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:acfb2470be4a35c3a5d63df3fa4e96ad2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_mini_pecan_single3__conf.html#acfb2470be4a35c3a5d63df3fa4e96ad2">default_options</a> ()</td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td></tr>
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+<tr class="separator:a0c6ccdb318ca662f0ead725ab661273e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a7072b951f3d57b690c0d2a2465d75d9b inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a639062a270bf3af88f896c9231f38133 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td></tr>
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+<tr class="separator:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a8b28b1e6e1ef24ac3d9143062ddc36d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a> ()</td></tr>
+<tr class="separator:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a> ()</td></tr>
+<tr class="separator:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> ()</td></tr>
+<tr class="separator:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_mini_pecan_single3__conf.html">MiniPecanSingle3_conf</a> -password <your_password></div>
+<div class="line"></div>
+<div class="line">init_pipeline.pl <a class="code" href="class_mini_pecan_single3__conf.html">MiniPecanSingle3_conf</a> -hive_driver sqlite -password <FOO></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is an example pipeline put together from basic building blocks:
+
+ Analysis_1: SystemCmd.pm is used to run Pecan on a set of files
+
+ the job is sent down the branch #1 into the second analysis
+
+ Analysis_2: SystemCmd.pm is used to run gerp_col on the resulting alignment
+
+ the job is sent down the branch #1 into the third analysis
+
+ Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="acfb2470be4a35c3a5d63df3fa4e96ad2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public MiniPecanSingle3_conf::default_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_mini_pecan_single3__conf.html#acfb2470be4a35c3a5d63df3fa4e96ad2">default_options()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that is used to initialize default options.
+ In addition to the standard things it defines three options:
+ o('capacity') defines how many files can be run in parallel</pre><pre> There are rules dependent on two options that do not have defaults (this makes them mandatory):
+ o('password') your read-write password for creation and maintenance of the hive database</pre><pre> </pre><div id="codesection-default_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_mini_pecan_single3__conf.html#acfb2470be4a35c3a5d63df3fa4e96ad2">default_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{ $self->SUPER::default_options() }, # inherit other stuff from the base <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'pipeline_name'</span> => <span class="stringliteral">'mini_pecan_single3'</span>, # name used by the beekeeper to prefix job names on the farm</div>
+<div class="line"></div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a7740c91be5f2d349a94909a7c152a998"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public MiniPecanSingle3_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_mini_pecan_single3__conf.html#a7740c91be5f2d349a94909a7c152a998">pipeline_analyses()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that defines the structure of the pipeline: analyses, jobs, rules, etc.
+ Here it defines two analyses:</pre><pre> 'pecan' aligns sequences with Pecan
+ Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.</pre><pre> 'gerp_col' runs gerp_col on Pecan output
+ Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.</pre><pre> 'gerp_elem' runs gerp_elem on gerp_col output</pre><pre> </pre><div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_mini_pecan_single3__conf.html#a7740c91be5f2d349a94909a7c152a998">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## First analysis: PECAN</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'pecan'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"><span class="preprocessor"> # The cmd parameter is required by the SystemCmd module. It defines the command line to be run.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # Note that some values are written between #hashes#. Those will be subtituted by the corresponding input values</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'java -cp /soft/pecan_v0.8/pecan_v0.8.jar bp.pecan.Pecan -E "#tree_string#" -F #input_files# -G #msa_file#'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> </div>
+<div class="line"> -input_ids => [</div>
+<div class="line"><span class="preprocessor"> # Each input_id is a new job for this analysis. Here we are defining the input_files and the msa_file for</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # the first and only job.</span></div>
+<div class="line"><span class="preprocessor"></span> {</div>
+<div class="line"> <span class="stringliteral">'tree_string'</span> => <span class="stringliteral">'((((HUMAN,(MOUSE,RAT)),COW),OPOSSUM),CHICKEN);'</span>,</div>
+<div class="line"> <span class="stringliteral">'input_files'</span> => <span class="stringliteral">'human.fa mouse.fa rat.fa cow.fa opossum.fa chicken.fa'</span>,</div>
+<div class="line"> <span class="stringliteral">'msa_file'</span> => <span class="stringliteral">"pecan3.mfa"</span>,</div>
+<div class="line"> <span class="stringliteral">'chr_name'</span> => <span class="stringliteral">"chr13"</span>,</div>
+<div class="line"> <span class="stringliteral">'chr_start'</span> => <span class="stringliteral">"32878016"</span>,</div>
+<div class="line"> },</div>
+<div class="line"> ],</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"><span class="preprocessor"> # dataflow rule. Once a 'pecan' job is done, it will create a new 'gerp_col' and</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # a new 'gerp_elem' job.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # Using the input_template, we are setting the input_file for the other two analyses</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'1->A'</span> => { <span class="stringliteral">'gerp_col'</span> => {<span class="stringliteral">'input_file'</span> => <span class="stringliteral">'#msa_file#'</span>} },</div>
+<div class="line"> <span class="stringliteral">'A->1'</span> => { <span class="stringliteral">'gerp_elem'</span> => {<span class="stringliteral">'input_file'</span> => <span class="stringliteral">'#msa_file#.rates'</span>,</div>
+<div class="line"> <span class="stringliteral">'chr_name'</span> => <span class="stringliteral">'#chr_name#'</span>,</div>
+<div class="line"> <span class="stringliteral">'chr_start'</span> => <span class="stringliteral">'#chr_start#'</span>}</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## Second analysis: GERP_COL</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'gerp_col'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"><span class="preprocessor"> # In this case, #msa_file# comes from the parent 'pecan' job.</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'gerpcol -t tree.nw -f #input_file# -a -e HUMAN'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## Third analysis: GERP_ELEM</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'gerp_elem'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'gerpelem -f #input_file# -c #chr_name# -s #chr_start# -x .bed'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>docs/presentations/HiveWorkshop_22Feb2013/<a class="el" href="_mini_pecan_single3__conf_8pm.html">MiniPecanSingle3_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="class_mini_pecan_single3__conf.html">MiniPecanSingle3_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+<div class="title">MiniPecanSingle_conf Member List</div> </div>
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+
+<p>This is the complete list of members for <a class="el" href="class_mini_pecan_single__conf.html">MiniPecanSingle_conf</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">beekeeper_extra_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">db_cmd</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">db_connect_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">db_execute_command</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">dbconn_2_mysql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">dbconn_2_pgsql</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">dbconn_2_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_mini_pecan_single__conf.html#a3c145006e519882ca8d9c95d965af7ff">default_options</a>()</td><td class="entry"><a class="el" href="class_mini_pecan_single__conf.html">MiniPecanSingle_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">hive_meta_table</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_mini_pecan_single__conf.html#aecd0653da35db4cc26178b9a5bbab306">pipeline_analyses</a>()</td><td class="entry"><a class="el" href="class_mini_pecan_single__conf.html">MiniPecanSingle_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">pipeline_create_commands</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">pipeline_name</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">pipeline_url</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">pipeline_wide_parameters</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">pre_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">process_options</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">resource_classes</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">root</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">run</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">use_cases</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="entry"></td></tr>
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+<div id="dynsection-0" onclick="return toggleVisibility(this)" class="dynheader closed" style="cursor:pointer;">
+ <img id="dynsection-0-trigger" src="closed.png" alt="+"/> Inheritance diagram for MiniPecanSingle_conf:</div>
+<div id="dynsection-0-summary" class="dynsummary" style="display:block;">
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+ <img id="dynsection-1-trigger" src="closed.png" alt="+"/> Collaboration diagram for MiniPecanSingle_conf:</div>
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+<center><span class="legend">[<a target="top" href="graph_legend.html">legend</a>]</span></center></div>
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a3c145006e519882ca8d9c95d965af7ff"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_mini_pecan_single__conf.html#a3c145006e519882ca8d9c95d965af7ff">default_options</a> ()</td></tr>
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+<tr class="memitem:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">load_cmdline_options</a> ()</td></tr>
+<tr class="separator:ac036ce35e64d7310b44481136fad5b18 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
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+<tr class="separator:a1191c5f58dd3ebbd26f4024b906ccfcf inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a8b28b1e6e1ef24ac3d9143062ddc36d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">is_fully_substituted_string</a> ()</td></tr>
+<tr class="separator:a8b28b1e6e1ef24ac3d9143062ddc36d6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">is_fully_substituted_structure</a> ()</td></tr>
+<tr class="separator:a35e7b3e74c6afda6e8f364b6b84f1348 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">hash_leaves</a> ()</td></tr>
+<tr class="separator:aaeb1b4b8db00aaa6a80126ff26cb7a0e inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">o</a> ()</td></tr>
+<tr class="separator:adca1f94c3e725c8f744517d14ac91853 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">substitute</a> ()</td></tr>
+<tr class="separator:a58f0a875a481ff975964bbd451773f11 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">merge_from_rules</a> ()</td></tr>
+<tr class="separator:a33d14b75b2adc800bbcc4451a7ca7819 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">process_options</a> ()</td></tr>
+<tr class="separator:a1832098d9531567eda925f5e108438a6 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">init_pipeline.pl <a class="code" href="class_mini_pecan_single__conf.html">MiniPecanSingle_conf</a> -password <your_password></div>
+<div class="line"></div>
+<div class="line">init_pipeline.pl <a class="code" href="class_mini_pecan_single__conf.html">MiniPecanSingle_conf</a> -hive_driver sqlite -password <FOO></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This is an example pipeline put together from basic building blocks:
+
+ Analysis_1: SystemCmd.pm is used to run Pecan on a set of files
+
+ the job is sent down the branch #1 into the second analysis
+
+ Analysis_2: SystemCmd.pm is used to run gerp_col on the resulting alignment
+
+ the job is sent down the branch #1 into the third analysis
+
+ Analysis_3: SystemCmd.pm is used to run gerp_elem on the GERP scores
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="a3c145006e519882ca8d9c95d965af7ff"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public MiniPecanSingle_conf::default_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_mini_pecan_single__conf.html#a3c145006e519882ca8d9c95d965af7ff">default_options()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that is used to initialize default options.
+ In addition to the standard things it defines three options:
+ o('capacity') defines how many files can be run in parallel</pre><pre> There are rules dependent on two options that do not have defaults (this makes them mandatory):
+ o('password') your read-write password for creation and maintenance of the hive database</pre><pre> </pre><div id="codesection-default_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-default_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-default_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-default_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_mini_pecan_single__conf.html#a3c145006e519882ca8d9c95d965af7ff">default_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> {</div>
+<div class="line"> %{ $self->SUPER::default_options() }, # inherit other stuff from the base <span class="keyword">class</span></div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'pipeline_name'</span> => <span class="stringliteral">'mini_pecan_single'</span>, # name used by the beekeeper to prefix job names on the farm</div>
+<div class="line"></div>
+<div class="line"> };</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="aecd0653da35db4cc26178b9a5bbab306"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public MiniPecanSingle_conf::pipeline_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<pre>
+ Description : Implements <a class="el" href="class_mini_pecan_single__conf.html#aecd0653da35db4cc26178b9a5bbab306">pipeline_analyses()</a> interface method of <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a> that defines the structure of the pipeline: analyses, jobs, rules, etc.
+ Here it defines two analyses:</pre><pre> 'pecan' aligns sequences with Pecan
+ Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_col' analysis.</pre><pre> 'gerp_col' runs gerp_col on Pecan output
+ Each job of this analysis will dataflow (create jobs) via branch #1 into 'gerp_elem' analysis.</pre><pre> 'gerp_elem' runs gerp_elem on gerp_col output</pre><pre> </pre><div id="codesection-pipeline_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-pipeline_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-pipeline_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-pipeline_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_mini_pecan_single__conf.html#aecd0653da35db4cc26178b9a5bbab306">pipeline_analyses</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> <span class="keywordflow">return</span> [</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## First analysis: PECAN</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'pecan'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"><span class="preprocessor"> # The cmd parameter is required by the SystemCmd module. It defines the command line to be run.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # Note that some values are written between #hashes#. Those will be subtituted by the corresponding input values</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'java -cp /soft/pecan_v0.8/pecan_v0.8.jar bp.pecan.Pecan -E "#tree_string#" -F #input_files# -G #msa_file#'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> </div>
+<div class="line"> -input_ids => [</div>
+<div class="line"><span class="preprocessor"> # Each input_id is a new job for this analysis. Here we are defining the input_files and the msa_file for</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # the first and only job.</span></div>
+<div class="line"><span class="preprocessor"></span> {</div>
+<div class="line"> <span class="stringliteral">'tree_string'</span> => <span class="stringliteral">'((((HUMAN,(MOUSE,RAT)),COW),OPOSSUM),CHICKEN);'</span>,</div>
+<div class="line"> <span class="stringliteral">'input_files'</span> => <span class="stringliteral">'human.fa mouse.fa rat.fa cow.fa opossum.fa chicken.fa'</span>,</div>
+<div class="line"> <span class="stringliteral">'msa_file'</span> => <span class="stringliteral">"pecan.mfa"</span>,</div>
+<div class="line"> },</div>
+<div class="line"> ],</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"><span class="preprocessor"> # dataflow rule. Once a 'pecan' job is done, it will create a new 'gerp_col' job.</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # The input_id for the new job will be the same as for the previous job (this is</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # only true for branch 1. In this case, 'tree_string', 'input_files' and 'msa_file'</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # values are used to create a new 'gerp_col' job (only msa_file is actually required).</span></div>
+<div class="line"><span class="preprocessor"></span> 1 => [ <span class="stringliteral">'gerp_col'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## Second analysis: GERP_COL</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'gerp_col'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"><span class="preprocessor"> # In this case, #msa_file# comes from the parent 'pecan' job.</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'gerpcol -t tree.nw -f #msa_file# -a -e HUMAN'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> -flow_into => {</div>
+<div class="line"><span class="preprocessor"> # dataflow rule, branch 1. The input_id for the new job will be the same as for the</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # previous job, i.e. 'tree_string', 'input_files' and 'msa_file' values are used to</span></div>
+<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # create a new 'gerp_elem' job (only msa_file is actually required).</span></div>
+<div class="line"><span class="preprocessor"></span> 1 => [ <span class="stringliteral">'gerp_elem'</span> ],</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> ## Third analysis: GERP_ELEM</span></div>
+<div class="line"><span class="preprocessor"></span> { -logic_name => <span class="stringliteral">'gerp_elem'</span>,</div>
+<div class="line"> -module => <span class="stringliteral">'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd'</span>,</div>
+<div class="line"> -parameters => {</div>
+<div class="line"><span class="preprocessor"> # In this case, #msa_file# comes from the parent 'gerp_col' job, which in turn comes from its parent 'pecan' job.</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="stringliteral">'cmd'</span> => <span class="stringliteral">'gerpelem -f #msa_file#.rates -c chr13 -s 32878016 -x .bed'</span>,</div>
+<div class="line"> },</div>
+<div class="line"> },</div>
+<div class="line"></div>
+<div class="line"> ];</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>docs/presentations/HiveWorkshop_22Feb2013/<a class="el" href="_mini_pecan_single__conf_8pm.html">MiniPecanSingle_conf.pm</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="class_mini_pecan_single__conf.html">MiniPecanSingle_conf</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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--- /dev/null
+++ b/docs/doxygen/class_script-members.html
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+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Member List</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
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+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+$(document).ready(function(){initNavTree('class_script.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Script Member List</div> </div>
+</div><!--header-->
+<div class="contents">
+
+<p>This is the complete list of members for <a class="el" href="class_script.html">Script</a>, including all inherited members.</p>
+<table class="directory">
+ <tr class="even"><td class="entry"><a class="el" href="class_script.html#ac470265a113d3130aa1699814c37df13">_options</a>()</td><td class="entry"><a class="el" href="class_script.html">Script</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_script.html#ab630c1fc26dd8c0aeef54acc78113515">_process_options</a>()</td><td class="entry"><a class="el" href="class_script.html">Script</a></td><td class="entry"></td></tr>
+ <tr class="even"><td class="entry"><a class="el" href="class_script.html#a1b841ee95221494ac0b4eb534f0e8c82">_write_graph</a>()</td><td class="entry"><a class="el" href="class_script.html">Script</a></td><td class="entry"></td></tr>
+ <tr><td class="entry"><a class="el" href="class_script.html#a1bd6f4c8c62743400cdc430f3e4d6c21">main</a>()</td><td class="entry"><a class="el" href="class_script.html">Script</a></td><td class="entry"></td></tr>
+</table></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_script.html b/docs/doxygen/class_script.html
new file mode 100644
index 0000000000000000000000000000000000000000..1c4c54cfd1145e2b7cdb25271d57af3752f01d45
--- /dev/null
+++ b/docs/doxygen/class_script.html
@@ -0,0 +1,321 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Script Class Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
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+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
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+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+ onmouseover="return searchBox.OnSearchSelectShow()"
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+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
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+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('class_script.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
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+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="summary">
+<a href="#pub-methods">Public Member Functions</a> |
+<a href="class_script-members.html">List of all members</a> </div>
+ <div class="headertitle">
+<div class="title">Script Class Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
+Public Member Functions</h2></td></tr>
+<tr class="memitem:a1bd6f4c8c62743400cdc430f3e4d6c21"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="class_script.html#a1bd6f4c8c62743400cdc430f3e4d6c21">main</a> ()</td></tr>
+<tr class="separator:a1bd6f4c8c62743400cdc430f3e4d6c21"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ac470265a113d3130aa1699814c37df13"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_script.html#ac470265a113d3130aa1699814c37df13">_options</a> ()</td></tr>
+<tr class="separator:ac470265a113d3130aa1699814c37df13"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:ab630c1fc26dd8c0aeef54acc78113515"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_script.html#ab630c1fc26dd8c0aeef54acc78113515">_process_options</a> ()</td></tr>
+<tr class="separator:ab630c1fc26dd8c0aeef54acc78113515"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a1b841ee95221494ac0b4eb534f0e8c82"><td class="memItemLeft" align="right" valign="top">protected </td><td class="memItemRight" valign="bottom"><a class="el" href="class_script.html#a1b841ee95221494ac0b4eb534f0e8c82">_write_graph</a> ()</td></tr>
+<tr class="separator:a1b841ee95221494ac0b4eb534f0e8c82"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
+<div class="textblock"><h1><a class="anchor" id="Synopsis"></a>
+Synopsis</h1>
+<div class="fragment"><div class="line">./generate_graph.pl -url mysql:<span class="comment">//user:pass@server:port/dbname -output OUTPUT_LOC [-help]</span></div>
+</div><!-- fragment --> <h1><a class="anchor" id="Description"></a>
+Description</h1>
+ <pre>
+ This program will generate a graphical representation of your hive pipeline.
+ This includes visalising the flow of data from the different analyses, blocking
+ rules & table writers. The graph is also coloured to indicate the stage
+ an analysis is at. The colours & fonts used can be configured via
+ hive_config.json configuration file.
+
+</pre> </div><h2 class="groupheader">Member Function Documentation</h2>
+<a class="anchor" id="ac470265a113d3130aa1699814c37df13"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Script::_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_script.html#ac470265a113d3130aa1699814c37df13">_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"> GetOptions(</div>
+<div class="line"> # connection parameters</div>
+<div class="line"> <span class="stringliteral">'url=s'</span> => \$self->{<span class="stringliteral">'url'</span>},</div>
+<div class="line"> <span class="stringliteral">'reg_conf|reg_file=s'</span> => \$self->{<span class="stringliteral">'reg_conf'</span>},</div>
+<div class="line"> <span class="stringliteral">'reg_type=s'</span> => \$self->{<span class="stringliteral">'reg_type'</span>},</div>
+<div class="line"> <span class="stringliteral">'reg_alias|reg_name=s'</span> => \$self->{<span class="stringliteral">'reg_alias'</span>},</div>
+<div class="line"> <span class="stringliteral">'nosqlvc=i'</span> => \$self->{<span class="stringliteral">'nosqlvc'</span>}, # <span class="keyword">using</span> <span class="stringliteral">"=i"</span> instead of <span class="stringliteral">"!"</span> <span class="keywordflow">for</span> consistency with scripts where it is a propagated option</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'f|format=s'</span> => \$self->{<span class="stringliteral">'format'</span>},</div>
+<div class="line"> <span class="stringliteral">'o|output=s'</span> => \$self->{<span class="stringliteral">'output'</span>},</div>
+<div class="line"></div>
+<div class="line"> <span class="stringliteral">'h|help'</span> => \$self->{<span class="stringliteral">'help'</span>},</div>
+<div class="line"> );</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="ab630c1fc26dd8c0aeef54acc78113515"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Script::_process_options </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_process_options" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_process_options-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_process_options-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_process_options-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_script.html#ab630c1fc26dd8c0aeef54acc78113515">_process_options</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"><span class="preprocessor"> #Check for help</span></div>
+<div class="line"><span class="preprocessor"></span> <span class="keywordflow">if</span>($self->{<span class="stringliteral">'help'</span>}) {</div>
+<div class="line"> pod2usage({-exitvalue => 0, -verbose => 2});</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($self->{<span class="stringliteral">'url'</span>} or $self->{<span class="stringliteral">'reg_alias'</span>}) {</div>
+<div class="line"> $self->{<span class="stringliteral">'dba'</span>} = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#abf2b541c5d7e3b124323a34356e3ace6">new</a>(</div>
+<div class="line"> -url => $self->{<span class="stringliteral">'url'</span>},</div>
+<div class="line"> -reg_conf => $self->{<span class="stringliteral">'reg_conf'</span>},</div>
+<div class="line"> -reg_type => $self->{<span class="stringliteral">'reg_type'</span>},</div>
+<div class="line"> -reg_alias => $self->{<span class="stringliteral">'reg_alias'</span>},</div>
+<div class="line"> -no_sql_schema_version_check => $self->{<span class="stringliteral">'nosqlvc'</span>},</div>
+<div class="line"> );</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> pod2usage({</div>
+<div class="line"> -message => <span class="stringliteral">'ERROR: Connection parameters (url or reg_conf+reg_alias) need to be specified'</span>,</div>
+<div class="line"> -exitvalue => 1,</div>
+<div class="line"> -verbose => 2</div>
+<div class="line"> });</div>
+<div class="line"> }</div>
+<div class="line"> </div>
+<div class="line"> <span class="keywordflow">if</span>(! $self->{<span class="stringliteral">'output'</span>}) {</div>
+<div class="line"> pod2usage({</div>
+<div class="line"> -message => <span class="stringliteral">'ERROR: No -output flag given'</span>,</div>
+<div class="line"> -exitvalue => 1,</div>
+<div class="line"> -verbose => 2</div>
+<div class="line"> });</div>
+<div class="line"> }</div>
+<div class="line"> </div>
+<div class="line"> <span class="keywordflow">if</span>(!$self->{<span class="stringliteral">'format'</span>}) {</div>
+<div class="line"> <span class="keywordflow">if</span>($self->{<span class="stringliteral">'output'</span>}=~/\.(\w+)$/) {</div>
+<div class="line"> $self->{<span class="stringliteral">'format'</span>} = $1;</div>
+<div class="line"> } <span class="keywordflow">else</span> {</div>
+<div class="line"> die <span class="stringliteral">"Format was not set and could not guess from "</span>.$self->output().<span class="stringliteral">". Please use either way to select it.\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1b841ee95221494ac0b4eb534f0e8c82"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">protected Script::_write_graph </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-_write_graph" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-_write_graph-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-_write_graph-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-_write_graph-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_script.html#a1b841ee95221494ac0b4eb534f0e8c82">_write_graph</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $graph = <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html">Bio::EnsEMBL::Hive::Utils::Graph</a>-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a0452e8098246f27173059b14600f190c">new</a>( $self->{<span class="stringliteral">'dba'</span>} );</div>
+<div class="line"> my $graphviz = $graph-><a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ad7fad3a0d313ae9d07c6b6e636876109">build</a>();</div>
+<div class="line"></div>
+<div class="line"> my $call = q{as_}.$self->{<span class="stringliteral">'format'</span>};</div>
+<div class="line"></div>
+<div class="line"> eval {$graphviz->$call($self->{<span class="stringliteral">'output'</span>});};</div>
+<div class="line"> <span class="keywordflow">if</span>($@) {</div>
+<div class="line"> warn $@;</div>
+<div class="line"> pod2usage({</div>
+<div class="line"> -message => <span class="stringliteral">'Error detected. Check '</span>.$self->{<span class="stringliteral">'format'</span>}.<span class="stringliteral">' is a valid format. Use a format name as supported by graphviz'</span>,</div>
+<div class="line"> -exitvalue => 1,</div>
+<div class="line"> -verbose => 2</div>
+<div class="line"> });</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a1bd6f4c8c62743400cdc430f3e4d6c21"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public Script::main </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-main" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-main-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-main-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-main-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="class_script.html#a1bd6f4c8c62743400cdc430f3e4d6c21">main</a> {</div>
+<div class="line"> my ($self) = @_;</div>
+<div class="line"></div>
+<div class="line"> $self->_options();</div>
+<div class="line"> $self->_process_options();</div>
+<div class="line"> $self->_write_graph();</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<hr/>The documentation for this class was generated from the following file:<ul>
+<li>scripts/<a class="el" href="generate__graph_8pl.html">generate_graph.pl</a></li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="class_script.html">Script</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/class_script.js b/docs/doxygen/class_script.js
new file mode 100644
index 0000000000000000000000000000000000000000..0ce20130932aed37bb769a7dfe8e0cbf14bdbad8
--- /dev/null
+++ b/docs/doxygen/class_script.js
@@ -0,0 +1,7 @@
+var class_script =
+[
+ [ "_options", "class_script.html#ac470265a113d3130aa1699814c37df13", null ],
+ [ "_process_options", "class_script.html#ab630c1fc26dd8c0aeef54acc78113515", null ],
+ [ "_write_graph", "class_script.html#a1b841ee95221494ac0b4eb534f0e8c82", null ],
+ [ "main", "class_script.html#a1bd6f4c8c62743400cdc430f3e4d6c21", null ]
+];
\ No newline at end of file
diff --git a/docs/doxygen/classes.html b/docs/doxygen/classes.html
new file mode 100644
index 0000000000000000000000000000000000000000..21711ffc99dcada5e85ae2402837b557bf79b278
--- /dev/null
+++ b/docs/doxygen/classes.html
@@ -0,0 +1,174 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Index</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li class="current"><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('classes.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="headertitle">
+<div class="title">Class Index</div> </div>
+</div><!--header-->
+<div class="contents">
+<div class="qindex"><a class="qindex" href="#letter_A">A</a> | <a class="qindex" href="#letter_B">B</a> | <a class="qindex" href="#letter_C">C</a> | <a class="qindex" href="#letter_D">D</a> | <a class="qindex" href="#letter_F">F</a> | <a class="qindex" href="#letter_G">G</a> | <a class="qindex" href="#letter_H">H</a> | <a class="qindex" href="#letter_J">J</a> | <a class="qindex" href="#letter_L">L</a> | <a class="qindex" href="#letter_M">M</a> | <a class="qindex" href="#letter_N">N</a> | <a class="qindex" href="#letter_O">O</a> | <a class="qindex" href="#letter_P">P</a> | <a class="qindex" href="#letter_Q">Q</a> | <a class="qindex" href="#letter_R">R</a> | <a class="qindex" href="#letter_S">S</a> | <a class="qindex" href="#letter_T">T</a> | <a class="qindex" href="#letter_U">U</a> | <a class="qindex" href="#letter_V">V</a> | <a class="qindex" href="#letter_W">W</a></div>
+<table style="margin: 10px; white-space: nowrap;" align="center" width="95%" border="0" cellspacing="0" cellpadding="0">
+<tr><td rowspan="2" valign="bottom"><a name="letter_A"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  A  </div></td></tr></table>
+</td><td rowspan="2" valign="bottom"><a name="letter_D"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  D  </div></td></tr></table>
+</td><td rowspan="2" valign="bottom"><a name="letter_L"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  L  </div></td></tr></table>
+</td><td rowspan="2" valign="bottom"><a name="letter_O"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  O  </div></td></tr></table>
+</td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html">SqlHealthcheck</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">Bio::EnsEMBL::Hive::RunnableDB</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html">SqlSchemaAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html">Accumulator</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html">DatabaseDumper</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">Bio::EnsEMBL::Hive::RunnableDB</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html">Limiter</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html">ObjectAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html">Utils::Stopwatch</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html">AccumulatorAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html">DataflowRule</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html">Meadow::LOCAL</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_P"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  P  </div></td></tr></table>
+</td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html">SystemCmd</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">Bio::EnsEMBL::Hive::RunnableDB</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html">AddTogether</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html">DataflowRuleAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html">LogMessageAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_T"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  T  </div></td></tr></table>
+</td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html">Analysis</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html">DBAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html">LongMult_conf</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">Bio::EnsEMBL::Hive::PipeConfig</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html">Params</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html">AnalysisAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html">DBConnection</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html">LongMultSt_conf</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">Bio::EnsEMBL::Hive::PipeConfig</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html">PartMultiply</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html">TableDumperZipper_conf</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">Bio::EnsEMBL::Hive::PipeConfig</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html">AnalysisCtrlRule</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html">DependentOptions</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html">Meadow::LSF</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html">Process</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_U"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  U  </div></td></tr></table>
+</td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html">AnalysisCtrlRuleAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html">DigitFactory</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult.html">Bio::EnsEMBL::Hive::RunnableDB::LongMult</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_M"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  M  </div></td></tr></table>
+</td><td rowspan="2" valign="bottom"><a name="letter_Q"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  Q  </div></td></tr></table>
+</td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html">AnalysisDataAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html">Dummy</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">Bio::EnsEMBL::Hive::RunnableDB</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l.html">Utils::URL</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html">AnalysisJob</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_F"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  F  </div></td></tr></table>
+</td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html">Meadow</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html">Queen</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html">URLFactory</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html">AnalysisJobAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html">MemlimitTest_conf</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">Bio::EnsEMBL::Hive::PipeConfig</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_R"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  R  </div></td></tr></table>
+</td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html">Utils</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html">AnalysisStats</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html">FailureTest</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">Bio::EnsEMBL::Hive::RunnableDB</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html">MetaAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_V"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  V  </div></td></tr></table>
+</td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html">AnalysisStatsAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html">FailureTest_conf</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">Bio::EnsEMBL::Hive::PipeConfig</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html">MetaContainer</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html">Utils::RedirectStack</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_any_commands__conf.html">AnyCommands_conf</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">Bio::EnsEMBL::Hive::PipeConfig</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html">FastaFactory</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">Bio::EnsEMBL::Hive::RunnableDB</a>)   </td><td valign="top"><a class="el" href="class_mini_pecan_multi__conf.html">MiniPecanMulti_conf</a>   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html">ResourceClass</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html">Valley</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_apply_to_databases__conf.html">ApplyToDatabases_conf</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">Bio::EnsEMBL::Hive::PipeConfig</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html">FastaSplitter_conf</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">Bio::EnsEMBL::Hive::PipeConfig</a>)   </td><td valign="top"><a class="el" href="class_mini_pecan_single2__conf.html">MiniPecanSingle2_conf</a>   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html">ResourceClassAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_version.html">Version</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td></tr>
+<tr><td rowspan="2" valign="bottom"><a name="letter_B"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  B  </div></td></tr></table>
+</td><td rowspan="2" valign="bottom"><a name="letter_G"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  G  </div></td></tr></table>
+</td><td valign="top"><a class="el" href="class_mini_pecan_single3__conf.html">MiniPecanSingle3_conf</a>   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html">ResourceDescription</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_W"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  W  </div></td></tr></table>
+</td></tr>
+<tr><td valign="top"><a class="el" href="class_mini_pecan_single__conf.html">MiniPecanSingle_conf</a>   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html">ResourceDescriptionAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html">BaseAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html">Utils::Graph</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html">MySQLTransfer</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">Bio::EnsEMBL::Hive::RunnableDB</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html">RunListOfCommandsOnFarm_conf</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">Bio::EnsEMBL::Hive::PipeConfig</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html">Worker</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td></tr>
+<tr><td rowspan="2" valign="bottom"><a name="letter_C"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  C  </div></td></tr></table>
+</td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html">Utils::GraphViz</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_N"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  N  </div></td></tr></table>
+</td><td rowspan="2" valign="bottom"><a name="letter_S"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  S  </div></td></tr></table>
+</td><td></td></tr>
+<tr><td rowspan="2" valign="bottom"><a name="letter_H"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  H  </div></td></tr></table>
+</td><td></td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html">CompressFiles_conf</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">Bio::EnsEMBL::Hive::PipeConfig</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html">NakedTable</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html">Scheduler</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td></td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html">Utils::Config</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html">HiveGeneric_conf</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config.html">Bio::EnsEMBL::Hive::PipeConfig</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html">NakedTableAdaptor</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l.html">Bio::EnsEMBL::Hive::DBSQL</a>)   </td><td valign="top"><a class="el" href="class_script.html">Script</a>   </td><td></td></tr>
+<tr><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html">Configurable</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive.html">Bio::EnsEMBL::Hive</a>)   </td><td rowspan="2" valign="bottom"><a name="letter_J"></a><table border="0" cellspacing="0" cellpadding="0"><tr><td><div class="ah">  J  </div></td></tr></table>
+</td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html">NotifyByEmail</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">Bio::EnsEMBL::Hive::RunnableDB</a>)   </td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html">SqlCmd</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">Bio::EnsEMBL::Hive::RunnableDB</a>)   </td><td></td></tr>
+<tr><td></td><td></td><td></td><td></td></tr>
+<tr><td></td><td valign="top"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html">JobFactory</a> (<a class="el" href="namespace_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b.html">Bio::EnsEMBL::Hive::RunnableDB</a>)   </td><td></td><td></td><td></td></tr>
+<tr><td></td><td></td><td></td><td></td><td></td></tr>
+</table>
+<div class="qindex"><a class="qindex" href="#letter_A">A</a> | <a class="qindex" href="#letter_B">B</a> | <a class="qindex" href="#letter_C">C</a> | <a class="qindex" href="#letter_D">D</a> | <a class="qindex" href="#letter_F">F</a> | <a class="qindex" href="#letter_G">G</a> | <a class="qindex" href="#letter_H">H</a> | <a class="qindex" href="#letter_J">J</a> | <a class="qindex" href="#letter_L">L</a> | <a class="qindex" href="#letter_M">M</a> | <a class="qindex" href="#letter_N">N</a> | <a class="qindex" href="#letter_O">O</a> | <a class="qindex" href="#letter_P">P</a> | <a class="qindex" href="#letter_Q">Q</a> | <a class="qindex" href="#letter_R">R</a> | <a class="qindex" href="#letter_S">S</a> | <a class="qindex" href="#letter_T">T</a> | <a class="qindex" href="#letter_U">U</a> | <a class="qindex" href="#letter_V">V</a> | <a class="qindex" href="#letter_W">W</a></div>
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+  <span id="projectnumber">1.9</span>
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+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:a3ce8b237b3bdb2817dac6f769e5768c2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="db__cmd_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">main</a> ()</td></tr>
+<tr class="separator:a3ce8b237b3bdb2817dac6f769e5768c2"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:aa9d6dbdd85d225abef029815f3ca0336"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="db__cmd_8pl.html#aa9d6dbdd85d225abef029815f3ca0336">dbc_hash_to_cmd</a> ()</td></tr>
+<tr class="separator:aa9d6dbdd85d225abef029815f3ca0336"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<h2 class="groupheader">Function Documentation</h2>
+<a class="anchor" id="aa9d6dbdd85d225abef029815f3ca0336"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public dbc_hash_to_cmd </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-dbc_hash_to_cmd" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-dbc_hash_to_cmd-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-dbc_hash_to_cmd-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-dbc_hash_to_cmd-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="db__cmd_8pl.html#aa9d6dbdd85d225abef029815f3ca0336">dbc_hash_to_cmd</a> {</div>
+<div class="line"> my ($dbc_hash, $sqlcmd, $extra, $to_params) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $driver = $dbc_hash->{<span class="stringliteral">'driver'</span>} || <span class="stringliteral">'mysql'</span>;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($sqlcmd) {</div>
+<div class="line"> <span class="keywordflow">if</span>($sqlcmd =~ /(DROP\s+DATABASE(?:\s+IF\s+EXISTS)?\s*?)(?:\s+(\w+))?/i) {</div>
+<div class="line"> my $dbname = $2 || $dbc_hash->{dbname};</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($driver eq <span class="stringliteral">'sqlite'</span>) {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">"rm -f $dbname"</span>;</div>
+<div class="line"> } elsif(!$2) {</div>
+<div class="line"> $sqlcmd = <span class="stringliteral">"$1 $dbname"</span>;</div>
+<div class="line"> $dbc_hash->{dbname} = <span class="stringliteral">''</span>;</div>
+<div class="line"> }</div>
+<div class="line"> } elsif($sqlcmd =~ /(CREATE\s+DATABASE\s*?)(?:\s+(\w+))?/i ) {</div>
+<div class="line"> my $dbname = $2 || $dbc_hash->{dbname};</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($driver eq <span class="stringliteral">'sqlite'</span>) {</div>
+<div class="line"> <span class="keywordflow">return</span> <span class="stringliteral">"touch $dbname"</span>;</div>
+<div class="line"> } elsif(!$2) {</div>
+<div class="line"> $sqlcmd = <span class="stringliteral">"$1 $dbname"</span>;</div>
+<div class="line"> $dbc_hash->{dbname} = <span class="stringliteral">''</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> my $cmd;</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">if</span>($driver eq <span class="stringliteral">'mysql'</span>) {</div>
+<div class="line"></div>
+<div class="line"> $cmd = ($to_params ? <span class="stringliteral">''</span> : <span class="stringliteral">'mysql '</span>)</div>
+<div class="line"> .<span class="stringliteral">"--host=$dbc_hash->{host} "</span></div>
+<div class="line"> .(defined($dbc_hash->{port}) ? <span class="stringliteral">"--port=$dbc_hash->{port} "</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> .<span class="stringliteral">"--user=$dbc_hash->{user} --password='$dbc_hash->{pass}' "</span></div>
+<div class="line"> .(defined($extra) ? <span class="stringliteral">"$extra "</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> .($dbc_hash->{dbname} || <span class="stringliteral">''</span>)</div>
+<div class="line"> .(defined($sqlcmd) ? <span class="stringliteral">" -e '$sqlcmd'"</span> : <span class="stringliteral">''</span>);</div>
+<div class="line"> } elsif($driver eq <span class="stringliteral">'pgsql'</span>) {</div>
+<div class="line"></div>
+<div class="line"> $cmd = ($to_params ? <span class="stringliteral">''</span> : <span class="stringliteral">"env PGPASSWORD='$dbc_hash->{pass}' psql "</span>)</div>
+<div class="line"> .<span class="stringliteral">"--host=$dbc_hash->{host} "</span></div>
+<div class="line"> .(defined($dbc_hash->{port}) ? <span class="stringliteral">"--port=$dbc_hash->{port} "</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> .<span class="stringliteral">"--username=$dbc_hash->{user} "</span></div>
+<div class="line"> .(defined($sqlcmd) ? <span class="stringliteral">"--command='$sqlcmd' "</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> .(defined($extra) ? <span class="stringliteral">"$extra "</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> .($dbc_hash->{dbname} || <span class="stringliteral">''</span>);</div>
+<div class="line"> } elsif($driver eq <span class="stringliteral">'sqlite'</span>) {</div>
+<div class="line"></div>
+<div class="line"> die <span class="stringliteral">"sqlite requires a database (file) name\n"</span> unless $dbc_hash->{dbname};</div>
+<div class="line"> $cmd = <span class="stringliteral">"sqlite3 "</span></div>
+<div class="line"> .(defined($extra) ? <span class="stringliteral">"$extra "</span> : <span class="stringliteral">''</span>)</div>
+<div class="line"> .$dbc_hash->{dbname}</div>
+<div class="line"> .(defined($sqlcmd) ? <span class="stringliteral">" '$sqlcmd'"</span> : <span class="stringliteral">''</span>);</div>
+<div class="line"> }</div>
+<div class="line"></div>
+<div class="line"> <span class="keywordflow">return</span> $cmd;</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+<a class="anchor" id="a3ce8b237b3bdb2817dac6f769e5768c2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public main </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+</div>
+</div>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="dir_5fc43faac24a7b81dcfb81b231064839.html">scripts</a></li><li class="navelem"><a class="el" href="db__cmd_8pl.html">db_cmd.pl</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/db__cmd_8pl.js b/docs/doxygen/db__cmd_8pl.js
new file mode 100644
index 0000000000000000000000000000000000000000..d60dbc69b6ee52dec056dd2f32acc14a6e60ee99
--- /dev/null
+++ b/docs/doxygen/db__cmd_8pl.js
@@ -0,0 +1,5 @@
+var db__cmd_8pl =
+[
+ [ "dbc_hash_to_cmd", "db__cmd_8pl.html#aa9d6dbdd85d225abef029815f3ca0336", null ],
+ [ "main", "db__cmd_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2", null ]
+];
\ No newline at end of file
diff --git a/docs/doxygen/deprecated.html b/docs/doxygen/deprecated.html
new file mode 100644
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--- /dev/null
+++ b/docs/doxygen/deprecated.html
@@ -0,0 +1,127 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
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+ onmouseover="return searchBox.OnSearchSelectShow()"
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+$(document).ready(function(){initNavTree('deprecated.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+ <div class="headertitle">
+<div class="title">Deprecated List </div> </div>
+</div><!--header-->
+<div class="contents">
+<div class="textblock"><dl class="reflist">
+<dt><a class="anchor" id="_deprecated000001"></a>Member <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a77f78d2fe7e5ac25737ff9322d40e4f9">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor::CreateNewJob</a> ()</dt>
+<dd>. Please use $job_adaptor->store_jobs_and_adjust_counters( @jobs_to_store ) instead </dd>
+<dt><a class="anchor" id="_deprecated000004"></a>Member <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::db_connect_command</a> ()</dt>
+<dd>method. Please use $self->db_cmd() instead. </dd>
+<dt><a class="anchor" id="_deprecated000005"></a>Member <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::db_execute_command</a> ()</dt>
+<dd>method. Please use $self->db_cmd() instead. </dd>
+<dt><a class="anchor" id="_deprecated000002"></a>Member <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::dbconn_2_mysql</a> ()</dt>
+<dd>method. Please use $self->db_cmd() instead. </dd>
+<dt><a class="anchor" id="_deprecated000003"></a>Member <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf::dbconn_2_pgsql</a> ()</dt>
+<dd>method. Please use $self->db_cmd() instead.</dd>
+</dl>
+</div></div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+<div class="levels">[detail level <span onclick="javascript:toggleLevel(1);">1</span><span onclick="javascript:toggleLevel(2);">2</span><span onclick="javascript:toggleLevel(3);">3</span><span onclick="javascript:toggleLevel(4);">4</span><span onclick="javascript:toggleLevel(5);">5</span><span onclick="javascript:toggleLevel(6);">6</span><span onclick="javascript:toggleLevel(7);">7</span>]</div><table class="directory">
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+<tr id="row_1_0_0_0_12_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2doc.png" alt="*" width="24" height="22" /><a class="el" href="_dependent_options_8pm.html" target="_self">DependentOptions.pm</a></td><td class="desc"></td></tr>
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+<tr id="row_1_0_0_0_14_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2doc.png" alt="*" width="24" height="22" /><a class="el" href="_limiter_8pm.html" target="_self">Limiter.pm</a></td><td class="desc"></td></tr>
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+<tr id="row_1_0_0_0_16_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2doc.png" alt="*" width="24" height="22" /><a class="el" href="_naked_table_8pm.html" target="_self">NakedTable.pm</a></td><td class="desc"></td></tr>
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+<tr id="row_1_0_0_0_20_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2doc.png" alt="*" width="24" height="22" /><a class="el" href="_resource_class_8pm.html" target="_self">ResourceClass.pm</a></td><td class="desc"></td></tr>
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+<tr id="row_1_0_0_0_22_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2doc.png" alt="*" width="24" height="22" /><a class="el" href="_scheduler_8pm.html" target="_self">Scheduler.pm</a></td><td class="desc"></td></tr>
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index__"></a>- _ -</h3><ul>
+<li>_add_analysis_node()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a15c083cbf55912f540a1a62c63f36ccd">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_add_hive_details()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ad0284a21114d9ea4bc9569b28b86b3ac">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_add_table_node()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f15e355d2750a68a1a219ef2decc55a">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_add_together()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a58596178ed9c2bb86dbaca822ce0f29a">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a>
+</li>
+<li>_allocate_to_subgraph()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a56fbf0b2d2c70f562cb8aaa6c430ee64">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_analysis_node_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_as_debug()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a65653a19ade3aa317b9a40dac5af679b">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>_control_rules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a0a4df43f72b40dfdbbd100f957a430c3">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_dataflow_rules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#af6624dc439ed366dc32f51716c1de48f">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_fisher_yates_shuffle_in_place()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a051cdcc9af5a857e02f899adf0736c46">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_get_rows_from_list()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a046e795740452e442df65849921da767">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_get_rows_from_open()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#ac5c6183dcd03bbfdb054253cbd4b7405">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_get_rows_from_query()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a66dd4176925958a32b1e09ec6b381f6e">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_get_table_list()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a8e55c7699aa239e5c5550427bed3eed9">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a>
+</li>
+<li>_midpoint_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a546d1e3d214a8c2ba2c25a8d94ac0813">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_options()
+: <a class="el" href="class_script.html#ac470265a113d3130aa1699814c37df13">Script</a>
+</li>
+<li>_param_possibly_overridden()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a0536cad5480d931d7982fe0f049ebfaf">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>_param_silent()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a416e12ae4a4511ba13ba427cfc2361d5">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>_process_options()
+: <a class="el" href="class_script.html#ab630c1fc26dd8c0aeef54acc78113515">Script</a>
+</li>
+<li>_rec_multiply()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aae56050726847606ccb5ea8c7516dc75">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a>
+</li>
+<li>_run_test()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a1341a510369536f2cbcd09fdd2050bf2">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a>
+</li>
+<li>_subst_one_hashpair()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a960052271c6be58027f13c1cadbe5ad8">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>_substitute_minibatched_rows()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a1d866fc6d59bb185b2a7630583b6a93a">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_substitute_rows()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a32b9467b5a794591dd41d0c471c1dab6">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_table_info_loader()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>_table_node_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#af860b66fd159323a7c507fa27b2f3794">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_unit()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a278a474770becadc0c47562beb111e4f">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>_validate_tests()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a3d33b3c3256122e564dfffc8b745f5af">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a>
+</li>
+<li>_write_graph()
+: <a class="el" href="class_script.html#a1b841ee95221494ac0b4eb534f0e8c82">Script</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_a.html b/docs/doxygen/functions_a.html
new file mode 100644
index 0000000000000000000000000000000000000000..b3958db9596c64328650ba0722b809ec68f7a9ff
--- /dev/null
+++ b/docs/doxygen/functions_a.html
@@ -0,0 +1,210 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li class="current"><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_a.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_a"></a>- a -</h3><ul>
+<li>accu_hash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1a33fd570abad2c0f79c22bc5d77d652">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>accu_id_stack()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52165b28650c26a24b621da4ff2e777a">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>accumulated()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a243a5222c2176291094dd9d83b51b7c3">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>adaptor()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a7dd96c5cf6b8c8c4b4b1447923250373">Bio::EnsEMBL::Hive::Accumulator</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ab689e0f33659659ebdc4396b237df113">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#ae26cea149a37ce38a76340febf821ea3">Bio::EnsEMBL::Hive::NakedTable</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a253a528483f463acf6db1e49f54c75a2">Bio::EnsEMBL::Hive::ResourceDescription</a>
+</li>
+<li>analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a9447a3ac1aa3c45822c8d495c405785e">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>analysis_capacity()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a0ecb60e98a4410c8bbf7bdb0784c9785">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>analysis_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ad43a29a7f535cc507f91702fad70b310">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a9dea5f797f92fa7dd1e06a67f0bcd401">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aa7b8e54f437a9427f268c91ed61626e5">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>autoflow()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ac5bab7c3ffa521e44370d1bdc34cf11a">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>autoinc_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>AUTOLOAD()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>available_capacity()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a6e64029524e47016b9db01936324f8d2">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>available_meadow_hash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a3d03fc09525b8349ab06bff8e387686e">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>avg_input_msec_per_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4015806ce9a0a952ec992386f323ecd4">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>avg_msec_per_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0aee41e0ab6ecb6e1726a2254a1c5256">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>avg_output_msec_per_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a763d7539d36a921ba14409ffdd805a04">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>avg_run_msec_per_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adc046b69d9e806527342f79319818631">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_b.html b/docs/doxygen/functions_b.html
new file mode 100644
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
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+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<script type="text/javascript" src="search/search.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
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+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
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+ <div id="navrow3" class="tabs2">
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+ <li class="current"><a href="functions.html"><span>All</span></a></li>
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+ </div>
+ <div id="navrow4" class="tabs3">
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+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li class="current"><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_b.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
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+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_b"></a>- b -</h3><ul>
+<li>balance_semaphores()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ac9e28226315228b396483078e3823515">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>batch_size()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4889ae9b5d00bcb53add084060676301">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>beekeeper_extra_cmdline_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>behaviour()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac5a95b82fd9ad6752c5eeb4527714d8e">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>born()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a0904a2e1b64e956c6400d8344eb6fc71">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>branch_code()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ad765dadb213174df11b5f31e3248b9db">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>branch_name_2_code()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a529c8c386c3e60cb1a737231775bf77c">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a>
+</li>
+<li>build()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ad7fad3a0d313ae9d07c6b6e636876109">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
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+ <li class="footer">Generated by
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+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_c.html b/docs/doxygen/functions_c.html
new file mode 100644
index 0000000000000000000000000000000000000000..d549bb79cf7aec0a7fbfdfefcf76e68eaeb89d91
--- /dev/null
+++ b/docs/doxygen/functions_c.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta name="generator" content="Doxygen 1.8.6"/>
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+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="dynsections.js"></script>
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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
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+ onmouseover="return searchBox.OnSearchSelectShow()"
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+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
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+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li class="current"><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
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+</script>
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_c"></a>- c -</h3><ul>
+<li>can_be_empty()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9371f668649753210a7a301b02f6f855">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>can_respecialize()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a0c047d0bd965ee20025093fa837ee897">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>cause_of_death()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3c525fb34ae49638bf9898949f995388">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>check_blocking_control_rules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a5d40dc556b755e7aed76e02fe6550b65">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>check_for_dead_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a020be70f3da4eca961fef537e68daca6">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>check_in_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a8ec0da9cd78a6fc994786f65b8710a7d">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>check_object_present_in_db()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>check_worker_is_alive_and_mine()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa5ed36b42e1e9a3eeb2f2474c37cab8f">Bio::EnsEMBL::Hive::Meadow</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a460348aa64020e5d8a747991f831cd05">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a9a3c0c5e45f0c8d8f39c353f3613366d">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>cleanup_worker_temp_directory()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>colour_offset()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a7b1487d4809792cc1322687655f2d984">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>colour_scheme()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#afe6a7243b9051c98db319ecbcf89d212">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>column_set()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>completed()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#adf437552d1a1b96a0fb1868b7ee58e0b">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>condition_analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#a7cec568f2499ba88040334c408efeb6b">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+</li>
+<li>condition_analysis_url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa1408c2380cfa9fc9d4b22458bdfd1cb">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+</li>
+<li>config()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">Bio::EnsEMBL::Hive::Configurable</a>
+</li>
+<li>config_get()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">Bio::EnsEMBL::Hive::Configurable</a>
+</li>
+<li>config_hash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#ab0ede51b2658eddc43a8f6e9fbf34509">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>config_set()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">Bio::EnsEMBL::Hive::Configurable</a>
+</li>
+<li>context()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">Bio::EnsEMBL::Hive::Configurable</a>
+</li>
+<li>continue()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#ad91a33ccd3234b64b19bc3083e9367f0">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>count_all()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>count_pending_workers_by_rc_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#ad61570016524a1d7411c8b3c64354964">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#aab163089fbc11ff4c488645833e0b89c">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>count_running_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a414f3e223753f1e7ce0225848ac33379">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a50fe0638cee223af901c6e4fcbb00ce1">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#afbb012326e074b38548ac7341404774b">Bio::EnsEMBL::Hive::Queen</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a7e7eed865f3ba9395495adf304668843">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>create_cached_dba()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a1cdc4eafa4fb5abf83942dfe21e3a7ff">Bio::EnsEMBL::Hive::URLFactory</a>
+</li>
+<li>create_new()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a>
+</li>
+<li>create_new_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a9cd9baa52f9e7a2240ffb979518cfee1">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>CreateNewJob()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a77f78d2fe7e5ac25737ff9322d40e4f9">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>csvq()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a77d324a4242b0c01f6f1288846db43d6">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>ctrled_analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa7553c12b9b1af1c15d147dd5f5d4fac">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+</li>
+<li>ctrled_analysis_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4c95d1a0114e3d438f8b3b71d40cd70">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_d.html b/docs/doxygen/functions_d.html
new file mode 100644
index 0000000000000000000000000000000000000000..ff3034b30028108d62f7431008568d62bfa48fd9
--- /dev/null
+++ b/docs/doxygen/functions_d.html
@@ -0,0 +1,286 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta name="generator" content="Doxygen 1.8.6"/>
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+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
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+ <div id="navrow1" class="tabs">
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+ <li><a href="files.html"><span>Files</span></a></li>
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+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
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+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li class="current"><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
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+$(document).ready(function(){initNavTree('functions_d.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
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+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_d"></a>- d -</h3><ul>
+<li>dangerous_math()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#add6d6e854b8d35f11810311490b17ab9">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+</li>
+<li>data_dbc()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>dataflow()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a16b156d26595a7d16e0e04b60d5f6f36">Bio::EnsEMBL::Hive::Accumulator</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a34c62ade6f73ec76a1b2e46eefdc3f41">Bio::EnsEMBL::Hive::NakedTable</a>
+</li>
+<li>dataflow_output_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a02aa287f1ac4ae8ff473bb550dcf5355">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>dataflow_rules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae830f1e7b046d1787e65ece0cebc30cd">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>db()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>db_cmd()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>db_connect_command()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>db_execute_command()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>dba()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#aae6bcf902b62b4a4b698c2ad04165cbe">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>dbc()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a704db480f27205d0cf17952fd54ffddf">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>dbconn_2_mysql()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>dbconn_2_pgsql()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>dbconn_2_url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>debug()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a274245e911fc8e5f0ef621993c96732a">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>decrease_required_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a98976d888957cc7231fcc50e44f21408">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>decrease_running_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a15fd023779f6e61df20d84d70dc3e28f">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>decrease_semaphore_count_for_jobid()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a1518bf5c281727593960180483f8554b">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>default_config_files()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a2bd177535ba7ff4f0d8990a6c50a1241">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>default_input_column_mapping()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a66f32625d1fbafc4fafbbc23ac11b442">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>default_insertion_method()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a462f42ba52299b0402dea71c1f265dba">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#a7a0b17cb2cc51e54df8397325bcc9b88">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#ac91050686189e4d62b84fc5ac21c9399">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#a66aa80f75c5e69493344e9b8f94142bc">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#ac3f259e9b0d6c54b67a3bd027e8e46f9">Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ab0c7e6cbb62054c0076d73a52efe9141">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>default_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_apply_to_databases__conf.html#a9e6433a752ae91242daaed87123f7ad3">Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html#a1763292c10a5df1d25ec8ffbbaeefd75">Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#a77596009fcf0b4b84e07090667b28e2f">Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a28568127780ecee07cde885f1ec1a1f3">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html#a2a5f21f07b20e9a7a2e188771f7e5400">Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf</a>
+, <a class="el" href="class_mini_pecan_multi__conf.html#a80b54e2491d5ea2289c81e3fc5e7745a">MiniPecanMulti_conf</a>
+, <a class="el" href="class_mini_pecan_single2__conf.html#ab1bb3850c9086897fc4f0cadf59b4cac">MiniPecanSingle2_conf</a>
+, <a class="el" href="class_mini_pecan_single3__conf.html#acfb2470be4a35c3a5d63df3fa4e96ad2">MiniPecanSingle3_conf</a>
+, <a class="el" href="class_mini_pecan_single__conf.html#a3c145006e519882ca8d9c95d965af7ff">MiniPecanSingle_conf</a>
+</li>
+<li>default_overflow_limit()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ad5638f98e14c623db7787ae6da2f38cf">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>default_table_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html#a300d9c9d8f8ade46655850dd61771472">Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a50439fb73efbfd5e2ec3cfd8839c483c">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#aa39019f2695173ed4d98c1e46277c1f7">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html#a32effe05fbc822b45f5505997faab25c">Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a0c5b6bbd627a70f5d1eb35b24b6e2d91">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a7d096d983b7596fa83094ebbb8ebb06a">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae3e95ef6cee275aa2ace188e45da854a">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a1ef36bbed301036800367e22c6895f13">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#a9c5a35a90a18728182e12a66503ced26">Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#afee7422722307560e830dd17c7065993">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a2b2f74be0c9bbc3330a2bfa1c97c5e99">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#ad87ef629a730873721e4486ab5176fd0">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#a06ce8d0d67b24247c234a7a9637a3b09">Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a545edfa6d9aa715376d5ed7d20767755">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>description()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afea6647d740defa4fe2f636cd24b02cd">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>destringify()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ac3350cd70c4187290ded88a59533e62d">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>DESTROY()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#acf08a2e7774e3dcc8643f8703d068c6a">Bio::EnsEMBL::Hive::URLFactory</a>
+</li>
+<li>determine_status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a2f551acaf61aa9bf888e5d2246002170">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>died()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abd46b21982209917b8fbace6d01ac0a5">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>dir_revhash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a8c682e65730f8bb07e2d6274958b640d">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>display_subgraph()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#af99b2f612b6d9e52dbbf721c0993c746">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>done_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a8cbcb7b573a6c3277ac69456dca161fa">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
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+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li class="current"><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
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+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
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+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_e"></a>- e -</h3><ul>
+<li>enter_status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a13e1e3b2aa2905efe3f7dfef55019d2c">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>execute_writes()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#acc3848e02dd266ca7c193257ec036701">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
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+</table>
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+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
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+ </li>
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+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li class="current"><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_f.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_f"></a>- f -</h3><ul>
+<li>failed_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a49f5385adef0220da9708e24eeba68e2">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>failed_job_tolerance()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a7ed5f556571a2e8e8b9eec34d19935e1">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>fan_cache()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a48bcb9722516ca9456c53dd1732c394d">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>fetch()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">Bio::EnsEMBL::Hive::URLFactory</a>
+</li>
+<li>fetch_all()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>fetch_all_by_analysis_id_status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#aad1bc73bd8052820705590bf853e34f0">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>fetch_all_by_suitability_rc_id_meadow_type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#ae2e16bd96ffd64af54c59ba31f6becb1">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>fetch_all_dead_workers_with_jobs()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a1ec8aba875ab47959d2714b32b04a5d2">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>fetch_all_failed_analyses()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#ae87626fc8dec5f006d35ee4d780c090a">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+</li>
+<li>fetch_all_incomplete_jobs_by_worker_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ae84a1895b984f71659306509aac7b3d3">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>fetch_by_dbID()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>fetch_by_logic_name_or_url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#afb5c2b354ab0889fff2d55ef7c87443e">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+</li>
+<li>fetch_by_url_query()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a59abab89460a304db992a7a19669fcbc">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ab3ffe9d373143c197120510bbd7f85d7">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>fetch_input()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#ae38dde4f24511a8913461f18ae56067b">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a0574c8877209e27b076ef7afe573baa2">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a9ca1fe4defa82d28bc60b64fb4c9cf71">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a364bc206bd7c1d93307258ff83b3fcce">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a18e25e086249fc4775be954efe8efaef">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#adf959e0495247f1455195ab4d5761725">Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aefd561f1a619b59d3b784bdb78a54439">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#a2b25c050ce8cf7f5b8a12e0a21f2203d">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#ae903a369bd861a15a9826fa15fa8fa08">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#a8796e11e1db7a6fd716e684198dfc282">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#acabf587c254445072170ed6c7858cbe3">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#ae29716145f0f87688b97e906c8247c5f">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a>
+</li>
+<li>fetch_input_ids_for_job_ids()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a33703ebaa739dc4c4924cad07e2abd25">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>fetch_overdue_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a47b088cb6be9493e6853b5ee0b20b522">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>fetch_some_by_analysis_id_limit()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a171ed08ff5a07ce88413d1257093f7e5">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>fetch_structures_for_job_ids()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html#a5ecf1d84e9aabb00cffc7c4df537b98c">Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor</a>
+</li>
+<li>fetch_value_by_key()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#a872fcb522c8b0322daf1033f7e2fa41e">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor</a>
+</li>
+<li>final_decision()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a968b5a54d803a5e4e291cd9510940309">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>find_all_sql_schema_patches()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a4dd0e15f6e51c889ed715aee9275e54d">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a>
+</li>
+<li>find_available_meadow_responsible_for_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#ae5d7a34a10c8f72107156a73d348b54f">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>find_out_causes()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#ae6030241c373e061f40881edf6e01878">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>find_submodules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a487b583d13e668734c35bcff7e427d9b">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>from_analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ad8140faa5aec71033ae2cc3e69571246">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>from_analysis_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ac13454a4f86e556f82560a7f2967fc53">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>funnel_dataflow_rule_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#aec851945dd9ebf3652224066b8d271e8">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func.html b/docs/doxygen/functions_func.html
new file mode 100644
index 0000000000000000000000000000000000000000..17f729b61ab7a10430a3ff8bfce4556879d01b7f
--- /dev/null
+++ b/docs/doxygen/functions_func.html
@@ -0,0 +1,243 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
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+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li class="current"><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
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+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
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+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index__"></a>- _ -</h3><ul>
+<li>_add_analysis_node()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a15c083cbf55912f540a1a62c63f36ccd">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_add_hive_details()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ad0284a21114d9ea4bc9569b28b86b3ac">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_add_table_node()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f15e355d2750a68a1a219ef2decc55a">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_add_together()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a58596178ed9c2bb86dbaca822ce0f29a">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a>
+</li>
+<li>_allocate_to_subgraph()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a56fbf0b2d2c70f562cb8aaa6c430ee64">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_analysis_node_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ab6415312e311c5a6fe8d7aa89ba3684a">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_as_debug()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a65653a19ade3aa317b9a40dac5af679b">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>_control_rules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a0a4df43f72b40dfdbbd100f957a430c3">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_dataflow_rules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#af6624dc439ed366dc32f51716c1de48f">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_fisher_yates_shuffle_in_place()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a051cdcc9af5a857e02f899adf0736c46">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_get_rows_from_list()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a046e795740452e442df65849921da767">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_get_rows_from_open()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#ac5c6183dcd03bbfdb054253cbd4b7405">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_get_rows_from_query()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a66dd4176925958a32b1e09ec6b381f6e">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_get_table_list()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a8e55c7699aa239e5c5550427bed3eed9">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a>
+</li>
+<li>_midpoint_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a546d1e3d214a8c2ba2c25a8d94ac0813">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_options()
+: <a class="el" href="class_script.html#ac470265a113d3130aa1699814c37df13">Script</a>
+</li>
+<li>_param_possibly_overridden()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a0536cad5480d931d7982fe0f049ebfaf">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>_param_silent()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a416e12ae4a4511ba13ba427cfc2361d5">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>_process_options()
+: <a class="el" href="class_script.html#ab630c1fc26dd8c0aeef54acc78113515">Script</a>
+</li>
+<li>_rec_multiply()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aae56050726847606ccb5ea8c7516dc75">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a>
+</li>
+<li>_run_test()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a1341a510369536f2cbcd09fdd2050bf2">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a>
+</li>
+<li>_subst_one_hashpair()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a960052271c6be58027f13c1cadbe5ad8">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>_substitute_minibatched_rows()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a1d866fc6d59bb185b2a7630583b6a93a">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_substitute_rows()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a32b9467b5a794591dd41d0c471c1dab6">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+</li>
+<li>_table_info_loader()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a348c46fdc789f2eb970dfcc5260aaa28">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>_table_node_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#af860b66fd159323a7c507fa27b2f3794">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>_unit()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a278a474770becadc0c47562beb111e4f">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>_validate_tests()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a3d33b3c3256122e564dfffc8b745f5af">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a>
+</li>
+<li>_write_graph()
+: <a class="el" href="class_script.html#a1b841ee95221494ac0b4eb534f0e8c82">Script</a>
+</li>
+</ul>
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+<title>ensembl-hive: Class Members - Functions</title>
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+ <li class="current"><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
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+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
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+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
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+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_a"></a>- a -</h3><ul>
+<li>accu_hash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1a33fd570abad2c0f79c22bc5d77d652">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>accu_id_stack()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52165b28650c26a24b621da4ff2e777a">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>accumulated()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a243a5222c2176291094dd9d83b51b7c3">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>adaptor()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a7dd96c5cf6b8c8c4b4b1447923250373">Bio::EnsEMBL::Hive::Accumulator</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ab689e0f33659659ebdc4396b237df113">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#ae26cea149a37ce38a76340febf821ea3">Bio::EnsEMBL::Hive::NakedTable</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a253a528483f463acf6db1e49f54c75a2">Bio::EnsEMBL::Hive::ResourceDescription</a>
+</li>
+<li>analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a21e51ec58fe708d8875617da6912ca46">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a9447a3ac1aa3c45822c8d495c405785e">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>analysis_capacity()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a0ecb60e98a4410c8bbf7bdb0784c9785">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>analysis_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ad43a29a7f535cc507f91702fad70b310">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a9dea5f797f92fa7dd1e06a67f0bcd401">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aa7b8e54f437a9427f268c91ed61626e5">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>autoflow()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ac5bab7c3ffa521e44370d1bdc34cf11a">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>autoinc_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a7da3298fc1c03c9e7e07123fb710e9a5">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>AUTOLOAD()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a4805f85a21ec6b85814f32312ee36711">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>available_capacity()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a6e64029524e47016b9db01936324f8d2">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>available_meadow_hash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a3d03fc09525b8349ab06bff8e387686e">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>avg_input_msec_per_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4015806ce9a0a952ec992386f323ecd4">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>avg_msec_per_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0aee41e0ab6ecb6e1726a2254a1c5256">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>avg_output_msec_per_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a763d7539d36a921ba14409ffdd805a04">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>avg_run_msec_per_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adc046b69d9e806527342f79319818631">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_b.html b/docs/doxygen/functions_func_b.html
new file mode 100644
index 0000000000000000000000000000000000000000..7c56eb72a22e4a79fb439397292113dab8a27fa7
--- /dev/null
+++ b/docs/doxygen/functions_func_b.html
@@ -0,0 +1,180 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
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+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+ <li>
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+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li class="current"><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
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+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func_b.html','');});
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+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_b"></a>- b -</h3><ul>
+<li>balance_semaphores()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ac9e28226315228b396483078e3823515">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>batch_size()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a4889ae9b5d00bcb53add084060676301">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>beekeeper_extra_cmdline_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7a8b253910f9f1bd288b4c1526353cd8">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>behaviour()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac5a95b82fd9ad6752c5eeb4527714d8e">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>born()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a0904a2e1b64e956c6400d8344eb6fc71">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>branch_code()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ad765dadb213174df11b5f31e3248b9db">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>branch_name_2_code()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a529c8c386c3e60cb1a737231775bf77c">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a>
+</li>
+<li>build()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#ad7fad3a0d313ae9d07c6b6e636876109">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_c.html b/docs/doxygen/functions_func_c.html
new file mode 100644
index 0000000000000000000000000000000000000000..1e4004bcb1f2b408cbb89c221f43fb60c168cc3d
--- /dev/null
+++ b/docs/doxygen/functions_func_c.html
@@ -0,0 +1,255 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
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+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
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+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li class="current"><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
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+ <div id="nav-sync" class="sync"></div>
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+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func_c.html','');});
+</script>
+<div id="doc-content">
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+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
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+
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+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_c"></a>- c -</h3><ul>
+<li>can_be_empty()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9371f668649753210a7a301b02f6f855">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>can_respecialize()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a0c047d0bd965ee20025093fa837ee897">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>cause_of_death()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3c525fb34ae49638bf9898949f995388">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>check_blocking_control_rules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a5d40dc556b755e7aed76e02fe6550b65">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>check_for_dead_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a020be70f3da4eca961fef537e68daca6">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>check_in_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a8ec0da9cd78a6fc994786f65b8710a7d">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>check_object_present_in_db()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a73ed3c029cb8e6ba86cfd3159de577b2">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>check_worker_is_alive_and_mine()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa5ed36b42e1e9a3eeb2f2474c37cab8f">Bio::EnsEMBL::Hive::Meadow</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a460348aa64020e5d8a747991f831cd05">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a9a3c0c5e45f0c8d8f39c353f3613366d">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>cleanup_worker_temp_directory()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a35dbbcb04656e835a31cbc927b2c8584">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>colour_offset()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a7b1487d4809792cc1322687655f2d984">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>colour_scheme()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#afe6a7243b9051c98db319ecbcf89d212">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>column_set()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ada55ab8c29c95535953efb0ca8c1d805">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>completed()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#adf437552d1a1b96a0fb1868b7ee58e0b">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>condition_analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#a7cec568f2499ba88040334c408efeb6b">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+</li>
+<li>condition_analysis_url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa1408c2380cfa9fc9d4b22458bdfd1cb">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+</li>
+<li>config()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a38c57142acfd31f32e87a94717620baf">Bio::EnsEMBL::Hive::Configurable</a>
+</li>
+<li>config_get()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#aeed405377caddb6a1aa3cb605ed6304f">Bio::EnsEMBL::Hive::Configurable</a>
+</li>
+<li>config_hash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#ab0ede51b2658eddc43a8f6e9fbf34509">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>config_set()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a3e556c76396430193c3f613c6f3e4079">Bio::EnsEMBL::Hive::Configurable</a>
+</li>
+<li>context()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html#a419025891535ecd7b2f05183cf2ce8e4">Bio::EnsEMBL::Hive::Configurable</a>
+</li>
+<li>continue()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#ad91a33ccd3234b64b19bc3083e9367f0">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>count_all()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a5675f57702aa4cae6bfc1e39eb420bde">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>count_pending_workers_by_rc_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#ad61570016524a1d7411c8b3c64354964">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#aab163089fbc11ff4c488645833e0b89c">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>count_running_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a414f3e223753f1e7ce0225848ac33379">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a50fe0638cee223af901c6e4fcbb00ce1">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#afbb012326e074b38548ac7341404774b">Bio::EnsEMBL::Hive::Queen</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a7e7eed865f3ba9395495adf304668843">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>create_cached_dba()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a1cdc4eafa4fb5abf83942dfe21e3a7ff">Bio::EnsEMBL::Hive::URLFactory</a>
+</li>
+<li>create_new()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a90b0359523ef5040fd0e839edd83cca4">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a>
+</li>
+<li>create_new_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a9cd9baa52f9e7a2240ffb979518cfee1">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>CreateNewJob()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a77f78d2fe7e5ac25737ff9322d40e4f9">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>csvq()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a77d324a4242b0c01f6f1288846db43d6">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>ctrled_analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#aa7553c12b9b1af1c15d147dd5f5d4fac">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+</li>
+<li>ctrled_analysis_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4c95d1a0114e3d438f8b3b71d40cd70">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_d.html b/docs/doxygen/functions_func_d.html
new file mode 100644
index 0000000000000000000000000000000000000000..6ce418f89786e45ae19b5791b8f39def1eec1248
--- /dev/null
+++ b/docs/doxygen/functions_func_d.html
@@ -0,0 +1,286 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li class="current"><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+$(document).ready(function(){initNavTree('functions_func_d.html','');});
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+ onmouseout="return searchBox.OnSearchSelectHide()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_d"></a>- d -</h3><ul>
+<li>dangerous_math()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#add6d6e854b8d35f11810311490b17ab9">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+</li>
+<li>data_dbc()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afe4af3210589a3123a939ceaf83c0462">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>dataflow()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a16b156d26595a7d16e0e04b60d5f6f36">Bio::EnsEMBL::Hive::Accumulator</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a34c62ade6f73ec76a1b2e46eefdc3f41">Bio::EnsEMBL::Hive::NakedTable</a>
+</li>
+<li>dataflow_output_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a02aa287f1ac4ae8ff473bb550dcf5355">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3fd5b992716a3aa9a5810da1f007aa5b">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>dataflow_rules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae830f1e7b046d1787e65ece0cebc30cd">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>db()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a8ca200c10405c13d535353f2646b49a1">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>db_cmd()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a766a75f28b07ea491d7e8fdc97ee2ad6">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>db_connect_command()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#afa08fa64e8dc50604507f72fece0b9e2">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>db_execute_command()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a96f20328299d6747be0b641087c012ee">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>dba()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#aae6bcf902b62b4a4b698c2ad04165cbe">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+<li>dbc()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a704db480f27205d0cf17952fd54ffddf">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#afb5ddec979f7e2ed1f2dc375e26c4456">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>dbconn_2_mysql()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a08af9a5dfe9c8a40757a6b3140d4a569">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>dbconn_2_pgsql()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a116f65a759b66589980b5c84b0cfe1c4">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>dbconn_2_url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#af4d7bd7b523fc76a3c58aa15141c5f2c">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>debug()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a4c9739f352e4eea538b17bb88de70285">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a274245e911fc8e5f0ef621993c96732a">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>decrease_required_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a98976d888957cc7231fcc50e44f21408">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>decrease_running_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a15fd023779f6e61df20d84d70dc3e28f">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>decrease_semaphore_count_for_jobid()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a1518bf5c281727593960180483f8554b">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>default_config_files()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a2bd177535ba7ff4f0d8990a6c50a1241">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>default_input_column_mapping()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a66f32625d1fbafc4fafbbc23ac11b442">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a2f77cbefb20d4b4e3a40cf75ce420036">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>default_insertion_method()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a462f42ba52299b0402dea71c1f265dba">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#a7a0b17cb2cc51e54df8397325bcc9b88">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a129b813103eead72607723d43d3a6567">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#ac91050686189e4d62b84fc5ac21c9399">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#a66aa80f75c5e69493344e9b8f94142bc">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#ac3f259e9b0d6c54b67a3bd027e8e46f9">Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ab0c7e6cbb62054c0076d73a52efe9141">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>default_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_apply_to_databases__conf.html#a9e6433a752ae91242daaed87123f7ad3">Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html#a1763292c10a5df1d25ec8ffbbaeefd75">Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#a77596009fcf0b4b84e07090667b28e2f">Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a28568127780ecee07cde885f1ec1a1f3">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html#a2a5f21f07b20e9a7a2e188771f7e5400">Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf</a>
+, <a class="el" href="class_mini_pecan_multi__conf.html#a80b54e2491d5ea2289c81e3fc5e7745a">MiniPecanMulti_conf</a>
+, <a class="el" href="class_mini_pecan_single2__conf.html#ab1bb3850c9086897fc4f0cadf59b4cac">MiniPecanSingle2_conf</a>
+, <a class="el" href="class_mini_pecan_single3__conf.html#acfb2470be4a35c3a5d63df3fa4e96ad2">MiniPecanSingle3_conf</a>
+, <a class="el" href="class_mini_pecan_single__conf.html#a3c145006e519882ca8d9c95d965af7ff">MiniPecanSingle_conf</a>
+</li>
+<li>default_overflow_limit()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ad5638f98e14c623db7787ae6da2f38cf">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac73267d0e33aad126c188108f7e7c468">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>default_table_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html#a300d9c9d8f8ade46655850dd61771472">Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a50439fb73efbfd5e2ec3cfd8839c483c">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#aa39019f2695173ed4d98c1e46277c1f7">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html#a32effe05fbc822b45f5505997faab25c">Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a0c5b6bbd627a70f5d1eb35b24b6e2d91">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a7d096d983b7596fa83094ebbb8ebb06a">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae3e95ef6cee275aa2ace188e45da854a">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a1ef36bbed301036800367e22c6895f13">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#a9c5a35a90a18728182e12a66503ced26">Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#afee7422722307560e830dd17c7065993">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a2b2f74be0c9bbc3330a2bfa1c97c5e99">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#ad87ef629a730873721e4486ab5176fd0">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#a06ce8d0d67b24247c234a7a9637a3b09">Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a545edfa6d9aa715376d5ed7d20767755">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>description()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afea6647d740defa4fe2f636cd24b02cd">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>destringify()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ac3350cd70c4187290ded88a59533e62d">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>DESTROY()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aeac6bf08072f89a153165ea39b8ed7a1">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#acf08a2e7774e3dcc8643f8703d068c6a">Bio::EnsEMBL::Hive::URLFactory</a>
+</li>
+<li>determine_status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a2f551acaf61aa9bf888e5d2246002170">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>died()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abd46b21982209917b8fbace6d01ac0a5">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>dir_revhash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a8c682e65730f8bb07e2d6274958b640d">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>display_subgraph()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#af99b2f612b6d9e52dbbf721c0993c746">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>done_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a8cbcb7b573a6c3277ac69456dca161fa">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_e.html b/docs/doxygen/functions_func_e.html
new file mode 100644
index 0000000000000000000000000000000000000000..f23c418cad00b9dda8170a36cca6325abbf27ea4
--- /dev/null
+++ b/docs/doxygen/functions_func_e.html
@@ -0,0 +1,164 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
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+ $(document).ready(initResizable);
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
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+ <div id="navrow1" class="tabs">
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
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+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li class="current"><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
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+ 
+
+<h3><a class="anchor" id="index_e"></a>- e -</h3><ul>
+<li>enter_status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2344d158b5ca1a21fa9975fd424a3e6b">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a13e1e3b2aa2905efe3f7dfef55019d2c">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>execute_writes()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a2172d0e9d3014f2ef8f117176904fde3">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#acc3848e02dd266ca7c193257ec036701">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
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+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
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+</body>
+</html>
diff --git a/docs/doxygen/functions_func_f.html b/docs/doxygen/functions_func_f.html
new file mode 100644
index 0000000000000000000000000000000000000000..758fa548145e218ae21b3ca8e90d48a0f6206549
--- /dev/null
+++ b/docs/doxygen/functions_func_f.html
@@ -0,0 +1,250 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
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+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li class="current"><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+$(document).ready(function(){initNavTree('functions_func_f.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
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+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_f"></a>- f -</h3><ul>
+<li>failed_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a49f5385adef0220da9708e24eeba68e2">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>failed_job_tolerance()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a7ed5f556571a2e8e8b9eec34d19935e1">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>fan_cache()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a48bcb9722516ca9456c53dd1732c394d">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>fetch()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#a9b61c3f379811a6695c8bf57510fe293">Bio::EnsEMBL::Hive::URLFactory</a>
+</li>
+<li>fetch_all()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a18c6bfae797d67669e16242c2390c379">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>fetch_all_by_analysis_id_status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#aad1bc73bd8052820705590bf853e34f0">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>fetch_all_by_suitability_rc_id_meadow_type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#ae2e16bd96ffd64af54c59ba31f6becb1">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>fetch_all_dead_workers_with_jobs()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a1ec8aba875ab47959d2714b32b04a5d2">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>fetch_all_failed_analyses()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#ae87626fc8dec5f006d35ee4d780c090a">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+</li>
+<li>fetch_all_incomplete_jobs_by_worker_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ae84a1895b984f71659306509aac7b3d3">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>fetch_by_dbID()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a29854e14eb6854bc6871db82fdb89d1f">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>fetch_by_logic_name_or_url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#afb5c2b354ab0889fff2d55ef7c87443e">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+</li>
+<li>fetch_by_url_query()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#a59abab89460a304db992a7a19669fcbc">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ab3ffe9d373143c197120510bbd7f85d7">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>fetch_input()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#acdd4d38526457335f615330593ab9329">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#ae38dde4f24511a8913461f18ae56067b">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a0574c8877209e27b076ef7afe573baa2">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a9ca1fe4defa82d28bc60b64fb4c9cf71">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a364bc206bd7c1d93307258ff83b3fcce">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a18e25e086249fc4775be954efe8efaef">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#adf959e0495247f1455195ab4d5761725">Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#aefd561f1a619b59d3b784bdb78a54439">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#a2b25c050ce8cf7f5b8a12e0a21f2203d">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#ae903a369bd861a15a9826fa15fa8fa08">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#a8796e11e1db7a6fd716e684198dfc282">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#acabf587c254445072170ed6c7858cbe3">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#ae29716145f0f87688b97e906c8247c5f">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a>
+</li>
+<li>fetch_input_ids_for_job_ids()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a33703ebaa739dc4c4924cad07e2abd25">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>fetch_overdue_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a47b088cb6be9493e6853b5ee0b20b522">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>fetch_some_by_analysis_id_limit()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a171ed08ff5a07ce88413d1257093f7e5">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>fetch_structures_for_job_ids()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html#a5ecf1d84e9aabb00cffc7c4df537b98c">Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor</a>
+</li>
+<li>fetch_value_by_key()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#a872fcb522c8b0322daf1033f7e2fa41e">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor</a>
+</li>
+<li>final_decision()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a968b5a54d803a5e4e291cd9510940309">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>find_all_sql_schema_patches()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a4dd0e15f6e51c889ed715aee9275e54d">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a>
+</li>
+<li>find_available_meadow_responsible_for_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#ae5d7a34a10c8f72107156a73d348b54f">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>find_out_causes()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#ae6030241c373e061f40881edf6e01878">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>find_submodules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a487b583d13e668734c35bcff7e427d9b">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>from_analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ad8140faa5aec71033ae2cc3e69571246">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>from_analysis_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ac13454a4f86e556f82560a7f2967fc53">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>funnel_dataflow_rule_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#aec851945dd9ebf3652224066b8d271e8">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_g.html b/docs/doxygen/functions_func_g.html
new file mode 100644
index 0000000000000000000000000000000000000000..4db37fb31b5364805f687cb6b44221b9a5011f7f
--- /dev/null
+++ b/docs/doxygen/functions_func_g.html
@@ -0,0 +1,247 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
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+<link href="doxygen.css" rel="stylesheet" type="text/css" />
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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+var searchBox = new SearchBox("searchBox", "search",false,'Search');
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li class="current"><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+ onmouseover="return searchBox.OnSearchSelectShow()"
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+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_g"></a>- g -</h3><ul>
+<li>gc_dataflow()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a64c5703becb2a1989bc85e449d961aba">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>generate_job_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#ab8b9ebeacf07bfcb38851edbfdd0ae2f">Bio::EnsEMBL::Hive::Meadow</a>
+</li>
+<li>get()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a61b3f0cfb4fb961204ed1be500a6443e">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>get_analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ab3a0f109fab512fdae003e708d4c28df">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>get_available_adaptors()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a0baccc85ec9695e7ffa80c16d54cb9d9">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
+</li>
+<li>get_available_meadow_list()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a77f0a0b7a8de56d43c0271065bef6ebe">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>get_code_sql_schema_version()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a0c2dc02c4e81944f9eb9fa7f670aa753">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a>
+</li>
+<li>get_code_version()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_version.html#a8ec4c346c160d25cab629a0c56af720b">Bio::EnsEMBL::Hive::Version</a>
+</li>
+<li>get_compiled_module_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#aa3cfa679262a347a86a83079bde1037d">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>get_current_worker_process_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a2fec4ae34aa12e9249775e5cc3e5ba1e">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a8f756d46474a89b07f63d23ac1b744f9">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>get_default_meadow()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a80eeade51960beb35d31f35cf61f4c79">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>get_elapsed()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#ad933938ea83c78477a8580d500fdec94">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>get_hive_current_load()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#abe36b590f923d7e82d3577f484bd6056">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>get_meadow_capacity_hash_by_meadow_type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a04d1116b668a322e92ad5c916cffe4b9">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>get_nodes_that_point_at()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a20c82c55eba3cfa7120208fe131a94d1">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>get_num_failed_analyses()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#afdadb6fce4eb7469f6de433612867dd5">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>get_or_estimate_batch_size()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac31170452fe2a74986b93ed13eb697c3">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>get_param_hash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a9b86c006546292af7280396e0e86ad41">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a>
+</li>
+<li>get_pending_worker_counts_by_meadow_type_rc_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#aee959b792ccd1f79a3edb5e0f53cd38b">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>get_remaining_jobs_show_hive_progress()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a51b365aa339df1f733167970be158c63">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>get_row_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#aadc21d596971f8edf7410fbeec1f77ba">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>
+</li>
+<li>get_sql_schema_patches()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#aa6e8545c8a07176e86265ac18f684060">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a>
+</li>
+<li>get_stderr_redirector()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a6b49c7779e183bd1e314bc76354cd569">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>get_stdout_redirector()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aa4629bbbaa4103888c05c5936ae2823e">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>get_top_clusters()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#ac3527fe831ae9d80d246ce20072eb10e">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>get_workers_rank()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ad5392456810e1f4bb16291b54a731c0a">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>go_figure_dbc()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#aa1cbcb45d800cf3c5b47079e0b27e237">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>grab_jobs_for_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#aa023b41587da0be31418d3d871df7cdc">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>grab_memory()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a76caed50af47567cd2fd93ea4b7b3f8a">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+</li>
+<li>graph()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f9efde876681aea12fc343faae97dab">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
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+ <li class="footer">Generated by
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+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_h.html b/docs/doxygen/functions_func_h.html
new file mode 100644
index 0000000000000000000000000000000000000000..483a3aa0442954aceb043f5aa1d03de9194a1327
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+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="dynsections.js"></script>
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ onmouseover="return searchBox.OnSearchSelectShow()"
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+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li class="current"><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_h"></a>- h -</h3><ul>
+<li>hash_leaves()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>hive_capacity()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adf47bc7ce9c36899897d76f526e26e72">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>hive_meta_table()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a354e9305c82d67b99b5d0b159f2382db">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a>
+</li>
+<li>hive_use_param_stack()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a364f93a3a3019a023c09f7fd02313970">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
+</li>
+<li>hive_use_triggers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a5169045d2592861884a452dec9f3dd06">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
+</li>
+<li>host()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3bf4200e3a8a6603db7ef6a544df3356">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_i.html b/docs/doxygen/functions_func_i.html
new file mode 100644
index 0000000000000000000000000000000000000000..5e32c14f4428ce81521430402a28ae4bc88a8b83
--- /dev/null
+++ b/docs/doxygen/functions_func_i.html
@@ -0,0 +1,206 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+ <li>
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+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
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+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li class="current"><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+ class="ui-resizable-handle">
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+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func_i.html','');});
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+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
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+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_i"></a>- i -</h3><ul>
+<li>incomplete()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a7ba3562d4484fea866441d7d501d4900">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>increase_required_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a08e32841d6e713fc8b4eada7a3057d8d">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>increase_running_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#aff5f1a7e1f8579cd228352678cce7b78">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>increase_semaphore_count_for_jobid()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ac693f76b13041b3709e5d6a11ac03820">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>init()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a85d390e244fcd69c62f4544d8b384e44">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>inprogress_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a859730fee45d764bdc4fbaa50be04ca3">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>input_capacity()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aa2d5e93ea9239788909138d5eecf044e">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>input_column_mapping()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>input_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a9dd7289999985b60a8299ac66327f3ce">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>input_id_template()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a7a2ba2f2f0e72775363943785b918b90">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>input_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>insertion_method()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a386c4340b8343abd91aaf33ad66d61a1">Bio::EnsEMBL::Hive::NakedTable</a>
+</li>
+<li>interval_update_work_done()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a57f38be49bb6727b4e1dd853b1ad77b3">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>is_counting()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a27af7e8ae932532af50bfee75b08d2f3">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>is_fully_substituted_string()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>is_fully_substituted_structure()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_j.html b/docs/doxygen/functions_func_j.html
new file mode 100644
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript">
+ $(document).ready(initResizable);
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li class="current"><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
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+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
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+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_j"></a>- j -</h3><ul>
+<li>job_count_breakout()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a9ef9078ce15a6892e795bf93643ff3cd">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>job_limiter()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a83d25a571d54e205e8707f27f3277b2c">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>job_name_prefix()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a8d9888b59ba0e3fe41ac963b6415b894">Bio::EnsEMBL::Hive::Meadow</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_k.html b/docs/doxygen/functions_func_k.html
new file mode 100644
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--- /dev/null
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+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
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+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
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+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
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+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li class="current"><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
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+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func_k.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_k"></a>- k -</h3><ul>
+<li>keys_to_columns()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a>
+</li>
+<li>kill_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aad175b19c6c543012f5455740b539ba2">Bio::EnsEMBL::Hive::Meadow</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a2b3d6f77f19e0a635a444d551715704e">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#accdb28c3a317e4ecc45368b83a426a0c">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_l.html b/docs/doxygen/functions_func_l.html
new file mode 100644
index 0000000000000000000000000000000000000000..5f4677ff031c90b9dde32820b973fb3ac09d9f5c
--- /dev/null
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@@ -0,0 +1,192 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+ <li>
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+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+ <input type="text" id="MSearchField" value="Search" accesskey="S"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li class="current"><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func_l.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_l"></a>- l -</h3><ul>
+<li>last_check_in()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a23a37f5e84b64bdeb435f726e20255fc">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>last_update()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a089b03c15eeb063a7cbae758f72f6637">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>lethal_for_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1fb261840767255efd596b84312532d1">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>life_cycle()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>life_span()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a83d94917e06cca7e9f59aa999bec0c45">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>life_span_limit_reached()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#affdf64209cfb2b62895ced6e678206a9">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>lifespan_stopwatch()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a529d571f05adaa243ced017ee4c51fd2">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>load_cmdline_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>load_file_or_module()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a1956b39203f4df86e8d7aac981462ee5">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>load_from_json()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a4d561e831fd88920ca38ba78582a7f93">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>log_dir()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a2ddf6136f8b9cb3fca032b2ba6f152ff">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>logic_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6528be48120416c630abe32227e70bdb">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_m.html b/docs/doxygen/functions_func_m.html
new file mode 100644
index 0000000000000000000000000000000000000000..fd31dd968be13cdd1bb45912abdcda10f663ca87
--- /dev/null
+++ b/docs/doxygen/functions_func_m.html
@@ -0,0 +1,208 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li class="current"><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func_m.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_m"></a>- m -</h3><ul>
+<li>main()
+: <a class="el" href="class_script.html#a1bd6f4c8c62743400cdc430f3e4d6c21">Script</a>
+</li>
+<li>mark_stored()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2a39cbb60a5021d1cd5a4e385da4000f">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a>
+</li>
+<li>max_retry_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9fbc0420b87a63af05d8e741b14ef14a">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>meadow_class_path()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a63cab22c63e3c5aa31191ec02f0a6bf1">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>meadow_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a21077df2d82c57eda4845c9ea1d153d0">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>meadow_type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac41c5978a943fb1bf45a7c42507460ef">Bio::EnsEMBL::Hive::Analysis</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a73ad6041bffcd835a77d9086b2ea1695">Bio::EnsEMBL::Hive::ResourceDescription</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abf98a83eafeb602f3109fb147f9a2c19">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>merge()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a74bd20559c70a83d01236591fc606691">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>merge_from_rules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>min_batch_time()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ab1aa9f23e9feaec53f6e404dfe19f000">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>module()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac491521c673320cec2ce7cecf1d841cd">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>monitor()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a422e896db7c973b0385bbafd2c8aa556">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>more_work_done()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a54f5f9c0d65d4e71c50fd1fdf3e702cc">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>multiplier()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afb7019e05c935b4eb437ab7aaad54f8c">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>mysql_conn()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7c9b7527f3745f962277b5022d1d09ca">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>mysql_conn_from_dbc()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a66b12a83a4107e2f9758fba932642f7b">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#ab2382b362b1dd698c6c7b0a8d02acabe">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>
+</li>
+<li>mysql_dbname()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7660586a322000f6f797927a3a216676">Bio::EnsEMBL::Hive::Params</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_n.html b/docs/doxygen/functions_func_n.html
new file mode 100644
index 0000000000000000000000000000000000000000..db08c607338830e9f0b4f232f0b952af4120324e
--- /dev/null
+++ b/docs/doxygen/functions_func_n.html
@@ -0,0 +1,191 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li class="current"><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
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+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func_n.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
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+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_n"></a>- n -</h3><ul>
+<li>name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a822009e9a5c178598aa5125475b95f18">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a8be5f1cdaa5eb9e07fc29610e678f836">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a4483fbceef09b5b032c54b797fdb73d9">Bio::EnsEMBL::Hive::ResourceClass</a>
+</li>
+<li>new()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#ac035312016653df35c35398474835764">Bio::EnsEMBL::Hive::Accumulator</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ad61a51a522d45f6a30e2a596b5165524">Bio::EnsEMBL::Hive::Analysis</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#a22338588d57d7bf475159a73b4fb10da">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb83a9f0a1fa1cd38bc5ae626bfd6b51">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a63bec749348099898cac9401d6af959b">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#af8321e0eec4a4057a4d103400e549df3">Bio::EnsEMBL::Hive::DataflowRule</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#abf2b541c5d7e3b124323a34356e3ace6">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">Bio::EnsEMBL::Hive::DependentOptions</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a89203ff40a85e13c7ef840a46dcf4487">Bio::EnsEMBL::Hive::Limiter</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#abaa21c35b875562cdf4258eee1b717b3">Bio::EnsEMBL::Hive::Meadow</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a86e40bedaa4255b62bb61b92e1b663c8">Bio::EnsEMBL::Hive::NakedTable</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a5be508c964ea50f555fbd9692a226f67">Bio::EnsEMBL::Hive::Params</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a76ab34ac067611e361c72614a8156cb7">Bio::EnsEMBL::Hive::ResourceClass</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a182572a7a902208f7b78653dbca05fa4">Bio::EnsEMBL::Hive::ResourceDescription</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#ab067dc5c5216255309138355ecb085ee">Bio::EnsEMBL::Hive::URLFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#ae74fdb113363f2f412a30ce66d1651e3">Bio::EnsEMBL::Hive::Utils::Config</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a0452e8098246f27173059b14600f190c">Bio::EnsEMBL::Hive::Utils::Graph</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#a11b71d1d7802b7c52d23f49b8dab377c">Bio::EnsEMBL::Hive::Utils::RedirectStack</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a1cbc5b3e6c40f0a5862e55e228dc34a3">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a51140e4714459dccef65cb34d97bfe13">Bio::EnsEMBL::Hive::Valley</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ac85bb24d028f6a102654f3fdbadf4c74">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>num_required_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0f14ca66c121617e2e6a4f2f7327caa1">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>num_running_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae2ece1ac33d251baa674803832bdae70">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_o.html b/docs/doxygen/functions_func_o.html
new file mode 100644
index 0000000000000000000000000000000000000000..d2a6ea6fb5e9c2fbba6ef238711ac552ee86b4b4
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li class="current"><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+<div id="MSearchSelectWindow"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_o"></a>- o -</h3><ul>
+<li>o()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>object_class()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#abba4ea6afa8067b7e9eefd3278923d6f">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#a944fe8aee65ea55ba1bd54ee77f97849">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#acaa839ac5ee54ada4e4e555205925592">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a9670adf2613b9d268ca2195c33099df5">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a6001078bcc7bcb8fb45f46c415fb65d8">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a834186b707376a4ead29771860ab440f">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#ae3a6f6b2a9e4e71f62d6f9233c522b06">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#aacaba93caa84332eb1713a2218e87b76">Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#af9d2e010bf4d53356d2efde2367c5472">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>objectify()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#ad90a452430769ce22f854fb0d195e905">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a>
+</li>
+<li>output_capacity()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac64ad37ccf27356c480b1d058315d4dd">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>overflow_limit()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_p.html b/docs/doxygen/functions_func_p.html
new file mode 100644
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
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+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
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+ <li>
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+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
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+ <input type="text" id="MSearchField" value="Search" accesskey="S"
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+ 
+
+<h3><a class="anchor" id="index_p"></a>- p -</h3><ul>
+<li>param()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#aacc3d8e3ec1b0f940cc274c95c93e834">Bio::EnsEMBL::Hive::Params</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>param_defaults()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a87f4c403bf90241054674b689d01dd33">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#aebd3288a79a288b73f8527c86fcd6fd9">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a2291deabf24d52906b30ec18d2dbb126">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a80bb69bad70a8a048e373c72621bd7f9">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a4d6debc4b842ca5cdde9707783c62f20">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#ac539ab7a01025992f908be787b08aebb">Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a4b5d3553e76345622fb3fddb0aac447f">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#af07560dd3842fc50a1c2381ab0e338d0">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a53d7a4e8cce22cfbe0eb51f041604ed9">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a454164834bbb0e68d7cd321a4416a506">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a>
+</li>
+<li>param_exists()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a46b02fdd5e620c96f4f8abe8e1bc017b">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>param_id_stack()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb5e9b464027c776b1bd01eaf7b9cfe7">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>param_init()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a03f67c01a12beaa839338be4da9bf9cb">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>param_is_defined()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#ad6dba01319677081085a59310e235c51">Bio::EnsEMBL::Hive::Params</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>param_required()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a82a8b3a737120fdf27b3152bc1c63bab">Bio::EnsEMBL::Hive::Params</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>param_substitute()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a261b12abc17c65fac5fd4ccffbb73d6d">Bio::EnsEMBL::Hive::Params</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>parameters()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#aa4d07a94412dd36e4dbb0d3db533c419">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>parse()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l.html#ac80cc911eba215fb0ed17104861fe5f7">Bio::EnsEMBL::Hive::Utils::URL</a>
+</li>
+<li>parse_cmdline_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad08ca8e7270cfe9c94e0865e3cf75862">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>pause()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a17462e9ef3668063b549484e293c7f24">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>perform_cleanup()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a23b1369583a49f99f47d654993775113">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>pipeline_analyses()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_any_commands__conf.html#a44f48f0a63c2c7b84a029e2f77f99786">Bio::EnsEMBL::Hive::PipeConfig::AnyCommands_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_apply_to_databases__conf.html#ad1acd6cf7955d0a0ed331020d25dbca8">Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html#a8420a6236b02bab63cb9cd160728ce72">Bio::EnsEMBL::Hive::PipeConfig::CompressFiles_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html#a3c0d2ac018f87a5adb6f78764154228f">Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#aaee0e442c23012ab2f414b85adb6a719">Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7072b951f3d57b690c0d2a2465d75d9b">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a0046c9bd300412bda32547458e60064d">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a3c2b04c792006bd1a20941e65aea45ef">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html#a828e67804c29620ff20f5774983a734a">Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html#a4cbb91c590ae6014d587728430df6d11">Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html#a34f0292081b57df3025252e36ba2afa2">Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf</a>
+, <a class="el" href="class_mini_pecan_multi__conf.html#a3f50a960f6c073b41cf825a2057628cc">MiniPecanMulti_conf</a>
+, <a class="el" href="class_mini_pecan_single2__conf.html#a45e6c49458b9a332221b8f49217f8fac">MiniPecanSingle2_conf</a>
+, <a class="el" href="class_mini_pecan_single3__conf.html#a7740c91be5f2d349a94909a7c152a998">MiniPecanSingle3_conf</a>
+, <a class="el" href="class_mini_pecan_single__conf.html#aecd0653da35db4cc26178b9a5bbab306">MiniPecanSingle_conf</a>
+</li>
+<li>pipeline_create_commands()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#ad8d93256c230c0134de507b0fc067dee">Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a031b9cfa37aaf95c3c83fba5c243cad2">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a4e1bcdc9dbc1cdcef52e15361d1ebd09">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a>
+</li>
+<li>pipeline_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3685ec781296c30f00d2a8c4f3efeffc">Bio::EnsEMBL::Hive::Meadow</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>pipeline_url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>pipeline_wide_parameters()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a5b977e0be30a4f60ec9429a399db0fc8">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a3fa7a29fdd8d17ceae1d20c828c85e9e">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html#a722ee2d7f0974ab6865a73290f55adf9">Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf</a>
+</li>
+<li>pop()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#a1f475d12cf96160a963d47c370618856">Bio::EnsEMBL::Hive::Utils::RedirectStack</a>
+</li>
+<li>post_cleanup()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a071768efd731a484438461e833bae07f">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+</li>
+<li>pre_cleanup()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a6d7e5437a262f09e5e9cc37965f07ed1">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+</li>
+<li>pre_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>preliminary_offer()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a344004cad3162eefaa6314cff26fa0b3">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>prev_job_error()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab71a53273f57e143655703eaee5bfdc5">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>prev_job_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a097e33f4921749e52972e051032809c4">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>primary_key()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>primary_key_constraint()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>print_analysis_status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ad396c5be7d6806c71b5740054325d5e6">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>print_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a6080b20b6f65b3a31e72de743db62dac">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>print_running_worker_counts()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#af91dbe0832893ec7ec3ecc8a7f7164dd">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>priority()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ab1e00ad283310e3e6870b133cb029183">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>process()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a45dd4f95b7b508ddf2ba2d620734d96c">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>process_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a631e3067f5825bf38d981150fac0512d">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>process_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">Bio::EnsEMBL::Hive::DependentOptions</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>protected_prepare_execute()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html#aa5dabd385b717af07205feec2e8fee41">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a>
+</li>
+<li>push()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#af152aba8ac48eb58a0a7e1901eb8d94b">Bio::EnsEMBL::Hive::Utils::RedirectStack</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_q.html b/docs/doxygen/functions_func_q.html
new file mode 100644
index 0000000000000000000000000000000000000000..f4940231d9ff8df631242ce5e7b7a4be9163ab8c
--- /dev/null
+++ b/docs/doxygen/functions_func_q.html
@@ -0,0 +1,159 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li class="current"><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func_q.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_q"></a>- q -</h3><ul>
+<li>query_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ab69fe83605e95a9dafb3025e655082b5">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_r.html b/docs/doxygen/functions_func_r.html
new file mode 100644
index 0000000000000000000000000000000000000000..bb4973e637b8772143af2b6148fa5be7151410e9
--- /dev/null
+++ b/docs/doxygen/functions_func_r.html
@@ -0,0 +1,247 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li class="current"><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func_r.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_r"></a>- r -</h3><ul>
+<li>reached()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#ab3f3e0a81d708e08b8c6a0db9d056aac">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>ready_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#af55400b3e85544df26608ac63d98f7bc">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>refresh()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac704b4deb0a318afca57dddff2d891df">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#aed7915b07ea5296ca56e90b46f08553b">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>register_all_workers_dead()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ab4f2cf470e0b3bbe732dd50c22e4deca">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>register_worker_death()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a1dc35ff50f5375e8796f12d17b372773">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>release_and_age_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a375c57130791087ff6781f4cc6cc9b9e">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>release_undone_jobs_from_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a25ddbb1f2f0fada5fc7c9078c887f7d8">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>remove()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>remove_all()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>report_versions()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ae4891d2eb87c70172c9d37b374647144">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>reset_job_by_dbID_and_sync()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a46f196406a5bd9c452a5f94361a2eebd">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>reset_jobs_for_analysis_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a122b718f7e51f923fb50a1c01cb69805">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>reset_or_grab_job_by_dbID()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a4dd834ac1243d05989bcb352021ede70">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>resource_class_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a30049fd09f42f0b709d6785191168587">Bio::EnsEMBL::Hive::Analysis</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a5c5bf7acac77e65b07761146d39bcc24">Bio::EnsEMBL::Hive::ResourceDescription</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aec650e3731644a420c7a2be8597e0250">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>resource_classes()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html#af4f9a637c96b4abb18b8139fff3e885b">Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf</a>
+</li>
+<li>responsible_for_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa65a2353dde2a128123f36543d5aa115">Bio::EnsEMBL::Hive::Meadow</a>
+</li>
+<li>restart()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a233743ce015c7df93ad06562fe3b35dd">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>retry_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae3bad87fd4aff80e2b4ee41185494c64">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>retry_throwing_jobs()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a03e3c2ca474c831a1700dbfdfb424fb6">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>root()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>run()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a0a727e827af0f003386490d0aa3b2af9">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a4be920b14ab4f65812887f02751e1a10">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a525479b5642b24c86208663fa2fd7d4a">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#ad2334d5ffe5a01936cb8c9c365da979c">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a8f3a3f15b7d15493a3e0522a27a2edf5">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#ad709c3f522582c4965ce53adb1499e15">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a12b9e75e3910ce20c4489fa8babe9b6a">Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a5cfb529f37ccb583abe0a1518a86ab2c">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#af26f682eca96b51923aa75c501f21d02">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a4eab23c711954e76734d980c40819726">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#af2232b93770b96595d7e042964379e2c">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a7a00da78d95fdd5a586770e0c6ec1d6b">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a732af3c6c5e3c3eb4f272d0135c073be">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab6456d819b72b807884df4b49ea30492">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>run_one_batch()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a7fe639feb3731120a1a66663e8c2a2e8">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>runnable_object()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a4bc0dde1eb43909e1e8f8a87fd0a3257">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>runtime_msec()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#af050b0e809253aef004926eeaf6cdf75">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_s.html b/docs/doxygen/functions_func_s.html
new file mode 100644
index 0000000000000000000000000000000000000000..6dfe6d5db204ba0fe9639a5446a6f0fcd33db565
--- /dev/null
+++ b/docs/doxygen/functions_func_s.html
@@ -0,0 +1,288 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li class="current"><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
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+ class="ui-resizable-handle">
+ </div>
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+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func_s.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
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+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
+<li>safe_synchronize_AnalysisStats()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#abe0354cbdbf898d95cf08cb2d167ba38">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>schedule_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ad37b01e88608cec39e5f883d95c8ea42">Bio::EnsEMBL::Hive::Scheduler</a>
+</li>
+<li>schedule_workers_resync_if_necessary()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#a65f7b429d0ffbda238faeda2451350a8">Bio::EnsEMBL::Hive::Scheduler</a>
+</li>
+<li>script_usage()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad8abe58a987444c45b366ef5dba4e218">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>seconds_since_last_update()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae96201f918c87593f69279e032fea2a5">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>semaphore_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a75263a4a15c449f509bf35cbead2c54c">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>semaphored_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0a75c8843ba392c7df7a213a0767739f">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>semaphored_job_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1e2d7fa5ae29570bfc2e389dc3abd824">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>set()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a97a169fff464c4653386c08b7df40496">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>set_default_meadow_type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#af85407f558029e59470a282e82c4f8ad">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>signature()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a0594b46314ad2a8894f055bd58ba923c">Bio::EnsEMBL::Hive::Meadow</a>
+</li>
+<li>signature_template()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a9348142e49053884868319ec512435cd">Bio::EnsEMBL::Hive::Accumulator</a>
+</li>
+<li>slicer()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a>
+</li>
+<li>special_batch()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab6470f448766be332f7e4d081e6d7cc2">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>specialize_and_compile_wrapper()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ae432e7a7dbc6a8b0109353d4f6938d9c">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>specialize_new_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#adcc937a7a48d51f801d65757bc55bda2">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>start_job_output_redirection()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aac9ba54b8924088ef41717fab6240ef4">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>stats()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6ff6efb50bd9f7dbb2d2b221920e73a1">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ab65c1a11b3be9af06c4e47a71294b757">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a08a4fb1e1066710e635b0b078f9e3adb">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a814f0afa7c9b155777e5267a4b4fa145">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>status_of_all_our_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#aec32efb161e4f34a44f3d7baf2f3e643">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a48885c8ee5f0225f6252b04d82e7b590">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>stderr_file()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a817a316519b8f04e340458abf0a0cf1e">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>stdout_file()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#aa110de6559e3966aa60049145b77be0c">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>stop_job_output_redirection()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#acb9fec0fad8f289eed242f5b1fe7e284">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>store()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>store_if_needed()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html#ac8c0dae5bdef78d715b0f4b94853e8d1">Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor</a>
+</li>
+<li>store_job_message()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#a4040dc342aa0c6f479a56970e8a6c911">Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor</a>
+</li>
+<li>store_jobs_and_adjust_counters()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a601af453349bdbe526fed38bcbbbe6af">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>store_out_files()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a67149e75208ca45c0df928213877ac53">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>store_pair()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#a68fb7396bf048cecf23f94e1d616f1a3">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a2f04643ded7a65f9b80887b78b0d40ab">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a>
+</li>
+<li>store_worker_message()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#ad9ad5fe362cffb2edaa31c3086ad7a40">Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor</a>
+</li>
+<li>strict_hash_format()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#aaeefc3b5e868e3302698ff162baf5b64">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#ac3261fa50430bea9fecee3755c4ea2fa">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a4768c0e4d52965b3dc1a34aef202d368">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a>
+</li>
+<li>stringify()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a38ef61e77ea6ba6bb1e08c35228cb7c3">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>struct_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a0a2118e2f81d95101bf4d0e69d90852a">Bio::EnsEMBL::Hive::Accumulator</a>
+</li>
+<li>subgraphs()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a3b6578d1cc8a3a1922fd92177690e904">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>submission_cmd_args()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a2e0e47ea126a9a4ce7d1340700919239">Bio::EnsEMBL::Hive::ResourceDescription</a>
+</li>
+<li>submit_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#aebb3d0f07dcab91a3f189c3f150d24ea">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a653c9100f50d013f0b761a20536cc67f">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>substitute()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>suggest_analysis_to_specialize_by_rc_id_meadow_type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ab56e0d78a8774c93dc262a5c63812891">Bio::EnsEMBL::Hive::Scheduler</a>
+</li>
+<li>sync_lock()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac66bdac33e42b171ca6917480de34063">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>synchronize_AnalysisStats()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a2f39e9a7a7eacf12c8c6262f32b7ffce">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>synchronize_hive()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a2892c256744ac4bdd4f90b9bcc238735">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_t.html b/docs/doxygen/functions_func_t.html
new file mode 100644
index 0000000000000000000000000000000000000000..a615a8d086f619140e83dd637403e61907f7d588
--- /dev/null
+++ b/docs/doxygen/functions_func_t.html
@@ -0,0 +1,185 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li class="current"><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
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+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_func_t.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_t"></a>- t -</h3><ul>
+<li>table_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a6442b5f290356a70eec3d0f15e5004ca">Bio::EnsEMBL::Hive::NakedTable</a>
+</li>
+<li>to_analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ae069a34e628c9f6348c5110a8e9b29b6">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>to_analysis_url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#abe8caedff6ad05cb325d8d7be4ff14ec">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>toString()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a19564942a29c32c01248d9b84bc15c83">Bio::EnsEMBL::Hive::Analysis</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4532406dd4e302fa5a2f2531ff3df73">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a65bafee37ae9da96499433c2dd73f9bd">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a8f23e63cd393a1d4b4fa7489e070a1e0">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a48471b18b5f0d91bbeb9fee9c468a523">Bio::EnsEMBL::Hive::DataflowRule</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a1bb8f3a9ff04edf71733a8cca5622080">Bio::EnsEMBL::Hive::ResourceClass</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#aff13953b8d3b80fcb2b72a8f03457259">Bio::EnsEMBL::Hive::ResourceDescription</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ac8931e351f68c7b4c927c9a400f595c3">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>total_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a97f57d2303a39d59fb6828c681d1302d">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>transient_error()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52d6385c42523ebbd5c42c75e892fa31">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3f921a54a1be9be90a8bb3cd7b7752a3">Bio::EnsEMBL::Hive::Meadow</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_u.html b/docs/doxygen/functions_func_u.html
new file mode 100644
index 0000000000000000000000000000000000000000..ecc4bfba66fd5f992f5526ba9a39996947bda9b2
--- /dev/null
+++ b/docs/doxygen/functions_func_u.html
@@ -0,0 +1,182 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members - Functions</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
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+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
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+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
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+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_u"></a>- u -</h3><ul>
+<li>updatable_column_list()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>update()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aea393680de6bbeeb5cea86e986887fdf">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#ab81f838278b0c4e6791cac46713939fa">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>update_status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae14890c144f67fd2ff32b99bbba8f121">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aae68800782db346b681387c0412dd05f">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ad6424e27663135dc9d7dcd17d3b1d569">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#ac0868a1d8302c76a87eb04f1975b89c7">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#af5ca59dde1b1f4f1dba1c9154490a23a">Bio::EnsEMBL::Hive::Accumulator</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9126fe194c13785419034751cf611c44">Bio::EnsEMBL::Hive::Analysis</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html#a0d1860ad6f23fb2e1806171d46dbc40a">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a2a7e0b5d326bdfbcbb8135bda2d2b842">Bio::EnsEMBL::Hive::NakedTable</a>
+</li>
+<li>url2dbconn_hash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#af7e04ac99c85db0534b11541b99c96da">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>use_cases()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_func_w.html b/docs/doxygen/functions_func_w.html
new file mode 100644
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
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+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
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+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li><a href="functions.html"><span>All</span></a></li>
+ <li class="current"><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions_func.html#index__"><span>_</span></a></li>
+ <li><a href="functions_func_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_func_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_func_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_func_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_func_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_func_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_func_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_func_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_func_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_func_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_func_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_func_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_func_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_func_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_func_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_func_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_func_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_func_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_func_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_func_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_func_u.html#index_u"><span>u</span></a></li>
+ <li class="current"><a href="functions_func_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+
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+</iframe>
+</div>
+
+<div class="contents">
+ 
+
+<h3><a class="anchor" id="index_w"></a>- w -</h3><ul>
+<li>warning()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a00e809b1c03cf9e47212905b4284c140">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>whereami()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a626d8f4a721513ef5d4e6b2172226719">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>work_done()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ae34a70dcbfd02a12e20b1285adcbad1b">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>worker_cmd_args()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a1b975bd9bfad96e24af7bc859a28d116">Bio::EnsEMBL::Hive::ResourceDescription</a>
+</li>
+<li>worker_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#af38047d73f933f30cde285c5dab5dffb">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>worker_say()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a91724c25ce62bea58013fd483aad3abe">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>worker_temp_directory()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>worker_temp_directory_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab007327305a8dc5294ff757cb3d50559">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>write_output()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c9525d489a6ef446c834ef3c08927a3">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a091a7496c19f579499f04ee9c7f78c77">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a0b3680ba302807ee3b9fc34de7b1449d">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#aac3d886006c17c1e6578d622455bda2f">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#adcb45127a2af2a4015d59e590e1eb061">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a51b40c598bc04b4df6e78c5fd1189fc5">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a8ef4b1260e767a0d1392e05c8753c59f">Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a8f715ad1e9dc777cb7dcbbbc6a35c24b">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#a14ae8df5996542778d3e2ef9f64052a8">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a268d6080f03e8ae23d7b1f31baf91d1a">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#a8701139930a22ab99b38e5786d1cef68">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#ab6378c2a90b17bc95ad26d994f63914b">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_g.html b/docs/doxygen/functions_g.html
new file mode 100644
index 0000000000000000000000000000000000000000..0e0bc94c75bbb7560a441a2e0020738676dc20f2
--- /dev/null
+++ b/docs/doxygen/functions_g.html
@@ -0,0 +1,247 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li class="current"><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
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+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_g.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_g"></a>- g -</h3><ul>
+<li>gc_dataflow()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a64c5703becb2a1989bc85e449d961aba">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>generate_job_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#ab8b9ebeacf07bfcb38851edbfdd0ae2f">Bio::EnsEMBL::Hive::Meadow</a>
+</li>
+<li>get()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a61b3f0cfb4fb961204ed1be500a6443e">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>get_analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ab3a0f109fab512fdae003e708d4c28df">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>get_available_adaptors()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a0baccc85ec9695e7ffa80c16d54cb9d9">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
+</li>
+<li>get_available_meadow_list()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a77f0a0b7a8de56d43c0271065bef6ebe">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>get_code_sql_schema_version()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#a0c2dc02c4e81944f9eb9fa7f670aa753">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a>
+</li>
+<li>get_code_version()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_version.html#a8ec4c346c160d25cab629a0c56af720b">Bio::EnsEMBL::Hive::Version</a>
+</li>
+<li>get_compiled_module_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#aa3cfa679262a347a86a83079bde1037d">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>get_current_worker_process_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a2fec4ae34aa12e9249775e5cc3e5ba1e">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a8f756d46474a89b07f63d23ac1b744f9">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>get_default_meadow()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a80eeade51960beb35d31f35cf61f4c79">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>get_elapsed()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#ad933938ea83c78477a8580d500fdec94">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>get_hive_current_load()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#abe36b590f923d7e82d3577f484bd6056">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>get_meadow_capacity_hash_by_meadow_type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a04d1116b668a322e92ad5c916cffe4b9">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>get_nodes_that_point_at()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a20c82c55eba3cfa7120208fe131a94d1">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>get_num_failed_analyses()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#afdadb6fce4eb7469f6de433612867dd5">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>get_or_estimate_batch_size()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac31170452fe2a74986b93ed13eb697c3">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>get_param_hash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a9b86c006546292af7280396e0e86ad41">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a>
+</li>
+<li>get_pending_worker_counts_by_meadow_type_rc_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#aee959b792ccd1f79a3edb5e0f53cd38b">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>get_remaining_jobs_show_hive_progress()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a51b365aa339df1f733167970be158c63">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>get_row_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#aadc21d596971f8edf7410fbeec1f77ba">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>
+</li>
+<li>get_sql_schema_patches()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html#aa6e8545c8a07176e86265ac18f684060">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a>
+</li>
+<li>get_stderr_redirector()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a6b49c7779e183bd1e314bc76354cd569">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>get_stdout_redirector()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aa4629bbbaa4103888c05c5936ae2823e">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>get_top_clusters()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#ac3527fe831ae9d80d246ce20072eb10e">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>get_workers_rank()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ad5392456810e1f4bb16291b54a731c0a">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>go_figure_dbc()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#aa1cbcb45d800cf3c5b47079e0b27e237">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>grab_jobs_for_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#aa023b41587da0be31418d3d871df7cdc">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>grab_memory()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a76caed50af47567cd2fd93ea4b7b3f8a">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+</li>
+<li>graph()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a5f9efde876681aea12fc343faae97dab">Bio::EnsEMBL::Hive::Utils::Graph</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_h.html b/docs/doxygen/functions_h.html
new file mode 100644
index 0000000000000000000000000000000000000000..749e2e5cc691c87e3009a8189fa49cb196aacb87
--- /dev/null
+++ b/docs/doxygen/functions_h.html
@@ -0,0 +1,175 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
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+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+ <li><a href="annotated.html"><span>Class List</span></a></li>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
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+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li class="current"><a href="functions_h.html#index_h"><span>h</span></a></li>
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+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
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+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
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+</div><!-- top -->
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+ class="ui-resizable-handle">
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+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_h.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
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+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_h"></a>- h -</h3><ul>
+<li>hash_leaves()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#aaeb1b4b8db00aaa6a80126ff26cb7a0e">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>hive_capacity()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#adf47bc7ce9c36899897d76f526e26e72">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>hive_meta_table()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a35edd8ed45d8aea1de4f5c5124455a21">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a354e9305c82d67b99b5d0b159f2382db">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a>
+</li>
+<li>hive_use_param_stack()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a364f93a3a3019a023c09f7fd02313970">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
+</li>
+<li>hive_use_triggers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#a5169045d2592861884a452dec9f3dd06">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
+</li>
+<li>host()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a3bf4200e3a8a6603db7ef6a544df3356">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_i.html b/docs/doxygen/functions_i.html
new file mode 100644
index 0000000000000000000000000000000000000000..bf3b878314be6d8722d0de75423e544cb726b7bd
--- /dev/null
+++ b/docs/doxygen/functions_i.html
@@ -0,0 +1,206 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
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+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
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+<link href="doxygen.css" rel="stylesheet" type="text/css" />
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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+ <div id="navrow4" class="tabs3">
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+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li class="current"><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
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+$(document).ready(function(){initNavTree('functions_i.html','');});
+</script>
+<div id="doc-content">
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+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_i"></a>- i -</h3><ul>
+<li>incomplete()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a7ba3562d4484fea866441d7d501d4900">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>increase_required_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a08e32841d6e713fc8b4eada7a3057d8d">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>increase_running_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#aff5f1a7e1f8579cd228352678cce7b78">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>increase_semaphore_count_for_jobid()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ac693f76b13041b3709e5d6a11ac03820">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>init()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a85d390e244fcd69c62f4544d8b384e44">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>inprogress_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a859730fee45d764bdc4fbaa50be04ca3">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>input_capacity()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aa2d5e93ea9239788909138d5eecf044e">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>input_column_mapping()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ac7e056384281180e1b314889fc7c317f">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>input_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a9dd7289999985b60a8299ac66327f3ce">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#aaa5d456135299916bbb43f4c8300a404">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>input_id_template()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a7a2ba2f2f0e72775363943785b918b90">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>input_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#abaf96e66f6740ec51a294e4164363166">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>insertion_method()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#acd1bde351fcbdfddf8fa9896c8716514">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a386c4340b8343abd91aaf33ad66d61a1">Bio::EnsEMBL::Hive::NakedTable</a>
+</li>
+<li>interval_update_work_done()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a57f38be49bb6727b4e1dd853b1ad77b3">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>is_counting()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a27af7e8ae932532af50bfee75b08d2f3">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>is_fully_substituted_string()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a8b28b1e6e1ef24ac3d9143062ddc36d6">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>is_fully_substituted_structure()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a35e7b3e74c6afda6e8f364b6b84f1348">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_j.html b/docs/doxygen/functions_j.html
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+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
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+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="dynsections.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
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+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li class="current"><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
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+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
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+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_k.html b/docs/doxygen/functions_k.html
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
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+<title>ensembl-hive: Class Members</title>
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+<script type="text/javascript" src="dynsections.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
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+<link href="doxygen.css" rel="stylesheet" type="text/css" />
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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+ </tr>
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+<script type="text/javascript">
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+ <span class="left">
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+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li class="current"><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
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+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+ class="ui-resizable-handle">
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+
+<!-- iframe showing the search results (closed by default) -->
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+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_k"></a>- k -</h3><ul>
+<li>keys_to_columns()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a74f3ead3ecf4d1183b667c5da544362b">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a>
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+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aad175b19c6c543012f5455740b539ba2">Bio::EnsEMBL::Hive::Meadow</a>
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+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
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+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
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+</body>
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
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+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+<script type="text/javascript" src="dynsections.js"></script>
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+<script type="text/javascript" src="search/search.js"></script>
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+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
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+ <ul class="tablist">
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
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+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
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+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li class="current"><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
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+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+ <div id="nav-sync" class="sync"></div>
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+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_l.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
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+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_l"></a>- l -</h3><ul>
+<li>last_check_in()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a23a37f5e84b64bdeb435f726e20255fc">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>last_update()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a089b03c15eeb063a7cbae758f72f6637">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>lethal_for_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1fb261840767255efd596b84312532d1">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>life_cycle()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a1c6fcf03a764b66577f4e33477525401">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>life_span()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a83d94917e06cca7e9f59aa999bec0c45">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>life_span_limit_reached()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#affdf64209cfb2b62895ced6e678206a9">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>lifespan_stopwatch()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a529d571f05adaa243ced017ee4c51fd2">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>load_cmdline_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#ac036ce35e64d7310b44481136fad5b18">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>load_file_or_module()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a1956b39203f4df86e8d7aac981462ee5">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>load_from_json()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a4d561e831fd88920ca38ba78582a7f93">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>log_dir()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a2ddf6136f8b9cb3fca032b2ba6f152ff">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>logic_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6528be48120416c630abe32227e70bdb">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_m.html b/docs/doxygen/functions_m.html
new file mode 100644
index 0000000000000000000000000000000000000000..11355ce3a540c3007c812bd5511153f04dc8c962
--- /dev/null
+++ b/docs/doxygen/functions_m.html
@@ -0,0 +1,208 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
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+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
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+ <li><a href="files.html"><span>Files</span></a></li>
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+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
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+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
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+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li class="current"><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
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+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_m.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
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+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_m"></a>- m -</h3><ul>
+<li>main()
+: <a class="el" href="class_script.html#a1bd6f4c8c62743400cdc430f3e4d6c21">Script</a>
+</li>
+<li>mark_stored()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2a39cbb60a5021d1cd5a4e385da4000f">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#aee5049447ae13e0e4f41a1843899c4a0">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a>
+</li>
+<li>max_retry_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9fbc0420b87a63af05d8e741b14ef14a">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>meadow_class_path()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a63cab22c63e3c5aa31191ec02f0a6bf1">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>meadow_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a21077df2d82c57eda4845c9ea1d153d0">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>meadow_type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac41c5978a943fb1bf45a7c42507460ef">Bio::EnsEMBL::Hive::Analysis</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a73ad6041bffcd835a77d9086b2ea1695">Bio::EnsEMBL::Hive::ResourceDescription</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#abf98a83eafeb602f3109fb147f9a2c19">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>merge()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a74bd20559c70a83d01236591fc606691">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>merge_from_rules()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a33d14b75b2adc800bbcc4451a7ca7819">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>min_batch_time()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ab1aa9f23e9feaec53f6e404dfe19f000">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>module()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac491521c673320cec2ce7cecf1d841cd">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>monitor()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a422e896db7c973b0385bbafd2c8aa556">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>more_work_done()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a54f5f9c0d65d4e71c50fd1fdf3e702cc">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>multiplier()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#afb7019e05c935b4eb437ab7aaad54f8c">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>mysql_conn()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7c9b7527f3745f962277b5022d1d09ca">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>mysql_conn_from_dbc()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a66b12a83a4107e2f9758fba932642f7b">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#ab2382b362b1dd698c6c7b0a8d02acabe">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>
+</li>
+<li>mysql_dbname()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a7660586a322000f6f797927a3a216676">Bio::EnsEMBL::Hive::Params</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_n.html b/docs/doxygen/functions_n.html
new file mode 100644
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--- /dev/null
+++ b/docs/doxygen/functions_n.html
@@ -0,0 +1,191 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<script type="text/javascript" src="search/search.js"></script>
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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
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+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li class="current"><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
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+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
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+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_n"></a>- n -</h3><ul>
+<li>name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#a822009e9a5c178598aa5125475b95f18">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a8be5f1cdaa5eb9e07fc29610e678f836">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a4483fbceef09b5b032c54b797fdb73d9">Bio::EnsEMBL::Hive::ResourceClass</a>
+</li>
+<li>new()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#ac035312016653df35c35398474835764">Bio::EnsEMBL::Hive::Accumulator</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ad61a51a522d45f6a30e2a596b5165524">Bio::EnsEMBL::Hive::Analysis</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#a22338588d57d7bf475159a73b4fb10da">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb83a9f0a1fa1cd38bc5ae626bfd6b51">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a63bec749348099898cac9401d6af959b">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#af8321e0eec4a4057a4d103400e549df3">Bio::EnsEMBL::Hive::DataflowRule</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html#abf2b541c5d7e3b124323a34356e3ace6">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a729f524427ef5292b7e980f134aa456f">Bio::EnsEMBL::Hive::DependentOptions</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a89203ff40a85e13c7ef840a46dcf4487">Bio::EnsEMBL::Hive::Limiter</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#abaa21c35b875562cdf4258eee1b717b3">Bio::EnsEMBL::Hive::Meadow</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a86e40bedaa4255b62bb61b92e1b663c8">Bio::EnsEMBL::Hive::NakedTable</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a5be508c964ea50f555fbd9692a226f67">Bio::EnsEMBL::Hive::Params</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a76ab34ac067611e361c72614a8156cb7">Bio::EnsEMBL::Hive::ResourceClass</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a182572a7a902208f7b78653dbca05fa4">Bio::EnsEMBL::Hive::ResourceDescription</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_u_r_l_factory.html#ab067dc5c5216255309138355ecb085ee">Bio::EnsEMBL::Hive::URLFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#ae74fdb113363f2f412a30ce66d1651e3">Bio::EnsEMBL::Hive::Utils::Config</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html#a0452e8098246f27173059b14600f190c">Bio::EnsEMBL::Hive::Utils::Graph</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#a11b71d1d7802b7c52d23f49b8dab377c">Bio::EnsEMBL::Hive::Utils::RedirectStack</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a1cbc5b3e6c40f0a5862e55e228dc34a3">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a51140e4714459dccef65cb34d97bfe13">Bio::EnsEMBL::Hive::Valley</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ac85bb24d028f6a102654f3fdbadf4c74">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>num_required_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0f14ca66c121617e2e6a4f2f7327caa1">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>num_running_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae2ece1ac33d251baa674803832bdae70">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_o.html b/docs/doxygen/functions_o.html
new file mode 100644
index 0000000000000000000000000000000000000000..1b71ea7eb78dcf3c8a14e9e76c175c533a055cbf
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+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
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+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
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+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
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+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
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+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li class="current"><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
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+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_o.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
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+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_o"></a>- o -</h3><ul>
+<li>o()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#adca1f94c3e725c8f744517d14ac91853">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>object_class()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html#abba4ea6afa8067b7e9eefd3278923d6f">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html#a944fe8aee65ea55ba1bd54ee77f97849">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#acaa839ac5ee54ada4e4e555205925592">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#a9670adf2613b9d268ca2195c33099df5">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html#a6001078bcc7bcb8fb45f46c415fb65d8">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a834186b707376a4ead29771860ab440f">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html#ae3a6f6b2a9e4e71f62d6f9233c522b06">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html#aacaba93caa84332eb1713a2218e87b76">Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#af9d2e010bf4d53356d2efde2367c5472">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>objectify()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#ad90a452430769ce22f854fb0d195e905">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#a02d847dd4df770edb4bdbc5ed309a2d5">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a>
+</li>
+<li>output_capacity()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac64ad37ccf27356c480b1d058315d4dd">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>overflow_limit()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1f8bbd7bad6d23b679d4c07ab4121085">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
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diff --git a/docs/doxygen/functions_p.html b/docs/doxygen/functions_p.html
new file mode 100644
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+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
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+<!-- end header part -->
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+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
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+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li class="current"><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
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+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_p"></a>- p -</h3><ul>
+<li>param()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#aacc3d8e3ec1b0f940cc274c95c93e834">Bio::EnsEMBL::Hive::Params</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a6217efee02c3fc309ae8705356e5d8dd">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>param_defaults()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab30a44eca469388da3db6df134ea1559">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a87f4c403bf90241054674b689d01dd33">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#aebd3288a79a288b73f8527c86fcd6fd9">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#a2291deabf24d52906b30ec18d2dbb126">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a80bb69bad70a8a048e373c72621bd7f9">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#a4d6debc4b842ca5cdde9707783c62f20">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#ac539ab7a01025992f908be787b08aebb">Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a4b5d3553e76345622fb3fddb0aac447f">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#af07560dd3842fc50a1c2381ab0e338d0">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a53d7a4e8cce22cfbe0eb51f041604ed9">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a454164834bbb0e68d7cd321a4416a506">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a>
+</li>
+<li>param_exists()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a46b02fdd5e620c96f4f8abe8e1bc017b">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>param_id_stack()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#abb5e9b464027c776b1bd01eaf7b9cfe7">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>param_init()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a03f67c01a12beaa839338be4da9bf9cb">Bio::EnsEMBL::Hive::Params</a>
+</li>
+<li>param_is_defined()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#ad6dba01319677081085a59310e235c51">Bio::EnsEMBL::Hive::Params</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a472fd524e446e292b836f7f73af250e9">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>param_required()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a82a8b3a737120fdf27b3152bc1c63bab">Bio::EnsEMBL::Hive::Params</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ac4d8269232076e9956fbf09e32680c48">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>param_substitute()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html#a261b12abc17c65fac5fd4ccffbb73d6d">Bio::EnsEMBL::Hive::Params</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a43ada6306f2f629c9d727ea5a0146f89">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>parameters()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#aa4d07a94412dd36e4dbb0d3db533c419">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>parse()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_u_r_l.html#ac80cc911eba215fb0ed17104861fe5f7">Bio::EnsEMBL::Hive::Utils::URL</a>
+</li>
+<li>parse_cmdline_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad08ca8e7270cfe9c94e0865e3cf75862">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>pause()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a17462e9ef3668063b549484e293c7f24">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>perform_cleanup()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a23b1369583a49f99f47d654993775113">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>pipeline_analyses()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_any_commands__conf.html#a44f48f0a63c2c7b84a029e2f77f99786">Bio::EnsEMBL::Hive::PipeConfig::AnyCommands_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_apply_to_databases__conf.html#ad1acd6cf7955d0a0ed331020d25dbca8">Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_compress_files__conf.html#a8420a6236b02bab63cb9cd160728ce72">Bio::EnsEMBL::Hive::PipeConfig::CompressFiles_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html#a3c0d2ac018f87a5adb6f78764154228f">Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#aaee0e442c23012ab2f414b85adb6a719">Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a7072b951f3d57b690c0d2a2465d75d9b">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a0046c9bd300412bda32547458e60064d">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a3c2b04c792006bd1a20941e65aea45ef">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html#a828e67804c29620ff20f5774983a734a">Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html#a4cbb91c590ae6014d587728430df6d11">Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html#a34f0292081b57df3025252e36ba2afa2">Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf</a>
+, <a class="el" href="class_mini_pecan_multi__conf.html#a3f50a960f6c073b41cf825a2057628cc">MiniPecanMulti_conf</a>
+, <a class="el" href="class_mini_pecan_single2__conf.html#a45e6c49458b9a332221b8f49217f8fac">MiniPecanSingle2_conf</a>
+, <a class="el" href="class_mini_pecan_single3__conf.html#a7740c91be5f2d349a94909a7c152a998">MiniPecanSingle3_conf</a>
+, <a class="el" href="class_mini_pecan_single__conf.html#aecd0653da35db4cc26178b9a5bbab306">MiniPecanSingle_conf</a>
+</li>
+<li>pipeline_create_commands()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_fasta_splitter__conf.html#ad8d93256c230c0134de507b0fc067dee">Bio::EnsEMBL::Hive::PipeConfig::FastaSplitter_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a24011bab6821ed4f89114444eb997215">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a031b9cfa37aaf95c3c83fba5c243cad2">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a4e1bcdc9dbc1cdcef52e15361d1ebd09">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a>
+</li>
+<li>pipeline_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3685ec781296c30f00d2a8c4f3efeffc">Bio::EnsEMBL::Hive::Meadow</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a194b948521dcdf1e6a8f83a4fc3b1c11">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>pipeline_url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#ab46a140ff5e2b90989979ea6cba6bf06">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>pipeline_wide_parameters()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a0c6ccdb318ca662f0ead725ab661273e">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html#a5b977e0be30a4f60ec9429a399db0fc8">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html#a3fa7a29fdd8d17ceae1d20c828c85e9e">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html#a722ee2d7f0974ab6865a73290f55adf9">Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf</a>
+</li>
+<li>pop()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#a1f475d12cf96160a963d47c370618856">Bio::EnsEMBL::Hive::Utils::RedirectStack</a>
+</li>
+<li>post_cleanup()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a071768efd731a484438461e833bae07f">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+</li>
+<li>pre_cleanup()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a6d7e5437a262f09e5e9cc37965f07ed1">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+</li>
+<li>pre_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a639062a270bf3af88f896c9231f38133">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>preliminary_offer()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#a344004cad3162eefaa6314cff26fa0b3">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>prev_job_error()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab71a53273f57e143655703eaee5bfdc5">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>prev_job_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a097e33f4921749e52972e051032809c4">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>primary_key()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae98ea2fa8c6a85c6df918b9816bd6cbf">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>primary_key_constraint()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#aadc8dac52ad2c57bff954060d60af436">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>print_analysis_status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ad396c5be7d6806c71b5740054325d5e6">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>print_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a6080b20b6f65b3a31e72de743db62dac">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>print_running_worker_counts()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#af91dbe0832893ec7ec3ecc8a7f7164dd">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>priority()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ab1e00ad283310e3e6870b133cb029183">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>process()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a45dd4f95b7b508ddf2ba2d620734d96c">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>process_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a631e3067f5825bf38d981150fac0512d">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>process_options()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1832098d9531567eda925f5e108438a6">Bio::EnsEMBL::Hive::DependentOptions</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a16457254eff693383b5e2a9dcc5b19b2">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+</li>
+<li>protected_prepare_execute()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html#aa5dabd385b717af07205feec2e8fee41">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a>
+</li>
+<li>push()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html#af152aba8ac48eb58a0a7e1901eb8d94b">Bio::EnsEMBL::Hive::Utils::RedirectStack</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_q.html b/docs/doxygen/functions_q.html
new file mode 100644
index 0000000000000000000000000000000000000000..a77c106d2216042d9d6a1b8f16689a7579beacc7
--- /dev/null
+++ b/docs/doxygen/functions_q.html
@@ -0,0 +1,159 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
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+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
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+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
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+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li class="current"><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_q.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_q"></a>- q -</h3><ul>
+<li>query_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ab69fe83605e95a9dafb3025e655082b5">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_r.html b/docs/doxygen/functions_r.html
new file mode 100644
index 0000000000000000000000000000000000000000..6f56c495e442ce028a9f1a9b8a87dc61612cdcfa
--- /dev/null
+++ b/docs/doxygen/functions_r.html
@@ -0,0 +1,247 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li class="current"><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_r.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_r"></a>- r -</h3><ul>
+<li>reached()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_limiter.html#ab3f3e0a81d708e08b8c6a0db9d056aac">Bio::EnsEMBL::Hive::Limiter</a>
+</li>
+<li>ready_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#af55400b3e85544df26608ac63d98f7bc">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>refresh()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac704b4deb0a318afca57dddff2d891df">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#aed7915b07ea5296ca56e90b46f08553b">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>register_all_workers_dead()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#ab4f2cf470e0b3bbe732dd50c22e4deca">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>register_worker_death()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a1dc35ff50f5375e8796f12d17b372773">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>release_and_age_job()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a375c57130791087ff6781f4cc6cc9b9e">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>release_undone_jobs_from_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a25ddbb1f2f0fada5fc7c9078c887f7d8">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>remove()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>remove_all()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a1e7b244d27dcc1244453f725d81d3e54">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>report_versions()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ae4891d2eb87c70172c9d37b374647144">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>reset_job_by_dbID_and_sync()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a46f196406a5bd9c452a5f94361a2eebd">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>reset_jobs_for_analysis_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a122b718f7e51f923fb50a1c01cb69805">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>reset_or_grab_job_by_dbID()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a4dd834ac1243d05989bcb352021ede70">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>resource_class_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a30049fd09f42f0b709d6785191168587">Bio::EnsEMBL::Hive::Analysis</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a5c5bf7acac77e65b07761146d39bcc24">Bio::EnsEMBL::Hive::ResourceDescription</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aec650e3731644a420c7a2be8597e0250">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>resource_classes()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#a6d9612ad9a85971bc0734cbfb26854d7">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html#af4f9a637c96b4abb18b8139fff3e885b">Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf</a>
+</li>
+<li>responsible_for_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#aa65a2353dde2a128123f36543d5aa115">Bio::EnsEMBL::Hive::Meadow</a>
+</li>
+<li>restart()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html#a233743ce015c7df93ad06562fe3b35dd">Bio::EnsEMBL::Hive::Utils::Stopwatch</a>
+</li>
+<li>retry_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae3bad87fd4aff80e2b4ee41185494c64">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>retry_throwing_jobs()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a03e3c2ca474c831a1700dbfdfb424fb6">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>root()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a1191c5f58dd3ebbd26f4024b906ccfcf">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>run()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html#adb95548d620d772327085f7bb96b8b3a">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a346410a6c7d0e5f2541bc304048efdb9">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_database_dumper.html#a0a727e827af0f003386490d0aa3b2af9">Bio::EnsEMBL::Hive::RunnableDB::DatabaseDumper</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#a4be920b14ab4f65812887f02751e1a10">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html#a525479b5642b24c86208663fa2fd7d4a">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html#ad2334d5ffe5a01936cb8c9c365da979c">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_job_factory.html#a8f3a3f15b7d15493a3e0522a27a2edf5">Bio::EnsEMBL::Hive::RunnableDB::JobFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html#ad709c3f522582c4965ce53adb1499e15">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html#a12b9e75e3910ce20c4489fa8babe9b6a">Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html#a5cfb529f37ccb583abe0a1518a86ab2c">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_my_s_q_l_transfer.html#af26f682eca96b51923aa75c501f21d02">Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html#a4eab23c711954e76734d980c40819726">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#af2232b93770b96595d7e042964379e2c">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html#a7a00da78d95fdd5a586770e0c6ec1d6b">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a732af3c6c5e3c3eb4f272d0135c073be">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab6456d819b72b807884df4b49ea30492">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>run_one_batch()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a7fe639feb3731120a1a66663e8c2a2e8">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>runnable_object()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a4bc0dde1eb43909e1e8f8a87fd0a3257">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>runtime_msec()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#af050b0e809253aef004926eeaf6cdf75">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
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+</html>
diff --git a/docs/doxygen/functions_s.html b/docs/doxygen/functions_s.html
new file mode 100644
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
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+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
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+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
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+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
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+ <li class="current"><a href="functions.html"><span>All</span></a></li>
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+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li class="current"><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
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+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_s"></a>- s -</h3><ul>
+<li>safe_synchronize_AnalysisStats()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#abe0354cbdbf898d95cf08cb2d167ba38">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>schedule_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ad37b01e88608cec39e5f883d95c8ea42">Bio::EnsEMBL::Hive::Scheduler</a>
+</li>
+<li>schedule_workers_resync_if_necessary()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#a65f7b429d0ffbda238faeda2451350a8">Bio::EnsEMBL::Hive::Scheduler</a>
+</li>
+<li>script_usage()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#ad8abe58a987444c45b366ef5dba4e218">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>seconds_since_last_update()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ae96201f918c87593f69279e032fea2a5">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>semaphore_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a75263a4a15c449f509bf35cbead2c54c">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>semaphored_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a0a75c8843ba392c7df7a213a0767739f">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>semaphored_job_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a1e2d7fa5ae29570bfc2e389dc3abd824">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>set()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html#a97a169fff464c4653386c08b7df40496">Bio::EnsEMBL::Hive::Utils::Config</a>
+</li>
+<li>set_default_meadow_type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#af85407f558029e59470a282e82c4f8ad">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>signature()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a0594b46314ad2a8894f055bd58ba923c">Bio::EnsEMBL::Hive::Meadow</a>
+</li>
+<li>signature_template()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a9348142e49053884868319ec512435cd">Bio::EnsEMBL::Hive::Accumulator</a>
+</li>
+<li>slicer()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html#a2fd8279544ff4bd78e9b3fd09495542c">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html#af1b4e5cdd9865d10338aafe4c6d047c0">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a>
+</li>
+<li>special_batch()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ab6470f448766be332f7e4d081e6d7cc2">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>specialize_and_compile_wrapper()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ae432e7a7dbc6a8b0109353d4f6938d9c">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>specialize_new_worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#adcc937a7a48d51f801d65757bc55bda2">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>start_job_output_redirection()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#aac9ba54b8924088ef41717fab6240ef4">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>stats()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6ff6efb50bd9f7dbb2d2b221920e73a1">Bio::EnsEMBL::Hive::Analysis</a>
+</li>
+<li>status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ab65c1a11b3be9af06c4e47a71294b757">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a08a4fb1e1066710e635b0b078f9e3adb">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a814f0afa7c9b155777e5267a4b4fa145">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>status_of_all_our_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#aec32efb161e4f34a44f3d7baf2f3e643">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a48885c8ee5f0225f6252b04d82e7b590">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>stderr_file()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a817a316519b8f04e340458abf0a0cf1e">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>stdout_file()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#aa110de6559e3966aa60049145b77be0c">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>stop_job_output_redirection()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#acb9fec0fad8f289eed242f5b1fe7e284">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>store()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a23e67bcbf6294126212da34c0c5a2a90">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>store_if_needed()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html#ac8c0dae5bdef78d715b0f4b94853e8d1">Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor</a>
+</li>
+<li>store_job_message()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#a4040dc342aa0c6f479a56970e8a6c911">Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor</a>
+</li>
+<li>store_jobs_and_adjust_counters()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a601af453349bdbe526fed38bcbbbe6af">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>store_out_files()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#a67149e75208ca45c0df928213877ac53">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+</li>
+<li>store_pair()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html#a68fb7396bf048cecf23f94e1d616f1a3">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html#a2f04643ded7a65f9b80887b78b0d40ab">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a>
+</li>
+<li>store_worker_message()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html#ad9ad5fe362cffb2edaa31c3086ad7a40">Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor</a>
+</li>
+<li>strict_hash_format()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ab6663081a21ccab06ee06c3d3d920846">Bio::EnsEMBL::Hive::Process</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html#aaeefc3b5e868e3302698ff162baf5b64">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_cmd.html#ac3261fa50430bea9fecee3755c4ea2fa">Bio::EnsEMBL::Hive::RunnableDB::SqlCmd</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_system_cmd.html#a4768c0e4d52965b3dc1a34aef202d368">Bio::EnsEMBL::Hive::RunnableDB::SystemCmd</a>
+</li>
+<li>stringify()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a38ef61e77ea6ba6bb1e08c35228cb7c3">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>struct_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a0a2118e2f81d95101bf4d0e69d90852a">Bio::EnsEMBL::Hive::Accumulator</a>
+</li>
+<li>subgraphs()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#a3b6578d1cc8a3a1922fd92177690e904">Bio::EnsEMBL::Hive::Utils::GraphViz</a>
+</li>
+<li>submission_cmd_args()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a2e0e47ea126a9a4ce7d1340700919239">Bio::EnsEMBL::Hive::ResourceDescription</a>
+</li>
+<li>submit_workers()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html#aebb3d0f07dcab91a3f189c3f150d24ea">Bio::EnsEMBL::Hive::Meadow::LOCAL</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html#a653c9100f50d013f0b761a20536cc67f">Bio::EnsEMBL::Hive::Meadow::LSF</a>
+</li>
+<li>substitute()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a58f0a875a481ff975964bbd451773f11">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+<li>suggest_analysis_to_specialize_by_rc_id_meadow_type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html#ab56e0d78a8774c93dc262a5c63812891">Bio::EnsEMBL::Hive::Scheduler</a>
+</li>
+<li>sync_lock()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#ac66bdac33e42b171ca6917480de34063">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>synchronize_AnalysisStats()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a2f39e9a7a7eacf12c8c6262f32b7ffce">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+<li>synchronize_hive()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a2892c256744ac4bdd4f90b9bcc238735">Bio::EnsEMBL::Hive::Queen</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_t.html b/docs/doxygen/functions_t.html
new file mode 100644
index 0000000000000000000000000000000000000000..b2bffe3106b417b964c35f2b541f8a014467ec42
--- /dev/null
+++ b/docs/doxygen/functions_t.html
@@ -0,0 +1,185 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
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+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
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+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
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+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
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+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li class="current"><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
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+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_t"></a>- t -</h3><ul>
+<li>table_name()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a9ee7f9cfe42ad4993d0b544acfb4e1f5">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a6442b5f290356a70eec3d0f15e5004ca">Bio::EnsEMBL::Hive::NakedTable</a>
+</li>
+<li>to_analysis()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#ae069a34e628c9f6348c5110a8e9b29b6">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>to_analysis_url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#abe8caedff6ad05cb325d8d7be4ff14ec">Bio::EnsEMBL::Hive::DataflowRule</a>
+</li>
+<li>toString()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a19564942a29c32c01248d9b84bc15c83">Bio::EnsEMBL::Hive::Analysis</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html#ac4532406dd4e302fa5a2f2531ff3df73">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a65bafee37ae9da96499433c2dd73f9bd">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a8f23e63cd393a1d4b4fa7489e070a1e0">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a48471b18b5f0d91bbeb9fee9c468a523">Bio::EnsEMBL::Hive::DataflowRule</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#a1bb8f3a9ff04edf71733a8cca5622080">Bio::EnsEMBL::Hive::ResourceClass</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#aff13953b8d3b80fcb2b72a8f03457259">Bio::EnsEMBL::Hive::ResourceDescription</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ac8931e351f68c7b4c927c9a400f595c3">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>total_job_count()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a97f57d2303a39d59fb6828c681d1302d">Bio::EnsEMBL::Hive::AnalysisStats</a>
+</li>
+<li>transient_error()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a52d6385c42523ebbd5c42c75e892fa31">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>type()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a3f921a54a1be9be90a8bb3cd7b7752a3">Bio::EnsEMBL::Hive::Meadow</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_u.html b/docs/doxygen/functions_u.html
new file mode 100644
index 0000000000000000000000000000000000000000..a77b2ef7b5ea139420bde517590e5a1eb6697111
--- /dev/null
+++ b/docs/doxygen/functions_u.html
@@ -0,0 +1,182 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li class="current"><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_u.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_u"></a>- u -</h3><ul>
+<li>updatable_column_list()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ae47ff32866fc8b69d8463680b5ead1d2">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>update()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aea393680de6bbeeb5cea86e986887fdf">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#ab81f838278b0c4e6791cac46713939fa">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab8f4cc3813b7d1ad259b02e4a24112f2">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>
+</li>
+<li>update_status()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#ae14890c144f67fd2ff32b99bbba8f121">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#aae68800782db346b681387c0412dd05f">Bio::EnsEMBL::Hive::AnalysisStats</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html#ad6424e27663135dc9d7dcd17d3b1d569">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html#ac0868a1d8302c76a87eb04f1975b89c7">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
+</li>
+<li>url()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#af5ca59dde1b1f4f1dba1c9154490a23a">Bio::EnsEMBL::Hive::Accumulator</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a9126fe194c13785419034751cf611c44">Bio::EnsEMBL::Hive::Analysis</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html#a0d1860ad6f23fb2e1806171d46dbc40a">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a2a7e0b5d326bdfbcbb8135bda2d2b842">Bio::EnsEMBL::Hive::NakedTable</a>
+</li>
+<li>url2dbconn_hash()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#af7e04ac99c85db0534b11541b99c96da">Bio::EnsEMBL::Hive::Utils</a>
+</li>
+<li>use_cases()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html#a12fa6e8360e2db6bd40dc318654b9d42">Bio::EnsEMBL::Hive::DependentOptions</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/functions_w.html b/docs/doxygen/functions_w.html
new file mode 100644
index 0000000000000000000000000000000000000000..8a97a58073f93f97a06c0c9c07c8590e7185c8cb
--- /dev/null
+++ b/docs/doxygen/functions_w.html
@@ -0,0 +1,198 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Class Members</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li class="current"><a href="annotated.html"><span>Classes</span></a></li>
+ <li><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="annotated.html"><span>Class List</span></a></li>
+ <li><a href="classes.html"><span>Class Index</span></a></li>
+ <li><a href="inherits.html"><span>Class Hierarchy</span></a></li>
+ <li class="current"><a href="functions.html"><span>Class Members</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow3" class="tabs2">
+ <ul class="tablist">
+ <li class="current"><a href="functions.html"><span>All</span></a></li>
+ <li><a href="functions_func.html"><span>Functions</span></a></li>
+ </ul>
+ </div>
+ <div id="navrow4" class="tabs3">
+ <ul class="tablist">
+ <li><a href="functions.html#index__"><span>_</span></a></li>
+ <li><a href="functions_a.html#index_a"><span>a</span></a></li>
+ <li><a href="functions_b.html#index_b"><span>b</span></a></li>
+ <li><a href="functions_c.html#index_c"><span>c</span></a></li>
+ <li><a href="functions_d.html#index_d"><span>d</span></a></li>
+ <li><a href="functions_e.html#index_e"><span>e</span></a></li>
+ <li><a href="functions_f.html#index_f"><span>f</span></a></li>
+ <li><a href="functions_g.html#index_g"><span>g</span></a></li>
+ <li><a href="functions_h.html#index_h"><span>h</span></a></li>
+ <li><a href="functions_i.html#index_i"><span>i</span></a></li>
+ <li><a href="functions_j.html#index_j"><span>j</span></a></li>
+ <li><a href="functions_k.html#index_k"><span>k</span></a></li>
+ <li><a href="functions_l.html#index_l"><span>l</span></a></li>
+ <li><a href="functions_m.html#index_m"><span>m</span></a></li>
+ <li><a href="functions_n.html#index_n"><span>n</span></a></li>
+ <li><a href="functions_o.html#index_o"><span>o</span></a></li>
+ <li><a href="functions_p.html#index_p"><span>p</span></a></li>
+ <li><a href="functions_q.html#index_q"><span>q</span></a></li>
+ <li><a href="functions_r.html#index_r"><span>r</span></a></li>
+ <li><a href="functions_s.html#index_s"><span>s</span></a></li>
+ <li><a href="functions_t.html#index_t"><span>t</span></a></li>
+ <li><a href="functions_u.html#index_u"><span>u</span></a></li>
+ <li class="current"><a href="functions_w.html#index_w"><span>w</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('functions_w.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="contents">
+<div class="textblock">Here is a list of all class members with links to the classes they belong to:</div>
+
+<h3><a class="anchor" id="index_w"></a>- w -</h3><ul>
+<li>warning()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#a00e809b1c03cf9e47212905b4284c140">Bio::EnsEMBL::Hive::AnalysisJob</a>
+, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a5fef0ffecdd8b254a622f83baa8e03e3">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>whereami()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html#a626d8f4a721513ef5d4e6b2172226719">Bio::EnsEMBL::Hive::Valley</a>
+</li>
+<li>work_done()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#ae34a70dcbfd02a12e20b1285adcbad1b">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>worker()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a9d01ac47d41d31f30aca69b0220e0d9d">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>worker_cmd_args()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a1b975bd9bfad96e24af7bc859a28d116">Bio::EnsEMBL::Hive::ResourceDescription</a>
+</li>
+<li>worker_id()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html#af38047d73f933f30cde285c5dab5dffb">Bio::EnsEMBL::Hive::AnalysisJob</a>
+</li>
+<li>worker_say()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a91724c25ce62bea58013fd483aad3abe">Bio::EnsEMBL::Hive::Worker</a>
+</li>
+<li>worker_temp_directory()
+: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a3ee5bd7ae4938b858a48b3812814a0a1">Bio::EnsEMBL::Hive::Process</a>
+</li>
+<li>worker_temp_directory_name()
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+: <a class="el" href="beekeeper_8pl.html#ad7de8680eb8b39e160cee04957ccd668">beekeeper.pl</a>
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+: <a class="el" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">beekeeper.pl</a>
+, <a class="el" href="seed__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">seed_pipeline.pl</a>
+, <a class="el" href="lsf__report_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">lsf_report.pl</a>
+, <a class="el" href="init__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">init_pipeline.pl</a>
+, <a class="el" href="hoover__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">hoover_pipeline.pl</a>
+, <a class="el" href="generate__timeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">generate_timeline.pl</a>
+, <a class="el" href="db__cmd_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">db_cmd.pl</a>
+</li>
+<li>run_autonomously()
+: <a class="el" href="beekeeper_8pl.html#af314298b28a69538fb25aa7eb1327c98">beekeeper.pl</a>
+</li>
+<li>show_seedable_analyses()
+: <a class="el" href="seed__pipeline_8pl.html#ae56eff1c83733ae5dcc4d7f7d6d25ff8">seed_pipeline.pl</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
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+<title>ensembl-hive: File Members</title>
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+<table cellspacing="0" cellpadding="0">
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+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+ <ul class="tablist">
+ <li><a href="files.html"><span>File List</span></a></li>
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+<li>dbc_hash_to_cmd()
+: <a class="el" href="db__cmd_8pl.html#aa9d6dbdd85d225abef029815f3ca0336">db_cmd.pl</a>
+</li>
+<li>generate_worker_cmd()
+: <a class="el" href="beekeeper_8pl.html#ad7de8680eb8b39e160cee04957ccd668">beekeeper.pl</a>
+</li>
+<li>main()
+: <a class="el" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">beekeeper.pl</a>
+, <a class="el" href="seed__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">seed_pipeline.pl</a>
+, <a class="el" href="lsf__report_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">lsf_report.pl</a>
+, <a class="el" href="init__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">init_pipeline.pl</a>
+, <a class="el" href="hoover__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">hoover_pipeline.pl</a>
+, <a class="el" href="generate__timeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">generate_timeline.pl</a>
+, <a class="el" href="db__cmd_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">db_cmd.pl</a>
+</li>
+<li>run_autonomously()
+: <a class="el" href="beekeeper_8pl.html#af314298b28a69538fb25aa7eb1327c98">beekeeper.pl</a>
+</li>
+<li>show_seedable_analyses()
+: <a class="el" href="seed__pipeline_8pl.html#ae56eff1c83733ae5dcc4d7f7d6d25ff8">seed_pipeline.pl</a>
+</li>
+</ul>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
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+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: Graph Legend</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
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+ $(document).ready(function() { searchBox.OnSelectItem(0); });
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+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
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+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li><a href="annotated.html"><span>Classes</span></a></li>
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+ <div id="MSearchBox" class="MSearchBoxInactive">
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+ onmouseover="return searchBox.OnSearchSelectShow()"
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+<!-- iframe showing the search results (closed by default) -->
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+ name="MSearchResults" id="MSearchResults">
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+<div class="header">
+ <div class="headertitle">
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
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+<title>ensembl-hive: Class Hierarchy</title>
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+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
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+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
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+<tr id="row_0_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html" target="_self">Bio::EnsEMBL::Hive::Accumulator</a></td><td class="desc"></td></tr>
+<tr id="row_1_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_ctrl_rule.html" target="_self">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a></td><td class="desc"></td></tr>
+<tr id="row_2_" class="even"><td class="entry"><img id="arr_2_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('2_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><b>BaseAdaptor</b></td><td class="desc"></td></tr>
+<tr id="row_2_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_2_0_" src="ftv2mlastnode.png" alt="\" width="16" height="22" onclick="toggleFolder('2_0_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img id="arr_2_0_0_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('2_0_0_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_naked_table_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_0_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_accumulator_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::AccumulatorAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_0_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_data_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_0_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_log_message_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_0_3_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::MetaAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_0_4_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img id="arr_2_0_1_" src="ftv2mlastnode.png" alt="\" width="16" height="22" onclick="toggleFolder('2_0_1_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_object_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_1_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_1_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_ctrl_rule_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_1_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_job_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_1_3_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_analysis_stats_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_1_4_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_dataflow_rule_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_1_5_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_class_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_1_6_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_resource_description_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_2_0_1_7_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html" target="_self">Bio::EnsEMBL::Hive::Queen</a></td><td class="desc"></td></tr>
+<tr id="row_3_"><td class="entry"><img id="arr_3_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('3_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><b>BaseMetaContainer</b></td><td class="desc"></td></tr>
+<tr id="row_3_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_meta_container.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::MetaContainer</a></td><td class="desc"></td></tr>
+<tr id="row_4_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_config.html" target="_self">Bio::EnsEMBL::Hive::Utils::Config</a></td><td class="desc"></td></tr>
+<tr id="row_5_" class="even"><td class="entry"><img id="arr_5_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('5_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_configurable.html" target="_self">Bio::EnsEMBL::Hive::Configurable</a></td><td class="desc"></td></tr>
+<tr id="row_5_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_5_0_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('5_0_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html" target="_self">Bio::EnsEMBL::Hive::Meadow</a></td><td class="desc"></td></tr>
+<tr id="row_5_0_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_o_c_a_l.html" target="_self">Bio::EnsEMBL::Hive::Meadow::LOCAL</a></td><td class="desc"></td></tr>
+<tr id="row_5_0_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow_1_1_l_s_f.html" target="_self">Bio::EnsEMBL::Hive::Meadow::LSF</a></td><td class="desc"></td></tr>
+<tr id="row_5_1_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph.html" target="_self">Bio::EnsEMBL::Hive::Utils::Graph</a></td><td class="desc"></td></tr>
+<tr id="row_5_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_valley.html" target="_self">Bio::EnsEMBL::Hive::Valley</a></td><td class="desc"></td></tr>
+<tr id="row_6_" class="even"><td class="entry"><img id="arr_6_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('6_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><b>DBAdaptor</b></td><td class="desc"></td></tr>
+<tr id="row_6_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_7_" class="even"><td class="entry"><img id="arr_7_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('7_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><b>DBConnection</b></td><td class="desc"></td></tr>
+<tr id="row_7_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_d_b_connection.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::DBConnection</a></td><td class="desc"></td></tr>
+<tr id="row_8_" class="even"><td class="entry"><img id="arr_8_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('8_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dependent_options.html" target="_self">Bio::EnsEMBL::Hive::DependentOptions</a></td><td class="desc"></td></tr>
+<tr id="row_8_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_8_0_" src="ftv2mlastnode.png" alt="\" width="16" height="22" onclick="toggleFolder('8_0_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_hive_generic__conf.html" target="_self">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a></td><td class="desc"></td></tr>
+<tr id="row_8_0_0_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_any_commands__conf.html" target="_self">Bio::EnsEMBL::Hive::PipeConfig::AnyCommands_conf</a></td><td class="desc"></td></tr>
+<tr id="row_8_0_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_apply_to_databases__conf.html" target="_self">Bio::EnsEMBL::Hive::PipeConfig::ApplyToDatabases_conf</a></td><td class="desc"></td></tr>
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+<tr id="row_8_0_3_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_failure_test__conf.html" target="_self">Bio::EnsEMBL::Hive::PipeConfig::FailureTest_conf</a></td><td class="desc"></td></tr>
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+<tr id="row_8_0_5_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult__conf.html" target="_self">Bio::EnsEMBL::Hive::PipeConfig::LongMult_conf</a></td><td class="desc"></td></tr>
+<tr id="row_8_0_6_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_long_mult_st__conf.html" target="_self">Bio::EnsEMBL::Hive::PipeConfig::LongMultSt_conf</a></td><td class="desc"></td></tr>
+<tr id="row_8_0_7_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_memlimit_test__conf.html" target="_self">Bio::EnsEMBL::Hive::PipeConfig::MemlimitTest_conf</a></td><td class="desc"></td></tr>
+<tr id="row_8_0_8_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_run_list_of_commands_on_farm__conf.html" target="_self">Bio::EnsEMBL::Hive::PipeConfig::RunListOfCommandsOnFarm_conf</a></td><td class="desc"></td></tr>
+<tr id="row_8_0_9_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipe_config_1_1_table_dumper_zipper__conf.html" target="_self">Bio::EnsEMBL::Hive::PipeConfig::TableDumperZipper_conf</a></td><td class="desc"></td></tr>
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+<tr id="row_8_0_11_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_mini_pecan_single2__conf.html" target="_self">MiniPecanSingle2_conf</a></td><td class="desc"></td></tr>
+<tr id="row_8_0_12_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_mini_pecan_single3__conf.html" target="_self">MiniPecanSingle3_conf</a></td><td class="desc"></td></tr>
+<tr id="row_8_0_13_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_mini_pecan_single__conf.html" target="_self">MiniPecanSingle_conf</a></td><td class="desc"></td></tr>
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+<tr id="row_9_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img id="arr_9_0_" src="ftv2mlastnode.png" alt="\" width="16" height="22" onclick="toggleFolder('9_0_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html" target="_self">Bio::EnsEMBL::Hive::Process</a></td><td class="desc"></td></tr>
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+<tr id="row_9_0_1_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_dummy.html" target="_self">Bio::EnsEMBL::Hive::RunnableDB::Dummy</a></td><td class="desc"></td></tr>
+<tr id="row_9_0_2_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_failure_test.html" target="_self">Bio::EnsEMBL::Hive::RunnableDB::FailureTest</a></td><td class="desc"></td></tr>
+<tr id="row_9_0_3_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_fasta_factory.html" target="_self">Bio::EnsEMBL::Hive::RunnableDB::FastaFactory</a></td><td class="desc"></td></tr>
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+<tr id="row_9_0_5_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_add_together.html" target="_self">Bio::EnsEMBL::Hive::RunnableDB::LongMult::AddTogether</a></td><td class="desc"></td></tr>
+<tr id="row_9_0_6_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_digit_factory.html" target="_self">Bio::EnsEMBL::Hive::RunnableDB::LongMult::DigitFactory</a></td><td class="desc"></td></tr>
+<tr id="row_9_0_7_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_long_mult_1_1_part_multiply.html" target="_self">Bio::EnsEMBL::Hive::RunnableDB::LongMult::PartMultiply</a></td><td class="desc"></td></tr>
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+<tr id="row_9_0_9_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_notify_by_email.html" target="_self">Bio::EnsEMBL::Hive::RunnableDB::NotifyByEmail</a></td><td class="desc"></td></tr>
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+<tr id="row_9_0_11_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt=" " width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_runnable_d_b_1_1_sql_healthcheck.html" target="_self">Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck</a></td><td class="desc"></td></tr>
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+<tr id="row_10_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html" target="_self">Bio::EnsEMBL::Hive::Utils::GraphViz</a></td><td class="desc"></td></tr>
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+<tr id="row_13_" class="even"><td class="entry"><img id="arr_13_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('13_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_params.html" target="_self">Bio::EnsEMBL::Hive::Params</a></td><td class="desc"></td></tr>
+<tr id="row_13_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2lastnode.png" alt="\" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_job.html" target="_self">Bio::EnsEMBL::Hive::AnalysisJob</a></td><td class="desc"></td></tr>
+<tr id="row_14_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_redirect_stack.html" target="_self">Bio::EnsEMBL::Hive::Utils::RedirectStack</a></td><td class="desc"></td></tr>
+<tr id="row_15_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html" target="_self">Bio::EnsEMBL::Hive::ResourceDescription</a></td><td class="desc"></td></tr>
+<tr id="row_16_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_scheduler.html" target="_self">Bio::EnsEMBL::Hive::Scheduler</a></td><td class="desc"></td></tr>
+<tr id="row_17_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_script.html" target="_self">Script</a></td><td class="desc"></td></tr>
+<tr id="row_18_" class="even"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_sql_schema_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::SqlSchemaAdaptor</a></td><td class="desc"></td></tr>
+<tr id="row_19_"><td class="entry"><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_stopwatch.html" target="_self">Bio::EnsEMBL::Hive::Utils::Stopwatch</a></td><td class="desc"></td></tr>
+<tr id="row_20_" class="even"><td class="entry"><img id="arr_20_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('20_')"/><img src="ftv2cl.png" alt="C" width="24" height="22" /><b>Storable</b></td><td class="desc"></td></tr>
+<tr id="row_20_0_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html" target="_self">Bio::EnsEMBL::Hive::Analysis</a></td><td class="desc"></td></tr>
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+<tr id="row_20_2_"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html" target="_self">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="desc"></td></tr>
+<tr id="row_20_3_" class="even"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2node.png" alt="o" width="16" height="22" /><img src="ftv2cl.png" alt="C" width="24" height="22" /><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html" target="_self">Bio::EnsEMBL::Hive::DataflowRule</a></td><td class="desc"></td></tr>
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+if(!bA||bv===3||bv===8||bv===2){return}if(bz&&bx in b.attrFn){return b(bA)[bx](bB)}if(typeof bA.getAttribute==="undefined"){return b.prop(bA,bx,bB)}by=bv!==1||!b.isXMLDoc(bA);if(by){bx=bx.toLowerCase();e=b.attrHooks[bx]||(ao.test(bx)?aY:be)}if(bB!==L){if(bB===null){b.removeAttr(bA,bx);return}else{if(e&&"set" in e&&by&&(bw=e.set(bA,bB,bx))!==L){return bw}else{bA.setAttribute(bx,""+bB);return bB}}}else{if(e&&"get" in e&&by&&(bw=e.get(bA,bx))!==null){return bw}else{bw=bA.getAttribute(bx);return bw===null?L:bw}}},removeAttr:function(bx,bz){var by,bA,bv,e,bw=0;if(bz&&bx.nodeType===1){bA=bz.toLowerCase().split(af);e=bA.length;for(;bw<e;bw++){bv=bA[bw];if(bv){by=b.propFix[bv]||bv;b.attr(bx,bv,"");bx.removeAttribute(F?bv:by);if(ao.test(bv)&&by in bx){bx[by]=false}}}}},attrHooks:{type:{set:function(e,bv){if(g.test(e.nodeName)&&e.parentNode){b.error("type property can't be changed")}else{if(!b.support.radioValue&&bv==="radio"&&b.nodeName(e,"input")){var bw=e.value;e.setAttribute("type",bv);if(bw){e.value=bw}return bv}}}},value:{get:function(bv,e){if(be&&b.nodeName(bv,"button")){return be.get(bv,e)}return e in bv?bv.value:null},set:function(bv,bw,e){if(be&&b.nodeName(bv,"button")){return be.set(bv,bw,e)}bv.value=bw}}},propFix:{tabindex:"tabIndex",readonly:"readOnly","for":"htmlFor","class":"className",maxlength:"maxLength",cellspacing:"cellSpacing",cellpadding:"cellPadding",rowspan:"rowSpan",colspan:"colSpan",usemap:"useMap",frameborder:"frameBorder",contenteditable:"contentEditable"},prop:function(bz,bx,bA){var bw,e,by,bv=bz.nodeType;if(!bz||bv===3||bv===8||bv===2){return}by=bv!==1||!b.isXMLDoc(bz);if(by){bx=b.propFix[bx]||bx;e=b.propHooks[bx]}if(bA!==L){if(e&&"set" in e&&(bw=e.set(bz,bA,bx))!==L){return bw}else{return(bz[bx]=bA)}}else{if(e&&"get" in e&&(bw=e.get(bz,bx))!==null){return bw}else{return bz[bx]}}},propHooks:{tabIndex:{get:function(bv){var e=bv.getAttributeNode("tabindex");return e&&e.specified?parseInt(e.value,10):D.test(bv.nodeName)||l.test(bv.nodeName)&&bv.href?0:L}}}});b.attrHooks.tabindex=b.propHooks.tabIndex;aY={get:function(bv,e){var bx,bw=b.prop(bv,e);return bw===true||typeof bw!=="boolean"&&(bx=bv.getAttributeNode(e))&&bx.nodeValue!==false?e.toLowerCase():L},set:function(bv,bx,e){var bw;if(bx===false){b.removeAttr(bv,e)}else{bw=b.propFix[e]||e;if(bw in bv){bv[bw]=true}bv.setAttribute(e,e.toLowerCase())}return e}};if(!F){aF={name:true,id:true};be=b.valHooks.button={get:function(bw,bv){var e;e=bw.getAttributeNode(bv);return e&&(aF[bv]?e.nodeValue!=="":e.specified)?e.nodeValue:L},set:function(bw,bx,bv){var e=bw.getAttributeNode(bv);if(!e){e=av.createAttribute(bv);bw.setAttributeNode(e)}return(e.nodeValue=bx+"")}};b.attrHooks.tabindex.set=be.set;b.each(["width","height"],function(bv,e){b.attrHooks[e]=b.extend(b.attrHooks[e],{set:function(bw,bx){if(bx===""){bw.setAttribute(e,"auto");return bx}}})});b.attrHooks.contenteditable={get:be.get,set:function(bv,bw,e){if(bw===""){bw="false"}be.set(bv,bw,e)}}}if(!b.support.hrefNormalized){b.each(["href","src","width","height"],function(bv,e){b.attrHooks[e]=b.extend(b.attrHooks[e],{get:function(bx){var bw=bx.getAttribute(e,2);return bw===null?L:bw}})})}if(!b.support.style){b.attrHooks.style={get:function(e){return e.style.cssText.toLowerCase()||L},set:function(e,bv){return(e.style.cssText=""+bv)}}}if(!b.support.optSelected){b.propHooks.selected=b.extend(b.propHooks.selected,{get:function(bv){var e=bv.parentNode;if(e){e.selectedIndex;if(e.parentNode){e.parentNode.selectedIndex}}return null}})}if(!b.support.enctype){b.propFix.enctype="encoding"}if(!b.support.checkOn){b.each(["radio","checkbox"],function(){b.valHooks[this]={get:function(e){return e.getAttribute("value")===null?"on":e.value}}})}b.each(["radio","checkbox"],function(){b.valHooks[this]=b.extend(b.valHooks[this],{set:function(e,bv){if(b.isArray(bv)){return(e.checked=b.inArray(b(e).val(),bv)>=0)}}})});var bd=/^(?:textarea|input|select)$/i,n=/^([^\.]*)?(?:\.(.+))?$/,J=/\bhover(\.\S+)?\b/,aO=/^key/,bf=/^(?:mouse|contextmenu)|click/,T=/^(?:focusinfocus|focusoutblur)$/,U=/^(\w*)(?:#([\w\-]+))?(?:\.([\w\-]+))?$/,Y=function(e){var bv=U.exec(e);if(bv){bv[1]=(bv[1]||"").toLowerCase();bv[3]=bv[3]&&new RegExp("(?:^|\\s)"+bv[3]+"(?:\\s|$)")}return bv},j=function(bw,e){var bv=bw.attributes||{};return((!e[1]||bw.nodeName.toLowerCase()===e[1])&&(!e[2]||(bv.id||{}).value===e[2])&&(!e[3]||e[3].test((bv["class"]||{}).value)))},bt=function(e){return b.event.special.hover?e:e.replace(J,"mouseenter$1 mouseleave$1")};b.event={add:function(bx,bC,bJ,bA,by){var bD,bB,bK,bI,bH,bF,e,bG,bv,bz,bw,bE;if(bx.nodeType===3||bx.nodeType===8||!bC||!bJ||!(bD=b._data(bx))){return}if(bJ.handler){bv=bJ;bJ=bv.handler}if(!bJ.guid){bJ.guid=b.guid++}bK=bD.events;if(!bK){bD.events=bK={}}bB=bD.handle;if(!bB){bD.handle=bB=function(bL){return typeof b!=="undefined"&&(!bL||b.event.triggered!==bL.type)?b.event.dispatch.apply(bB.elem,arguments):L};bB.elem=bx}bC=b.trim(bt(bC)).split(" ");for(bI=0;bI<bC.length;bI++){bH=n.exec(bC[bI])||[];bF=bH[1];e=(bH[2]||"").split(".").sort();bE=b.event.special[bF]||{};bF=(by?bE.delegateType:bE.bindType)||bF;bE=b.event.special[bF]||{};bG=b.extend({type:bF,origType:bH[1],data:bA,handler:bJ,guid:bJ.guid,selector:by,quick:Y(by),namespace:e.join(".")},bv);bw=bK[bF];if(!bw){bw=bK[bF]=[];bw.delegateCount=0;if(!bE.setup||bE.setup.call(bx,bA,e,bB)===false){if(bx.addEventListener){bx.addEventListener(bF,bB,false)}else{if(bx.attachEvent){bx.attachEvent("on"+bF,bB)}}}}if(bE.add){bE.add.call(bx,bG);if(!bG.handler.guid){bG.handler.guid=bJ.guid}}if(by){bw.splice(bw.delegateCount++,0,bG)}else{bw.push(bG)}b.event.global[bF]=true}bx=null},global:{},remove:function(bJ,bE,bv,bH,bB){var bI=b.hasData(bJ)&&b._data(bJ),bF,bx,bz,bL,bC,bA,bG,bw,by,bK,bD,e;if(!bI||!(bw=bI.events)){return}bE=b.trim(bt(bE||"")).split(" ");for(bF=0;bF<bE.length;bF++){bx=n.exec(bE[bF])||[];bz=bL=bx[1];bC=bx[2];if(!bz){for(bz in bw){b.event.remove(bJ,bz+bE[bF],bv,bH,true)}continue}by=b.event.special[bz]||{};bz=(bH?by.delegateType:by.bindType)||bz;bD=bw[bz]||[];bA=bD.length;bC=bC?new RegExp("(^|\\.)"+bC.split(".").sort().join("\\.(?:.*\\.)?")+"(\\.|$)"):null;for(bG=0;bG<bD.length;bG++){e=bD[bG];if((bB||bL===e.origType)&&(!bv||bv.guid===e.guid)&&(!bC||bC.test(e.namespace))&&(!bH||bH===e.selector||bH==="**"&&e.selector)){bD.splice(bG--,1);if(e.selector){bD.delegateCount--}if(by.remove){by.remove.call(bJ,e)}}}if(bD.length===0&&bA!==bD.length){if(!by.teardown||by.teardown.call(bJ,bC)===false){b.removeEvent(bJ,bz,bI.handle)}delete bw[bz]}}if(b.isEmptyObject(bw)){bK=bI.handle;if(bK){bK.elem=null}b.removeData(bJ,["events","handle"],true)}},customEvent:{getData:true,setData:true,changeData:true},trigger:function(bv,bD,bA,bJ){if(bA&&(bA.nodeType===3||bA.nodeType===8)){return}var bG=bv.type||bv,bx=[],e,bw,bC,bH,bz,by,bF,bE,bB,bI;if(T.test(bG+b.event.triggered)){return}if(bG.indexOf("!")>=0){bG=bG.slice(0,-1);bw=true}if(bG.indexOf(".")>=0){bx=bG.split(".");bG=bx.shift();bx.sort()}if((!bA||b.event.customEvent[bG])&&!b.event.global[bG]){return}bv=typeof bv==="object"?bv[b.expando]?bv:new b.Event(bG,bv):new b.Event(bG);bv.type=bG;bv.isTrigger=true;bv.exclusive=bw;bv.namespace=bx.join(".");bv.namespace_re=bv.namespace?new RegExp("(^|\\.)"+bx.join("\\.(?:.*\\.)?")+"(\\.|$)"):null;by=bG.indexOf(":")<0?"on"+bG:"";if(!bA){e=b.cache;for(bC in e){if(e[bC].events&&e[bC].events[bG]){b.event.trigger(bv,bD,e[bC].handle.elem,true)}}return}bv.result=L;if(!bv.target){bv.target=bA}bD=bD!=null?b.makeArray(bD):[];bD.unshift(bv);bF=b.event.special[bG]||{};if(bF.trigger&&bF.trigger.apply(bA,bD)===false){return}bB=[[bA,bF.bindType||bG]];if(!bJ&&!bF.noBubble&&!b.isWindow(bA)){bI=bF.delegateType||bG;bH=T.test(bI+bG)?bA:bA.parentNode;bz=null;for(;bH;bH=bH.parentNode){bB.push([bH,bI]);bz=bH}if(bz&&bz===bA.ownerDocument){bB.push([bz.defaultView||bz.parentWindow||bb,bI])}}for(bC=0;bC<bB.length&&!bv.isPropagationStopped();bC++){bH=bB[bC][0];bv.type=bB[bC][1];bE=(b._data(bH,"events")||{})[bv.type]&&b._data(bH,"handle");if(bE){bE.apply(bH,bD)}bE=by&&bH[by];if(bE&&b.acceptData(bH)&&bE.apply(bH,bD)===false){bv.preventDefault()}}bv.type=bG;if(!bJ&&!bv.isDefaultPrevented()){if((!bF._default||bF._default.apply(bA.ownerDocument,bD)===false)&&!(bG==="click"&&b.nodeName(bA,"a"))&&b.acceptData(bA)){if(by&&bA[bG]&&((bG!=="focus"&&bG!=="blur")||bv.target.offsetWidth!==0)&&!b.isWindow(bA)){bz=bA[by];if(bz){bA[by]=null}b.event.triggered=bG;bA[bG]();b.event.triggered=L;if(bz){bA[by]=bz}}}}return bv.result},dispatch:function(e){e=b.event.fix(e||bb.event);var bz=((b._data(this,"events")||{})[e.type]||[]),bA=bz.delegateCount,bG=[].slice.call(arguments,0),by=!e.exclusive&&!e.namespace,bH=[],bC,bB,bK,bx,bF,bE,bv,bD,bI,bw,bJ;bG[0]=e;e.delegateTarget=this;if(bA&&!e.target.disabled&&!(e.button&&e.type==="click")){bx=b(this);bx.context=this.ownerDocument||this;for(bK=e.target;bK!=this;bK=bK.parentNode||this){bE={};bD=[];bx[0]=bK;for(bC=0;bC<bA;bC++){bI=bz[bC];bw=bI.selector;if(bE[bw]===L){bE[bw]=(bI.quick?j(bK,bI.quick):bx.is(bw))}if(bE[bw]){bD.push(bI)}}if(bD.length){bH.push({elem:bK,matches:bD})}}}if(bz.length>bA){bH.push({elem:this,matches:bz.slice(bA)})}for(bC=0;bC<bH.length&&!e.isPropagationStopped();bC++){bv=bH[bC];e.currentTarget=bv.elem;for(bB=0;bB<bv.matches.length&&!e.isImmediatePropagationStopped();bB++){bI=bv.matches[bB];if(by||(!e.namespace&&!bI.namespace)||e.namespace_re&&e.namespace_re.test(bI.namespace)){e.data=bI.data;e.handleObj=bI;bF=((b.event.special[bI.origType]||{}).handle||bI.handler).apply(bv.elem,bG);if(bF!==L){e.result=bF;if(bF===false){e.preventDefault();e.stopPropagation()}}}}}return e.result},props:"attrChange attrName relatedNode srcElement altKey bubbles cancelable ctrlKey currentTarget eventPhase metaKey relatedTarget shiftKey target timeStamp view which".split(" "),fixHooks:{},keyHooks:{props:"char charCode key keyCode".split(" "),filter:function(bv,e){if(bv.which==null){bv.which=e.charCode!=null?e.charCode:e.keyCode}return bv}},mouseHooks:{props:"button buttons clientX clientY fromElement offsetX offsetY pageX pageY screenX screenY toElement".split(" "),filter:function(bx,bw){var by,bz,e,bv=bw.button,bA=bw.fromElement;if(bx.pageX==null&&bw.clientX!=null){by=bx.target.ownerDocument||av;bz=by.documentElement;e=by.body;bx.pageX=bw.clientX+(bz&&bz.scrollLeft||e&&e.scrollLeft||0)-(bz&&bz.clientLeft||e&&e.clientLeft||0);bx.pageY=bw.clientY+(bz&&bz.scrollTop||e&&e.scrollTop||0)-(bz&&bz.clientTop||e&&e.clientTop||0)}if(!bx.relatedTarget&&bA){bx.relatedTarget=bA===bx.target?bw.toElement:bA}if(!bx.which&&bv!==L){bx.which=(bv&1?1:(bv&2?3:(bv&4?2:0)))}return bx}},fix:function(bw){if(bw[b.expando]){return bw}var bv,bz,e=bw,bx=b.event.fixHooks[bw.type]||{},by=bx.props?this.props.concat(bx.props):this.props;bw=b.Event(e);for(bv=by.length;bv;){bz=by[--bv];bw[bz]=e[bz]}if(!bw.target){bw.target=e.srcElement||av}if(bw.target.nodeType===3){bw.target=bw.target.parentNode}if(bw.metaKey===L){bw.metaKey=bw.ctrlKey}return bx.filter?bx.filter(bw,e):bw},special:{ready:{setup:b.bindReady},load:{noBubble:true},focus:{delegateType:"focusin"},blur:{delegateType:"focusout"},beforeunload:{setup:function(bw,bv,e){if(b.isWindow(this)){this.onbeforeunload=e}},teardown:function(bv,e){if(this.onbeforeunload===e){this.onbeforeunload=null}}}},simulate:function(bw,by,bx,bv){var bz=b.extend(new b.Event(),bx,{type:bw,isSimulated:true,originalEvent:{}});if(bv){b.event.trigger(bz,null,by)}else{b.event.dispatch.call(by,bz)}if(bz.isDefaultPrevented()){bx.preventDefault()}}};b.event.handle=b.event.dispatch;b.removeEvent=av.removeEventListener?function(bv,e,bw){if(bv.removeEventListener){bv.removeEventListener(e,bw,false)}}:function(bv,e,bw){if(bv.detachEvent){bv.detachEvent("on"+e,bw)}};b.Event=function(bv,e){if(!(this instanceof b.Event)){return new b.Event(bv,e)}if(bv&&bv.type){this.originalEvent=bv;this.type=bv.type;this.isDefaultPrevented=(bv.defaultPrevented||bv.returnValue===false||bv.getPreventDefault&&bv.getPreventDefault())?i:bk}else{this.type=bv}if(e){b.extend(this,e)}this.timeStamp=bv&&bv.timeStamp||b.now();this[b.expando]=true};function bk(){return false}function i(){return true}b.Event.prototype={preventDefault:function(){this.isDefaultPrevented=i;var bv=this.originalEvent;if(!bv){return}if(bv.preventDefault){bv.preventDefault()}else{bv.returnValue=false}},stopPropagation:function(){this.isPropagationStopped=i;var bv=this.originalEvent;if(!bv){return}if(bv.stopPropagation){bv.stopPropagation()}bv.cancelBubble=true},stopImmediatePropagation:function(){this.isImmediatePropagationStopped=i;this.stopPropagation()},isDefaultPrevented:bk,isPropagationStopped:bk,isImmediatePropagationStopped:bk};b.each({mouseenter:"mouseover",mouseleave:"mouseout"},function(bv,e){b.event.special[bv]={delegateType:e,bindType:e,handle:function(bz){var bB=this,bA=bz.relatedTarget,by=bz.handleObj,bw=by.selector,bx;if(!bA||(bA!==bB&&!b.contains(bB,bA))){bz.type=by.origType;bx=by.handler.apply(this,arguments);bz.type=e}return bx}}});if(!b.support.submitBubbles){b.event.special.submit={setup:function(){if(b.nodeName(this,"form")){return false
+}b.event.add(this,"click._submit keypress._submit",function(bx){var bw=bx.target,bv=b.nodeName(bw,"input")||b.nodeName(bw,"button")?bw.form:L;if(bv&&!bv._submit_attached){b.event.add(bv,"submit._submit",function(e){if(this.parentNode&&!e.isTrigger){b.event.simulate("submit",this.parentNode,e,true)}});bv._submit_attached=true}})},teardown:function(){if(b.nodeName(this,"form")){return false}b.event.remove(this,"._submit")}}}if(!b.support.changeBubbles){b.event.special.change={setup:function(){if(bd.test(this.nodeName)){if(this.type==="checkbox"||this.type==="radio"){b.event.add(this,"propertychange._change",function(e){if(e.originalEvent.propertyName==="checked"){this._just_changed=true}});b.event.add(this,"click._change",function(e){if(this._just_changed&&!e.isTrigger){this._just_changed=false;b.event.simulate("change",this,e,true)}})}return false}b.event.add(this,"beforeactivate._change",function(bw){var bv=bw.target;if(bd.test(bv.nodeName)&&!bv._change_attached){b.event.add(bv,"change._change",function(e){if(this.parentNode&&!e.isSimulated&&!e.isTrigger){b.event.simulate("change",this.parentNode,e,true)}});bv._change_attached=true}})},handle:function(bv){var e=bv.target;if(this!==e||bv.isSimulated||bv.isTrigger||(e.type!=="radio"&&e.type!=="checkbox")){return bv.handleObj.handler.apply(this,arguments)}},teardown:function(){b.event.remove(this,"._change");return bd.test(this.nodeName)}}}if(!b.support.focusinBubbles){b.each({focus:"focusin",blur:"focusout"},function(bx,e){var bv=0,bw=function(by){b.event.simulate(e,by.target,b.event.fix(by),true)};b.event.special[e]={setup:function(){if(bv++===0){av.addEventListener(bx,bw,true)}},teardown:function(){if(--bv===0){av.removeEventListener(bx,bw,true)}}}})}b.fn.extend({on:function(bw,e,bz,by,bv){var bA,bx;if(typeof bw==="object"){if(typeof e!=="string"){bz=e;e=L}for(bx in bw){this.on(bx,e,bz,bw[bx],bv)}return this}if(bz==null&&by==null){by=e;bz=e=L}else{if(by==null){if(typeof e==="string"){by=bz;bz=L}else{by=bz;bz=e;e=L}}}if(by===false){by=bk}else{if(!by){return this}}if(bv===1){bA=by;by=function(bB){b().off(bB);return bA.apply(this,arguments)};by.guid=bA.guid||(bA.guid=b.guid++)}return this.each(function(){b.event.add(this,bw,by,bz,e)})},one:function(bv,e,bx,bw){return this.on.call(this,bv,e,bx,bw,1)},off:function(bw,e,by){if(bw&&bw.preventDefault&&bw.handleObj){var bv=bw.handleObj;b(bw.delegateTarget).off(bv.namespace?bv.type+"."+bv.namespace:bv.type,bv.selector,bv.handler);return this}if(typeof bw==="object"){for(var bx in bw){this.off(bx,e,bw[bx])}return this}if(e===false||typeof e==="function"){by=e;e=L}if(by===false){by=bk}return this.each(function(){b.event.remove(this,bw,by,e)})},bind:function(e,bw,bv){return this.on(e,null,bw,bv)},unbind:function(e,bv){return this.off(e,null,bv)},live:function(e,bw,bv){b(this.context).on(e,this.selector,bw,bv);return this},die:function(e,bv){b(this.context).off(e,this.selector||"**",bv);return this},delegate:function(e,bv,bx,bw){return this.on(bv,e,bx,bw)},undelegate:function(e,bv,bw){return arguments.length==1?this.off(e,"**"):this.off(bv,e,bw)},trigger:function(e,bv){return this.each(function(){b.event.trigger(e,bv,this)})},triggerHandler:function(e,bv){if(this[0]){return b.event.trigger(e,bv,this[0],true)}},toggle:function(bx){var bv=arguments,e=bx.guid||b.guid++,bw=0,by=function(bz){var bA=(b._data(this,"lastToggle"+bx.guid)||0)%bw;b._data(this,"lastToggle"+bx.guid,bA+1);bz.preventDefault();return bv[bA].apply(this,arguments)||false};by.guid=e;while(bw<bv.length){bv[bw++].guid=e}return this.click(by)},hover:function(e,bv){return this.mouseenter(e).mouseleave(bv||e)}});b.each(("blur focus focusin focusout load resize scroll unload click dblclick mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave change select submit keydown keypress keyup error contextmenu").split(" "),function(bv,e){b.fn[e]=function(bx,bw){if(bw==null){bw=bx;bx=null}return arguments.length>0?this.on(e,null,bx,bw):this.trigger(e)};if(b.attrFn){b.attrFn[e]=true}if(aO.test(e)){b.event.fixHooks[e]=b.event.keyHooks}if(bf.test(e)){b.event.fixHooks[e]=b.event.mouseHooks}});
+/*!
+ * Sizzle CSS Selector Engine
+ * Copyright 2011, The Dojo Foundation
+ * Released under the MIT, BSD, and GPL Licenses.
+ * More information: http://sizzlejs.com/
+ */
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+ * http://docs.jquery.com/UI
+ */
+(function(a,d){a.ui=a.ui||{};if(a.ui.version){return}a.extend(a.ui,{version:"1.8.18",keyCode:{ALT:18,BACKSPACE:8,CAPS_LOCK:20,COMMA:188,COMMAND:91,COMMAND_LEFT:91,COMMAND_RIGHT:93,CONTROL:17,DELETE:46,DOWN:40,END:35,ENTER:13,ESCAPE:27,HOME:36,INSERT:45,LEFT:37,MENU:93,NUMPAD_ADD:107,NUMPAD_DECIMAL:110,NUMPAD_DIVIDE:111,NUMPAD_ENTER:108,NUMPAD_MULTIPLY:106,NUMPAD_SUBTRACT:109,PAGE_DOWN:34,PAGE_UP:33,PERIOD:190,RIGHT:39,SHIFT:16,SPACE:32,TAB:9,UP:38,WINDOWS:91}});a.fn.extend({propAttr:a.fn.prop||a.fn.attr,_focus:a.fn.focus,focus:function(e,f){return typeof e==="number"?this.each(function(){var g=this;setTimeout(function(){a(g).focus();if(f){f.call(g)}},e)}):this._focus.apply(this,arguments)},scrollParent:function(){var e;if((a.browser.msie&&(/(static|relative)/).test(this.css("position")))||(/absolute/).test(this.css("position"))){e=this.parents().filter(function(){return(/(relative|absolute|fixed)/).test(a.curCSS(this,"position",1))&&(/(auto|scroll)/).test(a.curCSS(this,"overflow",1)+a.curCSS(this,"overflow-y",1)+a.curCSS(this,"overflow-x",1))}).eq(0)}else{e=this.parents().filter(function(){return(/(auto|scroll)/).test(a.curCSS(this,"overflow",1)+a.curCSS(this,"overflow-y",1)+a.curCSS(this,"overflow-x",1))}).eq(0)}return(/fixed/).test(this.css("position"))||!e.length?a(document):e},zIndex:function(h){if(h!==d){return this.css("zIndex",h)}if(this.length){var f=a(this[0]),e,g;while(f.length&&f[0]!==document){e=f.css("position");if(e==="absolute"||e==="relative"||e==="fixed"){g=parseInt(f.css("zIndex"),10);if(!isNaN(g)&&g!==0){return g}}f=f.parent()}}return 0},disableSelection:function(){return this.bind((a.support.selectstart?"selectstart":"mousedown")+".ui-disableSelection",function(e){e.preventDefault()})},enableSelection:function(){return this.unbind(".ui-disableSelection")}});a.each(["Width","Height"],function(g,e){var f=e==="Width"?["Left","Right"]:["Top","Bottom"],h=e.toLowerCase(),k={innerWidth:a.fn.innerWidth,innerHeight:a.fn.innerHeight,outerWidth:a.fn.outerWidth,outerHeight:a.fn.outerHeight};function j(m,l,i,n){a.each(f,function(){l-=parseFloat(a.curCSS(m,"padding"+this,true))||0;if(i){l-=parseFloat(a.curCSS(m,"border"+this+"Width",true))||0}if(n){l-=parseFloat(a.curCSS(m,"margin"+this,true))||0}});return l}a.fn["inner"+e]=function(i){if(i===d){return k["inner"+e].call(this)}return this.each(function(){a(this).css(h,j(this,i)+"px")})};a.fn["outer"+e]=function(i,l){if(typeof i!=="number"){return k["outer"+e].call(this,i)}return this.each(function(){a(this).css(h,j(this,i,true,l)+"px")})}});function c(g,e){var j=g.nodeName.toLowerCase();if("area"===j){var i=g.parentNode,h=i.name,f;if(!g.href||!h||i.nodeName.toLowerCase()!=="map"){return false}f=a("img[usemap=#"+h+"]")[0];return !!f&&b(f)}return(/input|select|textarea|button|object/.test(j)?!g.disabled:"a"==j?g.href||e:e)&&b(g)}function b(e){return !a(e).parents().andSelf().filter(function(){return a.curCSS(this,"visibility")==="hidden"||a.expr.filters.hidden(this)}).length}a.extend(a.expr[":"],{data:function(g,f,e){return !!a.data(g,e[3])},focusable:function(e){return c(e,!isNaN(a.attr(e,"tabindex")))},tabbable:function(g){var e=a.attr(g,"tabindex"),f=isNaN(e);return(f||e>=0)&&c(g,!f)}});a(function(){var e=document.body,f=e.appendChild(f=document.createElement("div"));f.offsetHeight;a.extend(f.style,{minHeight:"100px",height:"auto",padding:0,borderWidth:0});a.support.minHeight=f.offsetHeight===100;a.support.selectstart="onselectstart" in f;e.removeChild(f).style.display="none"});a.extend(a.ui,{plugin:{add:function(f,g,j){var h=a.ui[f].prototype;for(var e in j){h.plugins[e]=h.plugins[e]||[];h.plugins[e].push([g,j[e]])}},call:function(e,g,f){var j=e.plugins[g];if(!j||!e.element[0].parentNode){return}for(var h=0;h<j.length;h++){if(e.options[j[h][0]]){j[h][1].apply(e.element,f)}}}},contains:function(f,e){return document.compareDocumentPosition?f.compareDocumentPosition(e)&16:f!==e&&f.contains(e)},hasScroll:function(h,f){if(a(h).css("overflow")==="hidden"){return false}var e=(f&&f==="left")?"scrollLeft":"scrollTop",g=false;if(h[e]>0){return true}h[e]=1;g=(h[e]>0);h[e]=0;return g},isOverAxis:function(f,e,g){return(f>e)&&(f<(e+g))},isOver:function(j,f,i,h,e,g){return a.ui.isOverAxis(j,i,e)&&a.ui.isOverAxis(f,h,g)}})})(jQuery);/*!
+ * jQuery UI Widget 1.8.18
+ *
+ * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * http://docs.jquery.com/UI/Widget
+ */
+(function(b,d){if(b.cleanData){var c=b.cleanData;b.cleanData=function(f){for(var g=0,h;(h=f[g])!=null;g++){try{b(h).triggerHandler("remove")}catch(j){}}c(f)}}else{var a=b.fn.remove;b.fn.remove=function(e,f){return this.each(function(){if(!f){if(!e||b.filter(e,[this]).length){b("*",this).add([this]).each(function(){try{b(this).triggerHandler("remove")}catch(g){}})}}return a.call(b(this),e,f)})}}b.widget=function(f,h,e){var g=f.split(".")[0],j;f=f.split(".")[1];j=g+"-"+f;if(!e){e=h;h=b.Widget}b.expr[":"][j]=function(k){return !!b.data(k,f)};b[g]=b[g]||{};b[g][f]=function(k,l){if(arguments.length){this._createWidget(k,l)}};var i=new h();i.options=b.extend(true,{},i.options);b[g][f].prototype=b.extend(true,i,{namespace:g,widgetName:f,widgetEventPrefix:b[g][f].prototype.widgetEventPrefix||f,widgetBaseClass:j},e);b.widget.bridge(f,b[g][f])};b.widget.bridge=function(f,e){b.fn[f]=function(i){var g=typeof i==="string",h=Array.prototype.slice.call(arguments,1),j=this;i=!g&&h.length?b.extend.apply(null,[true,i].concat(h)):i;if(g&&i.charAt(0)==="_"){return j}if(g){this.each(function(){var k=b.data(this,f),l=k&&b.isFunction(k[i])?k[i].apply(k,h):k;if(l!==k&&l!==d){j=l;return false}})}else{this.each(function(){var k=b.data(this,f);if(k){k.option(i||{})._init()}else{b.data(this,f,new e(i,this))}})}return j}};b.Widget=function(e,f){if(arguments.length){this._createWidget(e,f)}};b.Widget.prototype={widgetName:"widget",widgetEventPrefix:"",options:{disabled:false},_createWidget:function(f,g){b.data(g,this.widgetName,this);this.element=b(g);this.options=b.extend(true,{},this.options,this._getCreateOptions(),f);var e=this;this.element.bind("remove."+this.widgetName,function(){e.destroy()});this._create();this._trigger("create");this._init()},_getCreateOptions:function(){return b.metadata&&b.metadata.get(this.element[0])[this.widgetName]},_create:function(){},_init:function(){},destroy:function(){this.element.unbind("."+this.widgetName).removeData(this.widgetName);this.widget().unbind("."+this.widgetName).removeAttr("aria-disabled").removeClass(this.widgetBaseClass+"-disabled ui-state-disabled")},widget:function(){return this.element},option:function(f,g){var e=f;if(arguments.length===0){return b.extend({},this.options)}if(typeof f==="string"){if(g===d){return this.options[f]}e={};e[f]=g}this._setOptions(e);return this},_setOptions:function(f){var e=this;b.each(f,function(g,h){e._setOption(g,h)});return this},_setOption:function(e,f){this.options[e]=f;if(e==="disabled"){this.widget()[f?"addClass":"removeClass"](this.widgetBaseClass+"-disabled ui-state-disabled").attr("aria-disabled",f)}return this},enable:function(){return this._setOption("disabled",false)},disable:function(){return this._setOption("disabled",true)},_trigger:function(e,f,g){var j,i,h=this.options[e];g=g||{};f=b.Event(f);f.type=(e===this.widgetEventPrefix?e:this.widgetEventPrefix+e).toLowerCase();f.target=this.element[0];i=f.originalEvent;if(i){for(j in i){if(!(j in f)){f[j]=i[j]}}}this.element.trigger(f,g);return !(b.isFunction(h)&&h.call(this.element[0],f,g)===false||f.isDefaultPrevented())}}})(jQuery);/*!
+ * jQuery UI Mouse 1.8.18
+ *
+ * Copyright 2011, AUTHORS.txt (http://jqueryui.com/about)
+ * Dual licensed under the MIT or GPL Version 2 licenses.
+ * http://jquery.org/license
+ *
+ * http://docs.jquery.com/UI/Mouse
+ *
+ * Depends:
+ * jquery.ui.widget.js
+ */
+(function(b,c){var a=false;b(document).mouseup(function(d){a=false});b.widget("ui.mouse",{options:{cancel:":input,option",distance:1,delay:0},_mouseInit:function(){var d=this;this.element.bind("mousedown."+this.widgetName,function(e){return d._mouseDown(e)}).bind("click."+this.widgetName,function(e){if(true===b.data(e.target,d.widgetName+".preventClickEvent")){b.removeData(e.target,d.widgetName+".preventClickEvent");e.stopImmediatePropagation();return false}});this.started=false},_mouseDestroy:function(){this.element.unbind("."+this.widgetName)},_mouseDown:function(f){if(a){return}(this._mouseStarted&&this._mouseUp(f));this._mouseDownEvent=f;var e=this,g=(f.which==1),d=(typeof this.options.cancel=="string"&&f.target.nodeName?b(f.target).closest(this.options.cancel).length:false);if(!g||d||!this._mouseCapture(f)){return true}this.mouseDelayMet=!this.options.delay;if(!this.mouseDelayMet){this._mouseDelayTimer=setTimeout(function(){e.mouseDelayMet=true},this.options.delay)}if(this._mouseDistanceMet(f)&&this._mouseDelayMet(f)){this._mouseStarted=(this._mouseStart(f)!==false);if(!this._mouseStarted){f.preventDefault();return true}}if(true===b.data(f.target,this.widgetName+".preventClickEvent")){b.removeData(f.target,this.widgetName+".preventClickEvent")}this._mouseMoveDelegate=function(h){return e._mouseMove(h)};this._mouseUpDelegate=function(h){return e._mouseUp(h)};b(document).bind("mousemove."+this.widgetName,this._mouseMoveDelegate).bind("mouseup."+this.widgetName,this._mouseUpDelegate);f.preventDefault();a=true;return true},_mouseMove:function(d){if(b.browser.msie&&!(document.documentMode>=9)&&!d.button){return this._mouseUp(d)}if(this._mouseStarted){this._mouseDrag(d);return d.preventDefault()}if(this._mouseDistanceMet(d)&&this._mouseDelayMet(d)){this._mouseStarted=(this._mouseStart(this._mouseDownEvent,d)!==false);(this._mouseStarted?this._mouseDrag(d):this._mouseUp(d))}return !this._mouseStarted},_mouseUp:function(d){b(document).unbind("mousemove."+this.widgetName,this._mouseMoveDelegate).unbind("mouseup."+this.widgetName,this._mouseUpDelegate);if(this._mouseStarted){this._mouseStarted=false;if(d.target==this._mouseDownEvent.target){b.data(d.target,this.widgetName+".preventClickEvent",true)}this._mouseStop(d)}return false},_mouseDistanceMet:function(d){return(Math.max(Math.abs(this._mouseDownEvent.pageX-d.pageX),Math.abs(this._mouseDownEvent.pageY-d.pageY))>=this.options.distance)},_mouseDelayMet:function(d){return this.mouseDelayMet},_mouseStart:function(d){},_mouseDrag:function(d){},_mouseStop:function(d){},_mouseCapture:function(d){return true}})})(jQuery);(function(c,d){c.widget("ui.resizable",c.ui.mouse,{widgetEventPrefix:"resize",options:{alsoResize:false,animate:false,animateDuration:"slow",animateEasing:"swing",aspectRatio:false,autoHide:false,containment:false,ghost:false,grid:false,handles:"e,s,se",helper:false,maxHeight:null,maxWidth:null,minHeight:10,minWidth:10,zIndex:1000},_create:function(){var f=this,k=this.options;this.element.addClass("ui-resizable");c.extend(this,{_aspectRatio:!!(k.aspectRatio),aspectRatio:k.aspectRatio,originalElement:this.element,_proportionallyResizeElements:[],_helper:k.helper||k.ghost||k.animate?k.helper||"ui-resizable-helper":null});if(this.element[0].nodeName.match(/canvas|textarea|input|select|button|img/i)){this.element.wrap(c('<div class="ui-wrapper" style="overflow: hidden;"></div>').css({position:this.element.css("position"),width:this.element.outerWidth(),height:this.element.outerHeight(),top:this.element.css("top"),left:this.element.css("left")}));this.element=this.element.parent().data("resizable",this.element.data("resizable"));this.elementIsWrapper=true;this.element.css({marginLeft:this.originalElement.css("marginLeft"),marginTop:this.originalElement.css("marginTop"),marginRight:this.originalElement.css("marginRight"),marginBottom:this.originalElement.css("marginBottom")});this.originalElement.css({marginLeft:0,marginTop:0,marginRight:0,marginBottom:0});this.originalResizeStyle=this.originalElement.css("resize");this.originalElement.css("resize","none");this._proportionallyResizeElements.push(this.originalElement.css({position:"static",zoom:1,display:"block"}));this.originalElement.css({margin:this.originalElement.css("margin")});this._proportionallyResize()}this.handles=k.handles||(!c(".ui-resizable-handle",this.element).length?"e,s,se":{n:".ui-resizable-n",e:".ui-resizable-e",s:".ui-resizable-s",w:".ui-resizable-w",se:".ui-resizable-se",sw:".ui-resizable-sw",ne:".ui-resizable-ne",nw:".ui-resizable-nw"});if(this.handles.constructor==String){if(this.handles=="all"){this.handles="n,e,s,w,se,sw,ne,nw"}var l=this.handles.split(",");this.handles={};for(var g=0;g<l.length;g++){var j=c.trim(l[g]),e="ui-resizable-"+j;var h=c('<div class="ui-resizable-handle '+e+'"></div>');if(/sw|se|ne|nw/.test(j)){h.css({zIndex:++k.zIndex})}if("se"==j){h.addClass("ui-icon ui-icon-gripsmall-diagonal-se")}this.handles[j]=".ui-resizable-"+j;this.element.append(h)}}this._renderAxis=function(q){q=q||this.element;for(var n in this.handles){if(this.handles[n].constructor==String){this.handles[n]=c(this.handles[n],this.element).show()}if(this.elementIsWrapper&&this.originalElement[0].nodeName.match(/textarea|input|select|button/i)){var o=c(this.handles[n],this.element),p=0;p=/sw|ne|nw|se|n|s/.test(n)?o.outerHeight():o.outerWidth();var m=["padding",/ne|nw|n/.test(n)?"Top":/se|sw|s/.test(n)?"Bottom":/^e$/.test(n)?"Right":"Left"].join("");q.css(m,p);this._proportionallyResize()}if(!c(this.handles[n]).length){continue}}};this._renderAxis(this.element);this._handles=c(".ui-resizable-handle",this.element).disableSelection();this._handles.mouseover(function(){if(!f.resizing){if(this.className){var i=this.className.match(/ui-resizable-(se|sw|ne|nw|n|e|s|w)/i)}f.axis=i&&i[1]?i[1]:"se"}});if(k.autoHide){this._handles.hide();c(this.element).addClass("ui-resizable-autohide").hover(function(){if(k.disabled){return}c(this).removeClass("ui-resizable-autohide");f._handles.show()},function(){if(k.disabled){return}if(!f.resizing){c(this).addClass("ui-resizable-autohide");f._handles.hide()}})}this._mouseInit()},destroy:function(){this._mouseDestroy();var e=function(g){c(g).removeClass("ui-resizable ui-resizable-disabled ui-resizable-resizing").removeData("resizable").unbind(".resizable").find(".ui-resizable-handle").remove()};if(this.elementIsWrapper){e(this.element);var f=this.element;f.after(this.originalElement.css({position:f.css("position"),width:f.outerWidth(),height:f.outerHeight(),top:f.css("top"),left:f.css("left")})).remove()}this.originalElement.css("resize",this.originalResizeStyle);e(this.originalElement);return this},_mouseCapture:function(f){var g=false;for(var e in this.handles){if(c(this.handles[e])[0]==f.target){g=true}}return !this.options.disabled&&g},_mouseStart:function(g){var j=this.options,f=this.element.position(),e=this.element;this.resizing=true;this.documentScroll={top:c(document).scrollTop(),left:c(document).scrollLeft()};if(e.is(".ui-draggable")||(/absolute/).test(e.css("position"))){e.css({position:"absolute",top:f.top,left:f.left})}this._renderProxy();var k=b(this.helper.css("left")),h=b(this.helper.css("top"));if(j.containment){k+=c(j.containment).scrollLeft()||0;h+=c(j.containment).scrollTop()||0}this.offset=this.helper.offset();this.position={left:k,top:h};this.size=this._helper?{width:e.outerWidth(),height:e.outerHeight()}:{width:e.width(),height:e.height()};this.originalSize=this._helper?{width:e.outerWidth(),height:e.outerHeight()}:{width:e.width(),height:e.height()};this.originalPosition={left:k,top:h};this.sizeDiff={width:e.outerWidth()-e.width(),height:e.outerHeight()-e.height()};this.originalMousePosition={left:g.pageX,top:g.pageY};this.aspectRatio=(typeof j.aspectRatio=="number")?j.aspectRatio:((this.originalSize.width/this.originalSize.height)||1);var i=c(".ui-resizable-"+this.axis).css("cursor");c("body").css("cursor",i=="auto"?this.axis+"-resize":i);e.addClass("ui-resizable-resizing");this._propagate("start",g);return true},_mouseDrag:function(e){var h=this.helper,g=this.options,m={},q=this,j=this.originalMousePosition,n=this.axis;var r=(e.pageX-j.left)||0,p=(e.pageY-j.top)||0;var i=this._change[n];if(!i){return false}var l=i.apply(this,[e,r,p]),k=c.browser.msie&&c.browser.version<7,f=this.sizeDiff;this._updateVirtualBoundaries(e.shiftKey);if(this._aspectRatio||e.shiftKey){l=this._updateRatio(l,e)}l=this._respectSize(l,e);this._propagate("resize",e);h.css({top:this.position.top+"px",left:this.position.left+"px",width:this.size.width+"px",height:this.size.height+"px"});if(!this._helper&&this._proportionallyResizeElements.length){this._proportionallyResize()}this._updateCache(l);this._trigger("resize",e,this.ui());return false},_mouseStop:function(h){this.resizing=false;var i=this.options,m=this;if(this._helper){var g=this._proportionallyResizeElements,e=g.length&&(/textarea/i).test(g[0].nodeName),f=e&&c.ui.hasScroll(g[0],"left")?0:m.sizeDiff.height,k=e?0:m.sizeDiff.width;var n={width:(m.helper.width()-k),height:(m.helper.height()-f)},j=(parseInt(m.element.css("left"),10)+(m.position.left-m.originalPosition.left))||null,l=(parseInt(m.element.css("top"),10)+(m.position.top-m.originalPosition.top))||null;if(!i.animate){this.element.css(c.extend(n,{top:l,left:j}))}m.helper.height(m.size.height);m.helper.width(m.size.width);if(this._helper&&!i.animate){this._proportionallyResize()}}c("body").css("cursor","auto");this.element.removeClass("ui-resizable-resizing");this._propagate("stop",h);if(this._helper){this.helper.remove()}return false},_updateVirtualBoundaries:function(g){var j=this.options,i,h,f,k,e;e={minWidth:a(j.minWidth)?j.minWidth:0,maxWidth:a(j.maxWidth)?j.maxWidth:Infinity,minHeight:a(j.minHeight)?j.minHeight:0,maxHeight:a(j.maxHeight)?j.maxHeight:Infinity};if(this._aspectRatio||g){i=e.minHeight*this.aspectRatio;f=e.minWidth/this.aspectRatio;h=e.maxHeight*this.aspectRatio;k=e.maxWidth/this.aspectRatio;if(i>e.minWidth){e.minWidth=i}if(f>e.minHeight){e.minHeight=f}if(h<e.maxWidth){e.maxWidth=h}if(k<e.maxHeight){e.maxHeight=k}}this._vBoundaries=e},_updateCache:function(e){var f=this.options;this.offset=this.helper.offset();if(a(e.left)){this.position.left=e.left}if(a(e.top)){this.position.top=e.top}if(a(e.height)){this.size.height=e.height}if(a(e.width)){this.size.width=e.width}},_updateRatio:function(h,g){var i=this.options,j=this.position,f=this.size,e=this.axis;if(a(h.height)){h.width=(h.height*this.aspectRatio)}else{if(a(h.width)){h.height=(h.width/this.aspectRatio)}}if(e=="sw"){h.left=j.left+(f.width-h.width);h.top=null}if(e=="nw"){h.top=j.top+(f.height-h.height);h.left=j.left+(f.width-h.width)}return h},_respectSize:function(l,g){var j=this.helper,i=this._vBoundaries,r=this._aspectRatio||g.shiftKey,q=this.axis,t=a(l.width)&&i.maxWidth&&(i.maxWidth<l.width),m=a(l.height)&&i.maxHeight&&(i.maxHeight<l.height),h=a(l.width)&&i.minWidth&&(i.minWidth>l.width),s=a(l.height)&&i.minHeight&&(i.minHeight>l.height);if(h){l.width=i.minWidth}if(s){l.height=i.minHeight}if(t){l.width=i.maxWidth}if(m){l.height=i.maxHeight}var f=this.originalPosition.left+this.originalSize.width,p=this.position.top+this.size.height;var k=/sw|nw|w/.test(q),e=/nw|ne|n/.test(q);if(h&&k){l.left=f-i.minWidth}if(t&&k){l.left=f-i.maxWidth}if(s&&e){l.top=p-i.minHeight}if(m&&e){l.top=p-i.maxHeight}var 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+<div class="title">eHive </div> </div>
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+<div class="textblock"><p>eHive is a system for running computation pipelines on distributed computing resources - clusters, farms or grids.</p>
+<p>The name comes from the way pipelines are processed by a swarm of autonomous agents.</p>
+<h2>Blackboard, Jobs and Workers </h2>
+<p>In the centre of each running pipeline is a database that acts as a blackboard with individual tasks to be run. These tasks (we call them Jobs) are claimed and processed by "Worker bees" or just Workers - autonomous processes that are continuously running on the compute farm and connect to the pipeline database to report about the progress of Jobs or claim some more. When a Worker discovers that its predefined time is up or that there are no more Jobs to do, it claims no more Jobs and exits the compute farm freeing the resources.</p>
+<h2>Beekeeper </h2>
+<p>A separate Beekeeper process makes sure there are always enough Workers on the farm. It regularly checks the states of both the blackboard and the farm and submits more Workers when needed. There is no direct communication between Beekeeper and Workers, which makes the system rather fault-tolerant, as crashing of any of the agents for whatever reason doesn't stop the rest of the system from running.</p>
+<h2>Analyses </h2>
+<p>Jobs that share same code, common parameters and resource requirements are typically grouped into Analyses, and generally an Analysis can be viewed as a "base class" for the Jobs that belong to it. However in some sense an Analysis also acts as a "container" for them.</p>
+<h2>PipeConfig file defines Analyses and dependency rules of the pipeline </h2>
+<p>eHive pipeline databases are molded according to PipeConfig files which are Perl modules conforming to a special interface. A PipeConfig file defines the stucture of the pipeline, which is a graph whose nodes are Analyses (with their code, parameters and resource requirements) and edges are various dependency rules:</p>
+<ul>
+<li>Dataflow rules define how data that flows out of an Analysis can be used to trigger creation of Jobs in other Analyses</li>
+<li>Control rules define dependencies between Analyses as Jobs' containers ("Jobs of Analysis Y can only start when all Jobs of Analysis X are done")</li>
+<li>Semaphore rules define dependencies between individual Jobs on a more fine-grained level</li>
+</ul>
+<p>There are also other parameters of Analyses that control, for example:</p>
+<ul>
+<li>how many Workers can simultaneously work on a given Analysis,</li>
+<li>how many times a Job should be tried until it is considered failed,</li>
+<li>what should be autimatically done with a Job if it needs more memory/time, etc.</li>
+</ul>
+<h2>Available documentation </h2>
+<ul>
+<li>eHive dependencies, installation and setup <a href="http://htmlpreview.github.io/?https://github.com/Ensembl/ensembl-hive/blob/version/1.9/docs/install.html">(on GitHub)</a> <a href="docs/install.html">(local)</a></li>
+<li>eHive database schema <a href="http://htmlpreview.github.io/?https://github.com/Ensembl/ensembl-hive/blob/version/1.9/docs/hive_schema.html">(on GitHub)</a> <a href="docs/hive_schema.html">(local)</a></li>
+</ul>
+<h2>Contact us (mailing list) </h2>
+<p>eHive was originally conceived and used within EnsEMBL Compara group for running Comparative Genomics pipelines, but since then it has been separated into a separate software tool and is used in many projects both in Genome Campus, Cambridge and outside. There is eHive users' mailing list for questions, suggestions, discussions and announcements.</p>
+<p>To subscribe to it please visit: <a href="http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users">http://listserver.ebi.ac.uk/mailman/listinfo/ehive-users</a> </p>
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+var namespaces =
+[
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+];
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index 0000000000000000000000000000000000000000..41a9cb96942beb392d6e62a1ec7a20aca467c602
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+#nav-tree .children_ul {
+ margin:0;
+ padding:4px;
+}
+
+#nav-tree ul {
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+ margin:0px;
+ padding:0px;
+}
+
+#nav-tree li {
+ white-space:nowrap;
+ margin:0px;
+ padding:0px;
+}
+
+#nav-tree .plus {
+ margin:0px;
+}
+
+#nav-tree .selected {
+ background-image: url('tab_a.png');
+ background-repeat:repeat-x;
+ color: #fff;
+ text-shadow: 0px 1px 1px rgba(0, 0, 0, 1.0);
+}
+
+#nav-tree img {
+ margin:0px;
+ padding:0px;
+ border:0px;
+ vertical-align: middle;
+}
+
+#nav-tree a {
+ text-decoration:none;
+ padding:0px;
+ margin:0px;
+ outline:none;
+}
+
+#nav-tree .label {
+ margin:0px;
+ padding:0px;
+ font: 12px 'Lucida Grande',Geneva,Helvetica,Arial,sans-serif;
+}
+
+#nav-tree .label a {
+ padding:2px;
+}
+
+#nav-tree .selected a {
+ text-decoration:none;
+ color:#fff;
+}
+
+#nav-tree .children_ul {
+ margin:0px;
+ padding:0px;
+}
+
+#nav-tree .item {
+ margin:0px;
+ padding:0px;
+}
+
+#nav-tree {
+ padding: 0px 0px;
+ background-color: #FAFAFF;
+ font-size:14px;
+ overflow:auto;
+}
+
+#doc-content {
+ overflow:auto;
+ display:block;
+ padding:0px;
+ margin:0px;
+ -webkit-overflow-scrolling : touch; /* iOS 5+ */
+}
+
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+ padding:0 6px 0 0;
+ margin: 0px;
+ display:block;
+ position: absolute;
+ left: 0px;
+ width: 250px;
+}
+
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+ display:block;
+}
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+ cursor:e-resize;
+ height:100%;
+ right:0;
+ top:0;
+ width:6px;
+}
+
+.ui-resizable-handle {
+ display:none;
+ font-size:0.1px;
+ position:absolute;
+ z-index:1;
+}
+
+#nav-tree-contents {
+ margin: 6px 0px 0px 0px;
+}
+
+#nav-tree {
+ background-image:url('nav_h.png');
+ background-repeat:repeat-x;
+ background-color: #F9FAFC;
+ -webkit-overflow-scrolling : touch; /* iOS 5+ */
+}
+
+#nav-sync {
+ position:absolute;
+ top:5px;
+ right:24px;
+ z-index:0;
+}
+
+#nav-sync img {
+ opacity:0.3;
+}
+
+#nav-sync img:hover {
+ opacity:0.9;
+}
+
+@media print
+{
+ #nav-tree { display: none; }
+ div.ui-resizable-handle { display: none; position: relative; }
+}
+
diff --git a/docs/doxygen/navtree.js b/docs/doxygen/navtree.js
new file mode 100644
index 0000000000000000000000000000000000000000..dc80f7d0c49c4f09013af909a38cbd64ab9fb652
--- /dev/null
+++ b/docs/doxygen/navtree.js
@@ -0,0 +1,552 @@
+var NAVTREE =
+[
+ [ "ensembl-hive", "index.html", [
+ [ "eHive", "md__r_e_a_d_m_e.html", null ],
+ [ "Deprecated List", "deprecated.html", null ],
+ [ "Namespaces", null, [
+ [ "Namespace List", "namespaces.html", "namespaces" ]
+ ] ],
+ [ "Classes", null, [
+ [ "Class List", "annotated.html", "annotated" ],
+ [ "Class Index", "classes.html", null ],
+ [ "Class Hierarchy", "hierarchy.html", "hierarchy" ],
+ [ "Class Members", "functions.html", [
+ [ "All", "functions.html", "functions_dup" ],
+ [ "Functions", "functions_func.html", "functions_func" ]
+ ] ]
+ ] ],
+ [ "Files", null, [
+ [ "File List", "files.html", "files" ],
+ [ "File Members", "globals.html", [
+ [ "All", "globals.html", null ],
+ [ "Functions", "globals_func.html", null ]
+ ] ]
+ ] ]
+ ] ]
+];
+
+var NAVTREEINDEX =
+[
+"_accumulator_8pm.html",
+"class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#ab19a4a6d447c8661574a97ae159234f3",
+"class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_description.html#a5c5bf7acac77e65b07761146d39bcc24",
+"functions_func.html"
+];
+
+var SYNCONMSG = 'click to disable panel synchronisation';
+var SYNCOFFMSG = 'click to enable panel synchronisation';
+var SYNCONMSG = 'click to disable panel synchronisation';
+var SYNCOFFMSG = 'click to enable panel synchronisation';
+var navTreeSubIndices = new Array();
+
+function getData(varName)
+{
+ var i = varName.lastIndexOf('/');
+ var n = i>=0 ? varName.substring(i+1) : varName;
+ return eval(n.replace(/\-/g,'_'));
+}
+
+function stripPath(uri)
+{
+ return uri.substring(uri.lastIndexOf('/')+1);
+}
+
+function stripPath2(uri)
+{
+ var i = uri.lastIndexOf('/');
+ var s = uri.substring(i+1);
+ var m = uri.substring(0,i+1).match(/\/d\w\/d\w\w\/$/);
+ return m ? uri.substring(i-6) : s;
+}
+
+function localStorageSupported()
+{
+ try {
+ return 'localStorage' in window && window['localStorage'] !== null && window.localStorage.getItem;
+ }
+ catch(e) {
+ return false;
+ }
+}
+
+
+function storeLink(link)
+{
+ if (!$("#nav-sync").hasClass('sync') && localStorageSupported()) {
+ window.localStorage.setItem('navpath',link);
+ }
+}
+
+function deleteLink()
+{
+ if (localStorageSupported()) {
+ window.localStorage.setItem('navpath','');
+ }
+}
+
+function cachedLink()
+{
+ if (localStorageSupported()) {
+ return window.localStorage.getItem('navpath');
+ } else {
+ return '';
+ }
+}
+
+function getScript(scriptName,func,show)
+{
+ var head = document.getElementsByTagName("head")[0];
+ var script = document.createElement('script');
+ script.id = scriptName;
+ script.type = 'text/javascript';
+ script.onload = func;
+ script.src = scriptName+'.js';
+ if ($.browser.msie && $.browser.version<=8) {
+ // script.onload does not work with older versions of IE
+ script.onreadystatechange = function() {
+ if (script.readyState=='complete' || script.readyState=='loaded') {
+ func(); if (show) showRoot();
+ }
+ }
+ }
+ head.appendChild(script);
+}
+
+function createIndent(o,domNode,node,level)
+{
+ var level=-1;
+ var n = node;
+ while (n.parentNode) { level++; n=n.parentNode; }
+ if (node.childrenData) {
+ var imgNode = document.createElement("img");
+ imgNode.style.paddingLeft=(16*level).toString()+'px';
+ imgNode.width = 16;
+ imgNode.height = 22;
+ imgNode.border = 0;
+ node.plus_img = imgNode;
+ node.expandToggle = document.createElement("a");
+ node.expandToggle.href = "javascript:void(0)";
+ node.expandToggle.onclick = function() {
+ if (node.expanded) {
+ $(node.getChildrenUL()).slideUp("fast");
+ node.plus_img.src = node.relpath+"ftv2pnode.png";
+ node.expanded = false;
+ } else {
+ expandNode(o, node, false, false);
+ }
+ }
+ node.expandToggle.appendChild(imgNode);
+ domNode.appendChild(node.expandToggle);
+ imgNode.src = node.relpath+"ftv2pnode.png";
+ } else {
+ var span = document.createElement("span");
+ span.style.display = 'inline-block';
+ span.style.width = 16*(level+1)+'px';
+ span.style.height = '22px';
+ span.innerHTML = ' ';
+ domNode.appendChild(span);
+ }
+}
+
+var animationInProgress = false;
+
+function gotoAnchor(anchor,aname,updateLocation)
+{
+ var pos, docContent = $('#doc-content');
+ if (anchor.parent().attr('class')=='memItemLeft' ||
+ anchor.parent().attr('class')=='fieldtype' ||
+ anchor.parent().is(':header'))
+ {
+ pos = anchor.parent().position().top;
+ } else if (anchor.position()) {
+ pos = anchor.position().top;
+ }
+ if (pos) {
+ var dist = Math.abs(Math.min(
+ pos-docContent.offset().top,
+ docContent[0].scrollHeight-
+ docContent.height()-docContent.scrollTop()));
+ animationInProgress=true;
+ docContent.animate({
+ scrollTop: pos + docContent.scrollTop() - docContent.offset().top
+ },Math.max(50,Math.min(500,dist)),function(){
+ if (updateLocation) window.location.href=aname;
+ animationInProgress=false;
+ });
+ }
+}
+
+function newNode(o, po, text, link, childrenData, lastNode)
+{
+ var node = new Object();
+ node.children = Array();
+ node.childrenData = childrenData;
+ node.depth = po.depth + 1;
+ node.relpath = po.relpath;
+ node.isLast = lastNode;
+
+ node.li = document.createElement("li");
+ po.getChildrenUL().appendChild(node.li);
+ node.parentNode = po;
+
+ node.itemDiv = document.createElement("div");
+ node.itemDiv.className = "item";
+
+ node.labelSpan = document.createElement("span");
+ node.labelSpan.className = "label";
+
+ createIndent(o,node.itemDiv,node,0);
+ node.itemDiv.appendChild(node.labelSpan);
+ node.li.appendChild(node.itemDiv);
+
+ var a = document.createElement("a");
+ node.labelSpan.appendChild(a);
+ node.label = document.createTextNode(text);
+ node.expanded = false;
+ a.appendChild(node.label);
+ if (link) {
+ var url;
+ if (link.substring(0,1)=='^') {
+ url = link.substring(1);
+ link = url;
+ } else {
+ url = node.relpath+link;
+ }
+ a.className = stripPath(link.replace('#',':'));
+ if (link.indexOf('#')!=-1) {
+ var aname = '#'+link.split('#')[1];
+ var srcPage = stripPath($(location).attr('pathname'));
+ var targetPage = stripPath(link.split('#')[0]);
+ a.href = srcPage!=targetPage ? url : "javascript:void(0)";
+ a.onclick = function(){
+ storeLink(link);
+ if (!$(a).parent().parent().hasClass('selected'))
+ {
+ $('.item').removeClass('selected');
+ $('.item').removeAttr('id');
+ $(a).parent().parent().addClass('selected');
+ $(a).parent().parent().attr('id','selected');
+ }
+ var anchor = $(aname);
+ gotoAnchor(anchor,aname,true);
+ };
+ } else {
+ a.href = url;
+ a.onclick = function() { storeLink(link); }
+ }
+ } else {
+ if (childrenData != null)
+ {
+ a.className = "nolink";
+ a.href = "javascript:void(0)";
+ a.onclick = node.expandToggle.onclick;
+ }
+ }
+
+ node.childrenUL = null;
+ node.getChildrenUL = function() {
+ if (!node.childrenUL) {
+ node.childrenUL = document.createElement("ul");
+ node.childrenUL.className = "children_ul";
+ node.childrenUL.style.display = "none";
+ node.li.appendChild(node.childrenUL);
+ }
+ return node.childrenUL;
+ };
+
+ return node;
+}
+
+function showRoot()
+{
+ var headerHeight = $("#top").height();
+ var footerHeight = $("#nav-path").height();
+ var windowHeight = $(window).height() - headerHeight - footerHeight;
+ (function (){ // retry until we can scroll to the selected item
+ try {
+ var navtree=$('#nav-tree');
+ navtree.scrollTo('#selected',0,{offset:-windowHeight/2});
+ } catch (err) {
+ setTimeout(arguments.callee, 0);
+ }
+ })();
+}
+
+function expandNode(o, node, imm, showRoot)
+{
+ if (node.childrenData && !node.expanded) {
+ if (typeof(node.childrenData)==='string') {
+ var varName = node.childrenData;
+ getScript(node.relpath+varName,function(){
+ node.childrenData = getData(varName);
+ expandNode(o, node, imm, showRoot);
+ }, showRoot);
+ } else {
+ if (!node.childrenVisited) {
+ getNode(o, node);
+ } if (imm || ($.browser.msie && $.browser.version>8)) {
+ // somehow slideDown jumps to the start of tree for IE9 :-(
+ $(node.getChildrenUL()).show();
+ } else {
+ $(node.getChildrenUL()).slideDown("fast");
+ }
+ if (node.isLast) {
+ node.plus_img.src = node.relpath+"ftv2mlastnode.png";
+ } else {
+ node.plus_img.src = node.relpath+"ftv2mnode.png";
+ }
+ node.expanded = true;
+ }
+ }
+}
+
+function glowEffect(n,duration)
+{
+ n.addClass('glow').delay(duration).queue(function(next){
+ $(this).removeClass('glow');next();
+ });
+}
+
+function highlightAnchor()
+{
+ var aname = $(location).attr('hash');
+ var anchor = $(aname);
+ if (anchor.parent().attr('class')=='memItemLeft'){
+ var rows = $('.memberdecls tr[class$="'+
+ window.location.hash.substring(1)+'"]');
+ glowEffect(rows.children(),300); // member without details
+ } else if (anchor.parents().slice(2).prop('tagName')=='TR') {
+ glowEffect(anchor.parents('div.memitem'),1000); // enum value
+ } else if (anchor.parent().attr('class')=='fieldtype'){
+ glowEffect(anchor.parent().parent(),1000); // struct field
+ } else if (anchor.parent().is(":header")) {
+ glowEffect(anchor.parent(),1000); // section header
+ } else {
+ glowEffect(anchor.next(),1000); // normal member
+ }
+ gotoAnchor(anchor,aname,false);
+}
+
+function selectAndHighlight(hash,n)
+{
+ var a;
+ if (hash) {
+ var link=stripPath($(location).attr('pathname'))+':'+hash.substring(1);
+ a=$('.item a[class$="'+link+'"]');
+ }
+ if (a && a.length) {
+ a.parent().parent().addClass('selected');
+ a.parent().parent().attr('id','selected');
+ highlightAnchor();
+ } else if (n) {
+ $(n.itemDiv).addClass('selected');
+ $(n.itemDiv).attr('id','selected');
+ }
+ if ($('#nav-tree-contents .item:first').hasClass('selected')) {
+ $('#nav-sync').css('top','30px');
+ } else {
+ $('#nav-sync').css('top','5px');
+ }
+ showRoot();
+}
+
+function showNode(o, node, index, hash)
+{
+ if (node && node.childrenData) {
+ if (typeof(node.childrenData)==='string') {
+ var varName = node.childrenData;
+ getScript(node.relpath+varName,function(){
+ node.childrenData = getData(varName);
+ showNode(o,node,index,hash);
+ },true);
+ } else {
+ if (!node.childrenVisited) {
+ getNode(o, node);
+ }
+ $(node.getChildrenUL()).css({'display':'block'});
+ if (node.isLast) {
+ node.plus_img.src = node.relpath+"ftv2mlastnode.png";
+ } else {
+ node.plus_img.src = node.relpath+"ftv2mnode.png";
+ }
+ node.expanded = true;
+ var n = node.children[o.breadcrumbs[index]];
+ if (index+1<o.breadcrumbs.length) {
+ showNode(o,n,index+1,hash);
+ } else {
+ if (typeof(n.childrenData)==='string') {
+ var varName = n.childrenData;
+ getScript(n.relpath+varName,function(){
+ n.childrenData = getData(varName);
+ node.expanded=false;
+ showNode(o,node,index,hash); // retry with child node expanded
+ },true);
+ } else {
+ var rootBase = stripPath(o.toroot.replace(/\..+$/, ''));
+ if (rootBase=="index" || rootBase=="pages" || rootBase=="search") {
+ expandNode(o, n, true, true);
+ }
+ selectAndHighlight(hash,n);
+ }
+ }
+ }
+ } else {
+ selectAndHighlight(hash);
+ }
+}
+
+function removeToInsertLater(element) {
+ var parentNode = element.parentNode;
+ var nextSibling = element.nextSibling;
+ parentNode.removeChild(element);
+ return function() {
+ if (nextSibling) {
+ parentNode.insertBefore(element, nextSibling);
+ } else {
+ parentNode.appendChild(element);
+ }
+ };
+}
+
+function getNode(o, po)
+{
+ var insertFunction = removeToInsertLater(po.li);
+ po.childrenVisited = true;
+ var l = po.childrenData.length-1;
+ for (var i in po.childrenData) {
+ var nodeData = po.childrenData[i];
+ po.children[i] = newNode(o, po, nodeData[0], nodeData[1], nodeData[2],
+ i==l);
+ }
+ insertFunction();
+}
+
+function gotoNode(o,subIndex,root,hash,relpath)
+{
+ var nti = navTreeSubIndices[subIndex][root+hash];
+ o.breadcrumbs = $.extend(true, [], nti ? nti : navTreeSubIndices[subIndex][root]);
+ if (!o.breadcrumbs && root!=NAVTREE[0][1]) { // fallback: show index
+ navTo(o,NAVTREE[0][1],"",relpath);
+ $('.item').removeClass('selected');
+ $('.item').removeAttr('id');
+ }
+ if (o.breadcrumbs) {
+ o.breadcrumbs.unshift(0); // add 0 for root node
+ showNode(o, o.node, 0, hash);
+ }
+}
+
+function navTo(o,root,hash,relpath)
+{
+ var link = cachedLink();
+ if (link) {
+ var parts = link.split('#');
+ root = parts[0];
+ if (parts.length>1) hash = '#'+parts[1];
+ else hash='';
+ }
+ if (hash.match(/^#l\d+$/)) {
+ var anchor=$('a[name='+hash.substring(1)+']');
+ glowEffect(anchor.parent(),1000); // line number
+ hash=''; // strip line number anchors
+ //root=root.replace(/_source\./,'.'); // source link to doc link
+ }
+ var url=root+hash;
+ var i=-1;
+ while (NAVTREEINDEX[i+1]<=url) i++;
+ if (i==-1) { i=0; root=NAVTREE[0][1]; } // fallback: show index
+ if (navTreeSubIndices[i]) {
+ gotoNode(o,i,root,hash,relpath)
+ } else {
+ getScript(relpath+'navtreeindex'+i,function(){
+ navTreeSubIndices[i] = eval('NAVTREEINDEX'+i);
+ if (navTreeSubIndices[i]) {
+ gotoNode(o,i,root,hash,relpath);
+ }
+ },true);
+ }
+}
+
+function showSyncOff(n,relpath)
+{
+ n.html('<img src="'+relpath+'sync_off.png" title="'+SYNCOFFMSG+'"/>');
+}
+
+function showSyncOn(n,relpath)
+{
+ n.html('<img src="'+relpath+'sync_on.png" title="'+SYNCONMSG+'"/>');
+}
+
+function toggleSyncButton(relpath)
+{
+ var navSync = $('#nav-sync');
+ if (navSync.hasClass('sync')) {
+ navSync.removeClass('sync');
+ showSyncOff(navSync,relpath);
+ storeLink(stripPath2($(location).attr('pathname'))+$(location).attr('hash'));
+ } else {
+ navSync.addClass('sync');
+ showSyncOn(navSync,relpath);
+ deleteLink();
+ }
+}
+
+function initNavTree(toroot,relpath)
+{
+ var o = new Object();
+ o.toroot = toroot;
+ o.node = new Object();
+ o.node.li = document.getElementById("nav-tree-contents");
+ o.node.childrenData = NAVTREE;
+ o.node.children = new Array();
+ o.node.childrenUL = document.createElement("ul");
+ o.node.getChildrenUL = function() { return o.node.childrenUL; };
+ o.node.li.appendChild(o.node.childrenUL);
+ o.node.depth = 0;
+ o.node.relpath = relpath;
+ o.node.expanded = false;
+ o.node.isLast = true;
+ o.node.plus_img = document.createElement("img");
+ o.node.plus_img.src = relpath+"ftv2pnode.png";
+ o.node.plus_img.width = 16;
+ o.node.plus_img.height = 22;
+
+ if (localStorageSupported()) {
+ var navSync = $('#nav-sync');
+ if (cachedLink()) {
+ showSyncOff(navSync,relpath);
+ navSync.removeClass('sync');
+ } else {
+ showSyncOn(navSync,relpath);
+ }
+ navSync.click(function(){ toggleSyncButton(relpath); });
+ }
+
+ $(window).load(function(){
+ navTo(o,toroot,window.location.hash,relpath);
+ showRoot();
+ });
+
+ $(window).bind('hashchange', function(){
+ if (window.location.hash && window.location.hash.length>1){
+ var a;
+ if ($(location).attr('hash')){
+ var clslink=stripPath($(location).attr('pathname'))+':'+
+ $(location).attr('hash').substring(1);
+ a=$('.item a[class$="'+clslink+'"]');
+ }
+ if (a==null || !$(a).parent().parent().hasClass('selected')){
+ $('.item').removeClass('selected');
+ $('.item').removeAttr('id');
+ }
+ var link=stripPath2($(location).attr('pathname'));
+ navTo(o,link,$(location).attr('hash'),relpath);
+ } else if (!animationInProgress) {
+ $('#doc-content').scrollTop(0);
+ $('.item').removeClass('selected');
+ $('.item').removeAttr('id');
+ navTo(o,toroot,window.location.hash,relpath);
+ }
+ })
+}
+
diff --git a/docs/doxygen/navtreeindex0.js b/docs/doxygen/navtreeindex0.js
new file mode 100644
index 0000000000000000000000000000000000000000..b5a5e9c130db2ef7d590d31c2fa62e76bb5263e2
--- /dev/null
+++ b/docs/doxygen/navtreeindex0.js
@@ -0,0 +1,253 @@
+var NAVTREEINDEX0 =
+{
+"_accumulator_8pm.html":[4,0,1,0,0,0,5],
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+"_add_together_8pm.html":[4,0,1,0,0,0,3,0,0],
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+ clearTimeout(this.keyTimeout);
+ this.keyTimeout = 0;
+ }
+
+ var e = (evt) ? evt : window.event; // for IE
+ if (e.keyCode==40 || e.keyCode==13)
+ {
+ if (e.shiftKey==1)
+ {
+ this.OnSearchSelectShow();
+ var win=this.DOMSearchSelectWindow();
+ for (i=0;i<win.childNodes.length;i++)
+ {
+ var child = win.childNodes[i]; // get span within a
+ if (child.className=='SelectItem')
+ {
+ child.focus();
+ return;
+ }
+ }
+ return;
+ }
+ else if (window.frames.MSearchResults.searchResults)
+ {
+ var elem = window.frames.MSearchResults.searchResults.NavNext(0);
+ if (elem) elem.focus();
+ }
+ }
+ else if (e.keyCode==27) // Escape out of the search field
+ {
+ this.DOMSearchField().blur();
+ this.DOMPopupSearchResultsWindow().style.display = 'none';
+ this.DOMSearchClose().style.display = 'none';
+ this.lastSearchValue = '';
+ this.Activate(false);
+ return;
+ }
+
+ // strip whitespaces
+ var searchValue = this.DOMSearchField().value.replace(/ +/g, "");
+
+ if (searchValue != this.lastSearchValue) // search value has changed
+ {
+ if (searchValue != "") // non-empty search
+ {
+ // set timer for search update
+ this.keyTimeout = setTimeout(this.name + '.Search()',
+ this.keyTimeoutLength);
+ }
+ else // empty search field
+ {
+ this.DOMPopupSearchResultsWindow().style.display = 'none';
+ this.DOMSearchClose().style.display = 'none';
+ this.lastSearchValue = '';
+ }
+ }
+ }
+
+ this.SelectItemCount = function(id)
+ {
+ var count=0;
+ var win=this.DOMSearchSelectWindow();
+ for (i=0;i<win.childNodes.length;i++)
+ {
+ var child = win.childNodes[i]; // get span within a
+ if (child.className=='SelectItem')
+ {
+ count++;
+ }
+ }
+ return count;
+ }
+
+ this.SelectItemSet = function(id)
+ {
+ var i,j=0;
+ var win=this.DOMSearchSelectWindow();
+ for (i=0;i<win.childNodes.length;i++)
+ {
+ var child = win.childNodes[i]; // get span within a
+ if (child.className=='SelectItem')
+ {
+ var node = child.firstChild;
+ if (j==id)
+ {
+ node.innerHTML='•';
+ }
+ else
+ {
+ node.innerHTML=' ';
+ }
+ j++;
+ }
+ }
+ }
+
+ // Called when an search filter selection is made.
+ // set item with index id as the active item
+ this.OnSelectItem = function(id)
+ {
+ this.searchIndex = id;
+ this.SelectItemSet(id);
+ var searchValue = this.DOMSearchField().value.replace(/ +/g, "");
+ if (searchValue!="" && this.searchActive) // something was found -> do a search
+ {
+ this.Search();
+ }
+ }
+
+ this.OnSearchSelectKey = function(evt)
+ {
+ var e = (evt) ? evt : window.event; // for IE
+ if (e.keyCode==40 && this.searchIndex<this.SelectItemCount()) // Down
+ {
+ this.searchIndex++;
+ this.OnSelectItem(this.searchIndex);
+ }
+ else if (e.keyCode==38 && this.searchIndex>0) // Up
+ {
+ this.searchIndex--;
+ this.OnSelectItem(this.searchIndex);
+ }
+ else if (e.keyCode==13 || e.keyCode==27)
+ {
+ this.OnSelectItem(this.searchIndex);
+ this.CloseSelectionWindow();
+ this.DOMSearchField().focus();
+ }
+ return false;
+ }
+
+ // --------- Actions
+
+ // Closes the results window.
+ this.CloseResultsWindow = function()
+ {
+ this.DOMPopupSearchResultsWindow().style.display = 'none';
+ this.DOMSearchClose().style.display = 'none';
+ this.Activate(false);
+ }
+
+ this.CloseSelectionWindow = function()
+ {
+ this.DOMSearchSelectWindow().style.display = 'none';
+ }
+
+ // Performs a search.
+ this.Search = function()
+ {
+ this.keyTimeout = 0;
+
+ // strip leading whitespace
+ var searchValue = this.DOMSearchField().value.replace(/^ +/, "");
+
+ var code = searchValue.toLowerCase().charCodeAt(0);
+ var idxChar = searchValue.substr(0, 1).toLowerCase();
+ if ( 0xD800 <= code && code <= 0xDBFF && searchValue > 1) // surrogate pair
+ {
+ idxChar = searchValue.substr(0, 2);
+ }
+
+ var resultsPage;
+ var resultsPageWithSearch;
+ var hasResultsPage;
+
+ var idx = indexSectionsWithContent[this.searchIndex].indexOf(idxChar);
+ if (idx!=-1)
+ {
+ var hexCode=idx.toString(16);
+ resultsPage = this.resultsPath + '/' + indexSectionNames[this.searchIndex] + '_' + hexCode + '.html';
+ resultsPageWithSearch = resultsPage+'?'+escape(searchValue);
+ hasResultsPage = true;
+ }
+ else // nothing available for this search term
+ {
+ resultsPage = this.resultsPath + '/nomatches.html';
+ resultsPageWithSearch = resultsPage;
+ hasResultsPage = false;
+ }
+
+ window.frames.MSearchResults.location = resultsPageWithSearch;
+ var domPopupSearchResultsWindow = this.DOMPopupSearchResultsWindow();
+
+ if (domPopupSearchResultsWindow.style.display!='block')
+ {
+ var domSearchBox = this.DOMSearchBox();
+ this.DOMSearchClose().style.display = 'inline';
+ if (this.insideFrame)
+ {
+ var domPopupSearchResults = this.DOMPopupSearchResults();
+ domPopupSearchResultsWindow.style.position = 'relative';
+ domPopupSearchResultsWindow.style.display = 'block';
+ var width = document.body.clientWidth - 8; // the -8 is for IE :-(
+ domPopupSearchResultsWindow.style.width = width + 'px';
+ domPopupSearchResults.style.width = width + 'px';
+ }
+ else
+ {
+ var domPopupSearchResults = this.DOMPopupSearchResults();
+ var left = getXPos(domSearchBox) + 150; // domSearchBox.offsetWidth;
+ var top = getYPos(domSearchBox) + 20; // domSearchBox.offsetHeight + 1;
+ domPopupSearchResultsWindow.style.display = 'block';
+ left -= domPopupSearchResults.offsetWidth;
+ domPopupSearchResultsWindow.style.top = top + 'px';
+ domPopupSearchResultsWindow.style.left = left + 'px';
+ }
+ }
+
+ this.lastSearchValue = searchValue;
+ this.lastResultsPage = resultsPage;
+ }
+
+ // -------- Activation Functions
+
+ // Activates or deactivates the search panel, resetting things to
+ // their default values if necessary.
+ this.Activate = function(isActive)
+ {
+ if (isActive || // open it
+ this.DOMPopupSearchResultsWindow().style.display == 'block'
+ )
+ {
+ this.DOMSearchBox().className = 'MSearchBoxActive';
+
+ var searchField = this.DOMSearchField();
+
+ if (searchField.value == this.searchLabel) // clear "Search" term upon entry
+ {
+ searchField.value = '';
+ this.searchActive = true;
+ }
+ }
+ else if (!isActive) // directly remove the panel
+ {
+ this.DOMSearchBox().className = 'MSearchBoxInactive';
+ this.DOMSearchField().value = this.searchLabel;
+ this.searchActive = false;
+ this.lastSearchValue = ''
+ this.lastResultsPage = '';
+ }
+ }
+}
+
+// -----------------------------------------------------------------------
+
+// The class that handles everything on the search results page.
+function SearchResults(name)
+{
+ // The number of matches from the last run of <Search()>.
+ this.lastMatchCount = 0;
+ this.lastKey = 0;
+ this.repeatOn = false;
+
+ // Toggles the visibility of the passed element ID.
+ this.FindChildElement = function(id)
+ {
+ var parentElement = document.getElementById(id);
+ var element = parentElement.firstChild;
+
+ while (element && element!=parentElement)
+ {
+ if (element.nodeName == 'DIV' && element.className == 'SRChildren')
+ {
+ return element;
+ }
+
+ if (element.nodeName == 'DIV' && element.hasChildNodes())
+ {
+ element = element.firstChild;
+ }
+ else if (element.nextSibling)
+ {
+ element = element.nextSibling;
+ }
+ else
+ {
+ do
+ {
+ element = element.parentNode;
+ }
+ while (element && element!=parentElement && !element.nextSibling);
+
+ if (element && element!=parentElement)
+ {
+ element = element.nextSibling;
+ }
+ }
+ }
+ }
+
+ this.Toggle = function(id)
+ {
+ var element = this.FindChildElement(id);
+ if (element)
+ {
+ if (element.style.display == 'block')
+ {
+ element.style.display = 'none';
+ }
+ else
+ {
+ element.style.display = 'block';
+ }
+ }
+ }
+
+ // Searches for the passed string. If there is no parameter,
+ // it takes it from the URL query.
+ //
+ // Always returns true, since other documents may try to call it
+ // and that may or may not be possible.
+ this.Search = function(search)
+ {
+ if (!search) // get search word from URL
+ {
+ search = window.location.search;
+ search = search.substring(1); // Remove the leading '?'
+ search = unescape(search);
+ }
+
+ search = search.replace(/^ +/, ""); // strip leading spaces
+ search = search.replace(/ +$/, ""); // strip trailing spaces
+ search = search.toLowerCase();
+ search = convertToId(search);
+
+ var resultRows = document.getElementsByTagName("div");
+ var matches = 0;
+
+ var i = 0;
+ while (i < resultRows.length)
+ {
+ var row = resultRows.item(i);
+ if (row.className == "SRResult")
+ {
+ var rowMatchName = row.id.toLowerCase();
+ rowMatchName = rowMatchName.replace(/^sr\d*_/, ''); // strip 'sr123_'
+
+ if (search.length<=rowMatchName.length &&
+ rowMatchName.substr(0, search.length)==search)
+ {
+ row.style.display = 'block';
+ matches++;
+ }
+ else
+ {
+ row.style.display = 'none';
+ }
+ }
+ i++;
+ }
+ document.getElementById("Searching").style.display='none';
+ if (matches == 0) // no results
+ {
+ document.getElementById("NoMatches").style.display='block';
+ }
+ else // at least one result
+ {
+ document.getElementById("NoMatches").style.display='none';
+ }
+ this.lastMatchCount = matches;
+ return true;
+ }
+
+ // return the first item with index index or higher that is visible
+ this.NavNext = function(index)
+ {
+ var focusItem;
+ while (1)
+ {
+ var focusName = 'Item'+index;
+ focusItem = document.getElementById(focusName);
+ if (focusItem && focusItem.parentNode.parentNode.style.display=='block')
+ {
+ break;
+ }
+ else if (!focusItem) // last element
+ {
+ break;
+ }
+ focusItem=null;
+ index++;
+ }
+ return focusItem;
+ }
+
+ this.NavPrev = function(index)
+ {
+ var focusItem;
+ while (1)
+ {
+ var focusName = 'Item'+index;
+ focusItem = document.getElementById(focusName);
+ if (focusItem && focusItem.parentNode.parentNode.style.display=='block')
+ {
+ break;
+ }
+ else if (!focusItem) // last element
+ {
+ break;
+ }
+ focusItem=null;
+ index--;
+ }
+ return focusItem;
+ }
+
+ this.ProcessKeys = function(e)
+ {
+ if (e.type == "keydown")
+ {
+ this.repeatOn = false;
+ this.lastKey = e.keyCode;
+ }
+ else if (e.type == "keypress")
+ {
+ if (!this.repeatOn)
+ {
+ if (this.lastKey) this.repeatOn = true;
+ return false; // ignore first keypress after keydown
+ }
+ }
+ else if (e.type == "keyup")
+ {
+ this.lastKey = 0;
+ this.repeatOn = false;
+ }
+ return this.lastKey!=0;
+ }
+
+ this.Nav = function(evt,itemIndex)
+ {
+ var e = (evt) ? evt : window.event; // for IE
+ if (e.keyCode==13) return true;
+ if (!this.ProcessKeys(e)) return false;
+
+ if (this.lastKey==38) // Up
+ {
+ var newIndex = itemIndex-1;
+ var focusItem = this.NavPrev(newIndex);
+ if (focusItem)
+ {
+ var child = this.FindChildElement(focusItem.parentNode.parentNode.id);
+ if (child && child.style.display == 'block') // children visible
+ {
+ var n=0;
+ var tmpElem;
+ while (1) // search for last child
+ {
+ tmpElem = document.getElementById('Item'+newIndex+'_c'+n);
+ if (tmpElem)
+ {
+ focusItem = tmpElem;
+ }
+ else // found it!
+ {
+ break;
+ }
+ n++;
+ }
+ }
+ }
+ if (focusItem)
+ {
+ focusItem.focus();
+ }
+ else // return focus to search field
+ {
+ parent.document.getElementById("MSearchField").focus();
+ }
+ }
+ else if (this.lastKey==40) // Down
+ {
+ var newIndex = itemIndex+1;
+ var focusItem;
+ var item = document.getElementById('Item'+itemIndex);
+ var elem = this.FindChildElement(item.parentNode.parentNode.id);
+ if (elem && elem.style.display == 'block') // children visible
+ {
+ focusItem = document.getElementById('Item'+itemIndex+'_c0');
+ }
+ if (!focusItem) focusItem = this.NavNext(newIndex);
+ if (focusItem) focusItem.focus();
+ }
+ else if (this.lastKey==39) // Right
+ {
+ var item = document.getElementById('Item'+itemIndex);
+ var elem = this.FindChildElement(item.parentNode.parentNode.id);
+ if (elem) elem.style.display = 'block';
+ }
+ else if (this.lastKey==37) // Left
+ {
+ var item = document.getElementById('Item'+itemIndex);
+ var elem = this.FindChildElement(item.parentNode.parentNode.id);
+ if (elem) elem.style.display = 'none';
+ }
+ else if (this.lastKey==27) // Escape
+ {
+ parent.searchBox.CloseResultsWindow();
+ parent.document.getElementById("MSearchField").focus();
+ }
+ else if (this.lastKey==13) // Enter
+ {
+ return true;
+ }
+ return false;
+ }
+
+ this.NavChild = function(evt,itemIndex,childIndex)
+ {
+ var e = (evt) ? evt : window.event; // for IE
+ if (e.keyCode==13) return true;
+ if (!this.ProcessKeys(e)) return false;
+
+ if (this.lastKey==38) // Up
+ {
+ if (childIndex>0)
+ {
+ var newIndex = childIndex-1;
+ document.getElementById('Item'+itemIndex+'_c'+newIndex).focus();
+ }
+ else // already at first child, jump to parent
+ {
+ document.getElementById('Item'+itemIndex).focus();
+ }
+ }
+ else if (this.lastKey==40) // Down
+ {
+ var newIndex = childIndex+1;
+ var elem = document.getElementById('Item'+itemIndex+'_c'+newIndex);
+ if (!elem) // last child, jump to parent next parent
+ {
+ elem = this.NavNext(itemIndex+1);
+ }
+ if (elem)
+ {
+ elem.focus();
+ }
+ }
+ else if (this.lastKey==27) // Escape
+ {
+ parent.searchBox.CloseResultsWindow();
+ parent.document.getElementById("MSearchField").focus();
+ }
+ else if (this.lastKey==13) // Enter
+ {
+ return true;
+ }
+ return false;
+ }
+}
+
+function setKeyActions(elem,action)
+{
+ elem.setAttribute('onkeydown',action);
+ elem.setAttribute('onkeypress',action);
+ elem.setAttribute('onkeyup',action);
+}
+
+function setClassAttr(elem,attr)
+{
+ elem.setAttribute('class',attr);
+ elem.setAttribute('className',attr);
+}
+
+function createResults()
+{
+ var results = document.getElementById("SRResults");
+ for (var e=0; e<searchData.length; e++)
+ {
+ var id = searchData[e][0];
+ var srResult = document.createElement('div');
+ srResult.setAttribute('id','SR_'+id);
+ setClassAttr(srResult,'SRResult');
+ var srEntry = document.createElement('div');
+ setClassAttr(srEntry,'SREntry');
+ var srLink = document.createElement('a');
+ srLink.setAttribute('id','Item'+e);
+ setKeyActions(srLink,'return searchResults.Nav(event,'+e+')');
+ setClassAttr(srLink,'SRSymbol');
+ srLink.innerHTML = searchData[e][1][0];
+ srEntry.appendChild(srLink);
+ if (searchData[e][1].length==2) // single result
+ {
+ srLink.setAttribute('href',searchData[e][1][1][0]);
+ if (searchData[e][1][1][1])
+ {
+ srLink.setAttribute('target','_parent');
+ }
+ var srScope = document.createElement('span');
+ setClassAttr(srScope,'SRScope');
+ srScope.innerHTML = searchData[e][1][1][2];
+ srEntry.appendChild(srScope);
+ }
+ else // multiple results
+ {
+ srLink.setAttribute('href','javascript:searchResults.Toggle("SR_'+id+'")');
+ var srChildren = document.createElement('div');
+ setClassAttr(srChildren,'SRChildren');
+ for (var c=0; c<searchData[e][1].length-1; c++)
+ {
+ var srChild = document.createElement('a');
+ srChild.setAttribute('id','Item'+e+'_c'+c);
+ setKeyActions(srChild,'return searchResults.NavChild(event,'+e+','+c+')');
+ setClassAttr(srChild,'SRScope');
+ srChild.setAttribute('href',searchData[e][1][c+1][0]);
+ if (searchData[e][1][c+1][1])
+ {
+ srChild.setAttribute('target','_parent');
+ }
+ srChild.innerHTML = searchData[e][1][c+1][2];
+ srChildren.appendChild(srChild);
+ }
+ srEntry.appendChild(srChildren);
+ }
+ srResult.appendChild(srEntry);
+ results.appendChild(srResult);
+ }
+}
+
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@@ -0,0 +1,187 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: scripts/seed_pipeline.pl File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="jquery.js"></script>
+<script type="text/javascript" src="dynsections.js"></script>
+<link href="navtree.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="resize.js"></script>
+<script type="text/javascript" src="navtree.js"></script>
+<script type="text/javascript">
+ $(document).ready(initResizable);
+ $(window).load(resizeHeight);
+</script>
+<link href="search/search.css" rel="stylesheet" type="text/css"/>
+<script type="text/javascript" src="search/search.js"></script>
+<script type="text/javascript">
+ $(document).ready(function() { searchBox.OnSelectItem(0); });
+</script>
+<link href="doxygen.css" rel="stylesheet" type="text/css" />
+</head>
+<body>
+<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+<div id="titlearea">
+<table cellspacing="0" cellpadding="0">
+ <tbody>
+ <tr style="height: 56px;">
+ <td style="padding-left: 0.5em;">
+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
+ </div>
+ </td>
+ </tr>
+ </tbody>
+</table>
+</div>
+<!-- end header part -->
+<!-- Generated by Doxygen 1.8.6 -->
+<script type="text/javascript">
+var searchBox = new SearchBox("searchBox", "search",false,'Search');
+</script>
+ <div id="navrow1" class="tabs">
+ <ul class="tablist">
+ <li><a href="index.html"><span>Main Page</span></a></li>
+ <li><a href="pages.html"><span>Related Pages</span></a></li>
+ <li><a href="namespaces.html"><span>Namespaces</span></a></li>
+ <li><a href="annotated.html"><span>Classes</span></a></li>
+ <li class="current"><a href="files.html"><span>Files</span></a></li>
+ <li>
+ <div id="MSearchBox" class="MSearchBoxInactive">
+ <span class="left">
+ <img id="MSearchSelect" src="search/mag_sel.png"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ alt=""/>
+ <input type="text" id="MSearchField" value="Search" accesskey="S"
+ onfocus="searchBox.OnSearchFieldFocus(true)"
+ onblur="searchBox.OnSearchFieldFocus(false)"
+ onkeyup="searchBox.OnSearchFieldChange(event)"/>
+ </span><span class="right">
+ <a id="MSearchClose" href="javascript:searchBox.CloseResultsWindow()"><img id="MSearchCloseImg" border="0" src="search/close.png" alt=""/></a>
+ </span>
+ </div>
+ </li>
+ </ul>
+ </div>
+ <div id="navrow2" class="tabs2">
+ <ul class="tablist">
+ <li><a href="files.html"><span>File List</span></a></li>
+ <li><a href="globals.html"><span>File Members</span></a></li>
+ </ul>
+ </div>
+</div><!-- top -->
+<div id="side-nav" class="ui-resizable side-nav-resizable">
+ <div id="nav-tree">
+ <div id="nav-tree-contents">
+ <div id="nav-sync" class="sync"></div>
+ </div>
+ </div>
+ <div id="splitbar" style="-moz-user-select:none;"
+ class="ui-resizable-handle">
+ </div>
+</div>
+<script type="text/javascript">
+$(document).ready(function(){initNavTree('seed__pipeline_8pl.html','');});
+</script>
+<div id="doc-content">
+<!-- window showing the filter options -->
+<div id="MSearchSelectWindow"
+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
+ onkeydown="return searchBox.OnSearchSelectKey(event)">
+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
+
+<!-- iframe showing the search results (closed by default) -->
+<div id="MSearchResultsWindow">
+<iframe src="javascript:void(0)" frameborder="0"
+ name="MSearchResults" id="MSearchResults">
+</iframe>
+</div>
+
+<div class="header">
+ <div class="summary">
+<a href="#func-members">Functions</a> </div>
+ <div class="headertitle">
+<div class="title">seed_pipeline.pl File Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+<table class="memberdecls">
+<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
+Functions</h2></td></tr>
+<tr class="memitem:ae56eff1c83733ae5dcc4d7f7d6d25ff8"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="seed__pipeline_8pl.html#ae56eff1c83733ae5dcc4d7f7d6d25ff8">show_seedable_analyses</a> ()</td></tr>
+<tr class="separator:ae56eff1c83733ae5dcc4d7f7d6d25ff8"><td class="memSeparator" colspan="2"> </td></tr>
+<tr class="memitem:a3ce8b237b3bdb2817dac6f769e5768c2"><td class="memItemLeft" align="right" valign="top">public </td><td class="memItemRight" valign="bottom"><a class="el" href="seed__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">main</a> ()</td></tr>
+<tr class="separator:a3ce8b237b3bdb2817dac6f769e5768c2"><td class="memSeparator" colspan="2"> </td></tr>
+</table>
+<h2 class="groupheader">Function Documentation</h2>
+<a class="anchor" id="a3ce8b237b3bdb2817dac6f769e5768c2"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public main </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+
+</div>
+</div>
+<a class="anchor" id="ae56eff1c83733ae5dcc4d7f7d6d25ff8"></a>
+<div class="memitem">
+<div class="memproto">
+ <table class="memname">
+ <tr>
+ <td class="memname">public show_seedable_analyses </td>
+ <td>(</td>
+ <td class="paramname"></td><td>)</td>
+ <td></td>
+ </tr>
+ </table>
+</div><div class="memdoc">
+<p>Undocumented method</p>
+<div id="codesection-show_seedable_analyses" class="dynheader closed" style="cursor:pointer;" onclick="return toggleVisibility(this)">
+ <img id='codesection-show_seedable_analyses-trigger' src='closed.png' style='display:inline'><b>Code:</b>
+</div>
+<div id='codesection-show_seedable_analyses-summary' class='dyncontent' style='display:block;font-size:small;'>click to view</div>
+<div id='codesection-show_seedable_analyses-content' class='dyncontent' style='display: none;'>
+ <div class="fragment"><div class="line">sub <a class="code" href="seed__pipeline_8pl.html#ae56eff1c83733ae5dcc4d7f7d6d25ff8">show_seedable_analyses</a> {</div>
+<div class="line"> my ($hive_dba) = @_;</div>
+<div class="line"></div>
+<div class="line"> my $analyses = $hive_dba->get_AnalysisAdaptor->fetch_all();</div>
+<div class="line"> my $incoming = $hive_dba->get_DataflowRuleAdaptor->fetch_HASHED_FROM_to_analysis_url_TO_dataflow_rule_id();</div>
+<div class="line"> my $job_adaptor = $hive_dba->get_AnalysisJobAdaptor;</div>
+<div class="line"></div>
+<div class="line"> print <span class="stringliteral">"\nYou haven't specified neither -logic_name nor -analysis_id of the analysis being seeded.\n"</span>;</div>
+<div class="line"> print <span class="stringliteral">"\nSeedable analyses without incoming dataflow:\n"</span>;</div>
+<div class="line"> <span class="keywordflow">foreach</span> my $analysis (@$analyses) {</div>
+<div class="line"> my $logic_name = $analysis->logic_name;</div>
+<div class="line"> unless($incoming->{$logic_name}) {</div>
+<div class="line"> my $analysis_id = $analysis->dbID;</div>
+<div class="line"> my ($example_job) = @{ $job_adaptor->fetch_some_by_analysis_id_limit( $analysis_id, 1 ) };</div>
+<div class="line"> print <span class="stringliteral">"\t$logic_name ($analysis_id)\t\t"</span>.($example_job ? <span class="stringliteral">"Example input_id: '"</span>.$example_job->input_id.<span class="stringliteral">"'"</span> : <span class="stringliteral">"[not populated yet]"</span>).<span class="stringliteral">"\n"</span>;</div>
+<div class="line"> }</div>
+<div class="line"> }</div>
+<div class="line">}</div>
+</div><!-- fragment --> </div>
+</div>
+</div>
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+ <ul>
+ <li class="navelem"><a class="el" href="dir_5fc43faac24a7b81dcfb81b231064839.html">scripts</a></li><li class="navelem"><a class="el" href="seed__pipeline_8pl.html">seed_pipeline.pl</a></li>
+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
+ </ul>
+</div>
+</body>
+</html>
diff --git a/docs/doxygen/seed__pipeline_8pl.js b/docs/doxygen/seed__pipeline_8pl.js
new file mode 100644
index 0000000000000000000000000000000000000000..8be5bc5a7098607b56e9283c73a03b9a81798b97
--- /dev/null
+++ b/docs/doxygen/seed__pipeline_8pl.js
@@ -0,0 +1,5 @@
+var seed__pipeline_8pl =
+[
+ [ "main", "seed__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2", null ],
+ [ "show_seedable_analyses", "seed__pipeline_8pl.html#ae56eff1c83733ae5dcc4d7f7d6d25ff8", null ]
+];
\ No newline at end of file
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+<meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen 1.8.6"/>
+<title>ensembl-hive: scripts/standaloneJob.pl File Reference</title>
+<link href="tabs.css" rel="stylesheet" type="text/css"/>
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+ <div id="projectname">ensembl-hive
+  <span id="projectnumber">1.9</span>
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+ <ul class="tablist">
+ <li><a href="files.html"><span>File List</span></a></li>
+ <li><a href="globals.html"><span>File Members</span></a></li>
+ </ul>
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+ onmouseover="return searchBox.OnSearchSelectShow()"
+ onmouseout="return searchBox.OnSearchSelectHide()"
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+<a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(0)"><span class="SelectionMark"> </span>All</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(1)"><span class="SelectionMark"> </span>Classes</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(2)"><span class="SelectionMark"> </span>Namespaces</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(3)"><span class="SelectionMark"> </span>Files</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(4)"><span class="SelectionMark"> </span>Functions</a><a class="SelectItem" href="javascript:void(0)" onclick="searchBox.OnSelectItem(5)"><span class="SelectionMark"> </span>Pages</a></div>
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+ name="MSearchResults" id="MSearchResults">
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+ <div class="headertitle">
+<div class="title">standaloneJob.pl File Reference</div> </div>
+</div><!--header-->
+<div class="contents">
+</div><!-- contents -->
+</div><!-- doc-content -->
+<!-- start footer part -->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
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+ <li class="footer">Generated by
+ <a href="http://www.doxygen.org/index.html">
+ <img class="footer" src="doxygen.png" alt="doxygen"/></a> 1.8.6 </li>
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diff --git a/docs/index.html b/docs/index.html
index fa737714cdfb4d0de9211ec74f5911ed3634212c..0191982ccc9f16de7dc4f5376cf99bb39caf349b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -17,6 +17,7 @@ The name "Hive" comes from the way pipelines are processed by a swarm
<li>Introduction to eHive: <a href="presentations/HiveWorkshop_Sept2013/">Sept. 2013 workshop</a> (parts <a href="presentations/HiveWorkshop_Sept2013/Slides_part1.pdf">1</a>, <a href="presentations/HiveWorkshop_Sept2013/Slides_part2.pdf">2</a> and <a href="presentations/HiveWorkshop_Sept2013/Slides_part3.pdf">3</a> in PDF)</li>
<li><a href="install.html">Dependencies, installation and setup</a></li>
<li><a href="hive_schema.html">Database schema</a></li>
+ <li><a href="doxygen/index.html">API Doxygen documentation</a></li>
<li class="tree">eHive scripts<br>
<div class="tree">
<span class="tree">│ </span><em>Execution</em><br>