Commit a50a080c authored by Leo Gordon's avatar Leo Gordon
Browse files

updated automatically-generated documentation for version/2.4

parent b21ca463

Too many changes to show.

To preserve performance only 1000 of 1000+ files are displayed.
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">2.3</span>
&#160;<span id="projectnumber">2.4</span>
</div>
</td>
</tr>
......@@ -171,6 +171,9 @@ $(document).ready(function(){initNavTree('functions_r.html','');});
<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>relative_display_name()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_cacheable.html#a292bc2bb488a6cea5c7fa044a658e4bf">Bio::EnsEMBL::Hive::Cacheable</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>
......@@ -196,16 +199,10 @@ $(document).ready(function(){initNavTree('functions_r.html','');});
: <a 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_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>
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_examples_1_1_failure_test_1_1_pipe_config_1_1_memlimit_test__conf.html#a0a51330672a79f01fcf6fd1cbf16a435">Bio::EnsEMBL::Hive::Examples::FailureTest::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_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_top_up__conf.html#ac1889f83a9261003583b02e9c68be619">Bio::EnsEMBL::Hive::PipeConfig::TopUp_conf</a>
</li>
<li>resources()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipeline.html#ad392930d051b5a3858de3b4d0ecb7e80">Bio::EnsEMBL::Hive::Pipeline</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>
......@@ -222,17 +219,18 @@ $(document).ready(function(){initNavTree('functions_r.html','');});
: <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_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_examples_1_1_failure_test_1_1_runnable_d_b_1_1_failure_test.html#a30e727f63b4ef006009479b6144cea11">Bio::EnsEMBL::Hive::Examples::FailureTest::RunnableDB::FailureTest</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_examples_1_1_g_c_1_1_runnable_d_b_1_1_calc_overall_percentage.html#a7ce8a47e9790f5d0d88964502a83fe63">Bio::EnsEMBL::Hive::Examples::GC::RunnableDB::CalcOverallPercentage</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_examples_1_1_g_c_1_1_runnable_d_b_1_1_count_a_t_g_c.html#a8cb2b3b32cb43be9810505a9ac3329cd">Bio::EnsEMBL::Hive::Examples::GC::RunnableDB::CountATGC</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_examples_1_1_long_mult_1_1_runnable_d_b_1_1_add_together.html#ae0dd335d7bb82f009c3539aa94202253">Bio::EnsEMBL::Hive::Examples::LongMult::RunnableDB::AddTogether</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_examples_1_1_long_mult_1_1_runnable_d_b_1_1_digit_factory.html#a407f83a62d4612713c8e8787ab7604d4">Bio::EnsEMBL::Hive::Examples::LongMult::RunnableDB::DigitFactory</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_examples_1_1_long_mult_1_1_runnable_d_b_1_1_part_multiply.html#a9ba521f65c80dfaa995b418cea25481a">Bio::EnsEMBL::Hive::Examples::LongMult::RunnableDB::PartMultiply</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_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_slack_notification.html#a853c71652d143a2b5534f65a7200658d">Bio::EnsEMBL::Hive::RunnableDB::SlackNotification</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>
......@@ -244,6 +242,9 @@ $(document).ready(function(){initNavTree('functions_r.html','');});
<li>run_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_hive_generic__conf.html#a6449dea7947a928206715abaab925a38">Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf</a>
</li>
<li>run_system_command()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a98a23f9308eb85ce1afcbbcad687aeb1">Bio::EnsEMBL::Hive::Process</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>
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">2.3</span>
&#160;<span id="projectnumber">2.4</span>
</div>
</td>
</tr>
......@@ -144,7 +144,7 @@ $(document).ready(function(){initNavTree('functions_s.html','');});
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a52679a6124cddf931f1882ed5b642259">Bio::EnsEMBL::Hive::Queen</a>
</li>
<li>save_collections()
: <a 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#adc3af59b42d7424b8c4b64a47e0e5c54">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_hive_pipeline.html#a74dca8d32aacd114a85074f020cfdd54">Bio::EnsEMBL::Hive::HivePipeline</a>
</li>
<li>say_with_header()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#a229788fa442d0070fdd3753b835f0e82">Bio::EnsEMBL::Hive::Process</a>
......@@ -167,6 +167,9 @@ $(document).ready(function(){initNavTree('functions_s.html','');});
<li>seconds_since_when_updated()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a51e82819489c15aa7952373c8a4ba3a8">Bio::EnsEMBL::Hive::AnalysisStats</a>
</li>
<li>semaphore_bgcolour()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_graph_viz.html#ade7c3ffeb4494d0f4919e2734748a1eb">Bio::EnsEMBL::Hive::Utils::GraphViz</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>
......@@ -176,9 +179,15 @@ $(document).ready(function(){initNavTree('functions_s.html','');});
<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>send_beekeeper_message_to_slack()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_slack.html#a0cb1ec687563e5226a6e58d19ccce82d">Bio::EnsEMBL::Hive::Utils::Slack</a>
</li>
<li>send_message()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_guest_process.html#a1ffb71047c020f5063bd9fdb7d847538">Bio::EnsEMBL::Hive::GuestProcess</a>
</li>
<li>send_message_to_slack()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_slack.html#a60195103eea8158952040db0773456e7">Bio::EnsEMBL::Hive::Utils::Slack</a>
</li>
<li>send_response()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_guest_process.html#aa45945f5e47cf67b83e69788ce788c3f">Bio::EnsEMBL::Hive::GuestProcess</a>
</li>
......@@ -195,9 +204,6 @@ $(document).ready(function(){initNavTree('functions_s.html','');});
<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>
......@@ -214,6 +220,12 @@ $(document).ready(function(){initNavTree('functions_s.html','');});
<li>specialize_worker()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_queen.html#a7d40ab66d3d6d591705a85fb791a34fe">Bio::EnsEMBL::Hive::Queen</a>
</li>
<li>species()
: <a 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#aaed4a915dbb554a8dfef9b9b54d446ba">Bio::EnsEMBL::Hive::DBSQL::DBAdaptor</a>
</li>
<li>split_for_bash()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#a436607946c20c76c08db79c35a3f7d93">Bio::EnsEMBL::Hive::Utils</a>
</li>
<li>sql()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_statement_handle.html#a2205b03c134fd7113a848ecff1165df5">Bio::EnsEMBL::Hive::DBSQL::StatementHandle</a>
</li>
......@@ -228,13 +240,15 @@ $(document).ready(function(){initNavTree('functions_s.html','');});
: <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.html#a748d037f4333b04d0c7f22bd418ada65">Bio::EnsEMBL::Hive::Analysis</a>
, <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>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a61ff24dd90b7e9b8afbbc6b19c6fbbed">Bio::EnsEMBL::Hive::Meadow</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>
......@@ -247,7 +261,6 @@ $(document).ready(function(){initNavTree('functions_s.html','');});
</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>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipeline.html#a751246601e079a764fe4b1f9c27846ff">Bio::EnsEMBL::Hive::Pipeline</a>
</li>
<li>store_hive_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#a33d1673af4663f17d99a19f838f02863">Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor</a>
......@@ -276,15 +289,13 @@ $(document).ready(function(){initNavTree('functions_s.html','');});
<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>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>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meadow.html#a52f236f5c57edb6ba8789d0ac593bf7a">Bio::EnsEMBL::Hive::Meadow</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>
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">2.3</span>
&#160;<span id="projectnumber">2.4</span>
</div>
</td>
</tr>
......@@ -149,20 +149,23 @@ $(document).ready(function(){initNavTree('functions_t.html','');});
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils.html#af71b51b03c60163952912de68e5eabf6">Bio::EnsEMBL::Hive::Utils</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>
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_target.html#a7ec23078eef60898a556d456a0d969aa">Bio::EnsEMBL::Hive::DataflowTarget</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>
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_target.html#a0d7b1614bc76bdee4ef38625b1199499">Bio::EnsEMBL::Hive::DataflowTarget</a>
</li>
<li>to_cmd()
: <a 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#ac340d3f67966c10819810ee5c8900e97">Bio::EnsEMBL::Hive::DBSQL::DBConnection</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_accumulator.html#a007c3da4f94bc7790734ed394b8a943c">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#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_dataflow_target.html#a6344470b14ec34399dcd3764f5c1daae">Bio::EnsEMBL::Hive::DataflowTarget</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#ad114ad8d8fa20f9404b58d81e2cb5c01">Bio::EnsEMBL::Hive::NakedTable</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>
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">2.3</span>
&#160;<span id="projectnumber">2.4</span>
</div>
</td>
</tr>
......@@ -141,24 +141,32 @@ $(document).ready(function(){initNavTree('functions_u.html','');});
<h3><a class="anchor" id="index_u"></a>- u -</h3><ul>
<li>unikey()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6bf0a011415c5ee82d30203dbad49be8">Bio::EnsEMBL::Hive::Analysis</a>
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator.html#a208a1a838d0d34828360caa57c4c0101">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#a6bf0a011415c5ee82d30203dbad49be8">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#a50f711438956e86414ca8a298215b72e">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis_stats.html#a982bd322e03a2a1146189c002ff6b046">Bio::EnsEMBL::Hive::AnalysisStats</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_cacheable.html#a2faa60df1b75b8c05e08975146e35412">Bio::EnsEMBL::Hive::Cacheable</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a586e5b260ddde283a976c34889e6534d">Bio::EnsEMBL::Hive::DataflowRule</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_target.html#a5318e1c2471d7440962f4228beb60d10">Bio::EnsEMBL::Hive::DataflowTarget</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_meta_parameters.html#a197a843099d7e5a32b267cdc69910f69">Bio::EnsEMBL::Hive::MetaParameters</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_naked_table.html#a088ab8dabc2c619457198a118544f260">Bio::EnsEMBL::Hive::NakedTable</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipeline_wide_parameters.html#a196b5b073b77d63e3e0b5ca76e42f14a">Bio::EnsEMBL::Hive::PipelineWideParameters</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_resource_class.html#aa14b80fd20e3958366f84bc8232d53de">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#a8fd8ce4c55fb4ef335aec8de2e2f5992">Bio::EnsEMBL::Hive::ResourceDescription</a>
</li>
<li>unitargets()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_dataflow_rule.html#a279f017ec8dbb148a38b577acd0c69af">Bio::EnsEMBL::Hive::DataflowRule</a>
</li>
<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_stats_and_monitor()
: <a 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#a90ac3e14a808eb949674ca989aa7a31c">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
</li>
<li>update_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_stats_adaptor.html#ac0868a1d8302c76a87eb04f1975b89c7">Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor</a>
</li>
......@@ -167,10 +175,6 @@ $(document).ready(function(){initNavTree('functions_u.html','');});
, <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>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_pipeline.html#a74bc6ec1c16af731b4c7f2b8d4a5d63c">Bio::EnsEMBL::Hive::Pipeline</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>
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">2.3</span>
&#160;<span id="projectnumber">2.4</span>
</div>
</td>
</tr>
......@@ -149,6 +149,9 @@ $(document).ready(function(){initNavTree('functions_w.html','');});
<li>warning()
: <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>WHEN()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_utils_1_1_p_c_l.html#a2070f0d353a4ce7a8cc7aeec02a1ebfd">Bio::EnsEMBL::Hive::Utils::PCL</a>
</li>
<li>when_born()
: <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_worker.html#a17e19566a821d29eb6e75db8ed7c00c1">Bio::EnsEMBL::Hive::Worker</a>
</li>
......@@ -199,14 +202,16 @@ $(document).ready(function(){initNavTree('functions_w.html','');});
, <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_examples_1_1_failure_test_1_1_runnable_d_b_1_1_failure_test.html#a97cbf5cfcd8cec4ec5a3e9948ab227b3">Bio::EnsEMBL::Hive::Examples::FailureTest::RunnableDB::FailureTest</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_examples_1_1_g_c_1_1_runnable_d_b_1_1_calc_overall_percentage.html#a27a6dc232da23d607ca46512efd06dd3">Bio::EnsEMBL::Hive::Examples::GC::RunnableDB::CalcOverallPercentage</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_examples_1_1_g_c_1_1_runnable_d_b_1_1_count_a_t_g_c.html#a4f77b2359841fa95107ece0bf7cd30ed">Bio::EnsEMBL::Hive::Examples::GC::RunnableDB::CountATGC</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_examples_1_1_long_mult_1_1_runnable_d_b_1_1_add_together.html#afc80be1b7f8551e12ff4ef9331b1a373">Bio::EnsEMBL::Hive::Examples::LongMult::RunnableDB::AddTogether</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_examples_1_1_long_mult_1_1_runnable_d_b_1_1_digit_factory.html#ac660b08ddfad486c04aed7965926d9aa">Bio::EnsEMBL::Hive::Examples::LongMult::RunnableDB::DigitFactory</a>
, <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_examples_1_1_long_mult_1_1_runnable_d_b_1_1_part_multiply.html#a815ca84af6066471e1d065a1eba17c09">Bio::EnsEMBL::Hive::Examples::LongMult::RunnableDB::PartMultiply</a>
, <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>
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">2.3</span>
&#160;<span id="projectnumber">2.4</span>
</div>
</td>
</tr>
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">2.3</span>
&#160;<span id="projectnumber">2.4</span>
</div>
</td>
</tr>
......@@ -148,7 +148,7 @@ Functions</h2></td></tr>
<div class="line"> <span class="keywordflow">foreach</span> my $row (@$data_timings) {</div>
<div class="line"> my $y = sum(map {$row-&gt;{$_} || 0} @$key_ids_to_sum) || $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> push @ydata, $y &lt; 0.05 ? $pseudo_zero_value : $y;</div>
<div class="line"><span class="preprocessor"></span> push @ydata, $y &lt; $rounding_error_threshold ? $pseudo_zero_value : $y;</div>
<div class="line"> }</div>
<div class="line"> my $dataset = Chart::Gnuplot::DataSet-&gt;new(</div>
<div class="line"> xdata =&gt; $xdata,</div>
......@@ -171,7 +171,7 @@ Functions</h2></td></tr>
<div class="line"> <span class="keywordflow">foreach</span> my $i (@$analysis_ids_pattern) {</div>
<div class="line"> $y += ($lt-&gt;{$i} || 0) - ($dt-&gt;{$i} || 0);</div>
<div class="line"> }</div>
<div class="line"> $ydatal[$j-1] = $y &lt; 0.05 ? $pseudo_zero_value : $y;</div>
<div class="line"> $ydatal[$j-1] = $y &lt; $rounding_error_threshold ? $pseudo_zero_value : $y;</div>
<div class="line"> }</div>
<div class="line"> $dataset = Chart::Gnuplot::DataSet-&gt;new(</div>
<div class="line"> xdata =&gt; $xdata,</div>
......@@ -311,25 +311,29 @@ Functions</h2></td></tr>
<div class="line"> last <span class="keywordflow">if</span> $end_date and ($event_date gt $end_date);</div>
<div class="line"> next unless exists $events-&gt;{$event_date};</div>
<div class="line"></div>
<div class="line"> <span class="keywordflow">if</span> ((scalar(@data_timings) == 0) and $start_date and ($event_date gt $start_date)) {</div>
<div class="line"> push @data_timings, [$start_date, { %hash_curr_workers }];</div>
<div class="line"> %tot_area = %hash_curr_workers;</div>
<div class="line"> }</div>
<div class="line"></div>
<div class="line"> my $topup_hash = $events-&gt;{$event_date};</div>
<div class="line"> <span class="keywordflow">foreach</span> my $key_id (keys %$topup_hash) {</div>
<div class="line"> $hash_curr_workers{$key_id} += $topup_hash-&gt;{$key_id};</div>
<div class="line"> $num_curr_workers += $topup_hash-&gt;{$key_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">&quot;!=$num_curr_workers&quot;</span> <span class="keywordflow">if</span> abs(sum(values %hash_curr_workers) - $num_curr_workers) &gt; 0.05;</div>
<div class="line"><span class="preprocessor"></span> die sum(values %hash_curr_workers).<span class="stringliteral">&quot;!=$num_curr_workers&quot;</span> <span class="keywordflow">if</span> abs(sum(values %hash_curr_workers) - $num_curr_workers) &gt; $rounding_error_threshold;</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_area{$_} += $hash_interval{$_}} keys %hash_interval;</div>
<div class="line"><span class="preprocessor"></span> map {$tot_area{$_} += $hash_curr_workers{$_}} keys %hash_curr_workers;</div>
<div class="line"></div>
<div class="line"> $max_workers = $num_curr_workers <span class="keywordflow">if</span> ($num_curr_workers &gt; $max_workers);</div>
<div class="line"></div>
<div class="line"><span class="preprocessor"> # We need to repeat the previous value to have an histogram shape</span></div>
<div class="line"><span class="preprocessor"></span> push @data_timings, [$event_date, { %{$data_timings[-1]-&gt;[1]} }] <span class="keywordflow">if</span> @data_timings;</div>
<div class="line"> push @data_timings, [$event_date, \%hash_interval];</div>
<div class="line"> push @data_timings, [$event_date, { %hash_curr_workers }];</div>
<div class="line"> }</div>
<div class="line"> push @data_timings, [$end_date, { %{$data_timings[-1]-&gt;[1]} }] <span class="keywordflow">if</span> @data_timings and $end_date and ($data_timings[-1]-&gt;[0] lt $end_date);</div>
<div class="line"> warn <span class="stringliteral">&quot;Last timing: &quot;</span>, Dumper $data_timings[-1] <span class="keywordflow">if</span> $verbose and @data_timings;</div>
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">2.3</span>
&#160;<span id="projectnumber">2.4</span>
</div>
</td>
</tr>
......@@ -115,9 +115,6 @@ $(document).ready(function(){initNavTree('globals.html','');});
<li>add_event()
: <a class="el" href="generate__timeline_8pl.html#af9173ecf6f7c033aa8704be6d5aa1019">generate_timeline.pl</a>
</li>
<li>clean()
: <a class="el" href="all__tests_8pl.html#a422ef8d1a748ca4ffbcd453fbf22ba8b">all_tests.pl</a>
</li>
<li>count_number_relevant_sets()
: <a class="el" href="generate__timeline_8pl.html#ac70218a8fce3a55255272b1552f00d3e">generate_timeline.pl</a>
</li>
......@@ -139,15 +136,14 @@ $(document).ready(function(){initNavTree('globals.html','');});
<li>generate_worker_cmd()
: <a class="el" href="beekeeper_8pl.html#ad7de8680eb8b39e160cee04957ccd668">beekeeper.pl</a>
</li>
<li>get_all_tests()
: <a class="el" href="all__tests_8pl.html#afec6f985b18aa1e7edb785fb6c35aada">all_tests.pl</a>
</li>
<li>main()
: <a class="el" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">beekeeper.pl</a>
, <a class="el" href="patch__2015-01-12_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">patch_2015-01-12.pl</a>
, <a class="el" href="tweak__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">tweak_pipeline.pl</a>
, <a class="el" href="standalone_job_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">standaloneJob.pl</a>
, <a class="el" href="seed__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">seed_pipeline.pl</a>
, <a class="el" href="run_worker_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">runWorker.pl</a>
, <a class="el" href="make__docs_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">make_docs.pl</a>
, <a class="el" href="load__resource__usage_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">load_resource_usage.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>
......@@ -162,8 +158,7 @@ $(document).ready(function(){initNavTree('globals.html','');});
: <a class="el" href="seed__pipeline_8pl.html#ae56eff1c83733ae5dcc4d7f7d6d25ff8">seed_pipeline.pl</a>
</li>
<li>usage()
: <a class="el" href="all__tests_8pl.html#a9449f3118943816afb79e9c3394972ca">all_tests.pl</a>
, <a class="el" href="create__sql__patches_8pl.html#a9449f3118943816afb79e9c3394972ca">create_sql_patches.pl</a>
: <a class="el" href="create__sql__patches_8pl.html#a9449f3118943816afb79e9c3394972ca">create_sql_patches.pl</a>
</li>
</ul>
</div><!-- contents -->
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">2.3</span>
&#160;<span id="projectnumber">2.4</span>
</div>
</td>
</tr>
......@@ -115,9 +115,6 @@ $(document).ready(function(){initNavTree('globals_func.html','');});
<li>add_event()
: <a class="el" href="generate__timeline_8pl.html#af9173ecf6f7c033aa8704be6d5aa1019">generate_timeline.pl</a>
</li>
<li>clean()
: <a class="el" href="all__tests_8pl.html#a422ef8d1a748ca4ffbcd453fbf22ba8b">all_tests.pl</a>
</li>
<li>count_number_relevant_sets()
: <a class="el" href="generate__timeline_8pl.html#ac70218a8fce3a55255272b1552f00d3e">generate_timeline.pl</a>
</li>
......@@ -139,15 +136,14 @@ $(document).ready(function(){initNavTree('globals_func.html','');});
<li>generate_worker_cmd()
: <a class="el" href="beekeeper_8pl.html#ad7de8680eb8b39e160cee04957ccd668">beekeeper.pl</a>
</li>
<li>get_all_tests()
: <a class="el" href="all__tests_8pl.html#afec6f985b18aa1e7edb785fb6c35aada">all_tests.pl</a>
</li>
<li>main()
: <a class="el" href="beekeeper_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">beekeeper.pl</a>
, <a class="el" href="patch__2015-01-12_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">patch_2015-01-12.pl</a>
, <a class="el" href="tweak__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">tweak_pipeline.pl</a>
, <a class="el" href="standalone_job_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">standaloneJob.pl</a>
, <a class="el" href="seed__pipeline_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">seed_pipeline.pl</a>
, <a class="el" href="run_worker_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">runWorker.pl</a>
, <a class="el" href="make__docs_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">make_docs.pl</a>
, <a class="el" href="load__resource__usage_8pl.html#a3ce8b237b3bdb2817dac6f769e5768c2">load_resource_usage.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>
......@@ -162,8 +158,7 @@ $(document).ready(function(){initNavTree('globals_func.html','');});
: <a class="el" href="seed__pipeline_8pl.html#ae56eff1c83733ae5dcc4d7f7d6d25ff8">seed_pipeline.pl</a>
</li>
<li>usage()
: <a class="el" href="all__tests_8pl.html#a9449f3118943816afb79e9c3394972ca">all_tests.pl</a>
, <a class="el" href="create__sql__patches_8pl.html#a9449f3118943816afb79e9c3394972ca">create_sql_patches.pl</a>
: <a class="el" href="create__sql__patches_8pl.html#a9449f3118943816afb79e9c3394972ca">create_sql_patches.pl</a>
</li>
</ul>
</div><!-- contents -->
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">2.3</span>
&#160;<span id="projectnumber">2.4</span>
</div>
</td>
</tr>
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">2.3</span>
&#160;<span id="projectnumber">2.4</span>
</div>
</td>
</tr>
......@@ -125,19 +125,24 @@ This inheritance list is sorted roughly, but not completely, alphabetically:</di
<tr id="row_0_1_2_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_0_1_3_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_0_1_4_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_0_1_5_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_0_1_6_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_0_1_7_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_role_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::RoleAdaptor</a></td><td class="desc"></td></tr>
<tr id="row_0_1_8_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_0_1_5_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_target_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::DataflowTargetAdaptor</a></td><td class="desc"></td></tr>
<tr id="row_0_1_6_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_0_1_7_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_0_1_8_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_role_adaptor.html" target="_self">Bio::EnsEMBL::Hive::DBSQL::RoleAdaptor</a></td><td class="desc"></td></tr>
<tr id="row_0_1_9_" style="display:none;"><td class="entry"><img src="ftv2vertline.png" alt="|" width="16" height="22" /><img src="ftv2blank.png" alt="&#160;" 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_1_"><td class="entry"><img id="arr_1_" src="ftv2mnode.png" alt="o" width="16" height="22" onclick="toggleFolder('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_cacheable.html" target="_self">Bio::EnsEMBL::Hive::Cacheable</a></td><td class="desc"></td></tr>
<tr id="row_1_0_" 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_analysis.html" target="_self">Bio::EnsEMBL::Hive::Analysis</a></td><td class="desc"></td></tr>
<tr id="row_1_1_"><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_ctrl_rule.html" target="_self">Bio::EnsEMBL::Hive::AnalysisCtrlRule</a></td><td class="desc"></td></tr>
<tr id="row_1_2_" 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_analysis_stats.html" target="_self">Bio::EnsEMBL::Hive::AnalysisStats</a></td><td class="desc"></td></tr>
<tr id="row_1_3_"><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>
<tr id="row_1_4_" 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_meta_parameters.html" target="_self">Bio::EnsEMBL::Hive::MetaParameters</a></td><td class="desc"></td></tr>
<tr id="row_1_5_"><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_pipeline_wide_parameters.html" target="_self">Bio::EnsEMBL::Hive::PipelineWideParameters</a></td><td class="desc"></td></tr>
<tr id="row_1_6_" 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_resource_class.html" target="_self">Bio::EnsEMBL::Hive::ResourceClass</a></td><td class="desc"></td></tr>
<tr id="row_1_7_"><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_resource_description.html" target="_self">Bio::EnsEMBL::Hive::ResourceDescription</a></td><td class="desc"></td></tr>
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<tr id="row_1_1_"><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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......@@ -152,73 +157,96 @@ This inheritance list is sorted roughly, but not completely, alphabetically:</di
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