Commit 481ab801 authored by Matthieu Muffato's avatar Matthieu Muffato
Browse files

Updated the Doxygen doc for 2.0

parent c9050154
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">1.9</span>
&#160;<span id="projectnumber">2.0</span>
</div>
</td>
</tr>
......@@ -130,7 +130,7 @@ Namespaces</h2></td></tr>
<!-- start footer part -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="navelem"><a class="el" href="dir_67a94abf6e99d454046c3675e3bd1175.html">modules</a></li><li class="navelem"><a class="el" href="dir_2fb356b2600b67fb4ecdf615049082a3.html">Bio</a></li><li class="navelem"><a class="el" href="dir_f09fa94c377b37d40ac85c9124ee4df7.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="dir_6043810977801faf48a2b9bf5611c94b.html">Hive</a></li><li class="navelem"><a class="el" href="_valley_8pm.html">Valley.pm</a></li>
<li class="navelem"><a class="el" href="dir_6ebb522408489b2f8d403221bdd352ef.html">modules</a></li><li class="navelem"><a class="el" href="dir_3f1a5943108f8f570f78b93dd62c0c7c.html">Bio</a></li><li class="navelem"><a class="el" href="dir_b054d96fb2e130911ab7d5638fe95547.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="dir_a9e0aa06350c0954648fef9d9cd79db9.html">Hive</a></li><li class="navelem"><a class="el" href="_valley_8pm.html">Valley.pm</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>
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">1.9</span>
&#160;<span id="projectnumber">2.0</span>
</div>
</td>
</tr>
......@@ -130,7 +130,7 @@ Namespaces</h2></td></tr>
<!-- start footer part -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="navelem"><a class="el" href="dir_67a94abf6e99d454046c3675e3bd1175.html">modules</a></li><li class="navelem"><a class="el" href="dir_2fb356b2600b67fb4ecdf615049082a3.html">Bio</a></li><li class="navelem"><a class="el" href="dir_f09fa94c377b37d40ac85c9124ee4df7.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="dir_6043810977801faf48a2b9bf5611c94b.html">Hive</a></li><li class="navelem"><a class="el" href="_version_8pm.html">Version.pm</a></li>
<li class="navelem"><a class="el" href="dir_6ebb522408489b2f8d403221bdd352ef.html">modules</a></li><li class="navelem"><a class="el" href="dir_3f1a5943108f8f570f78b93dd62c0c7c.html">Bio</a></li><li class="navelem"><a class="el" href="dir_b054d96fb2e130911ab7d5638fe95547.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="dir_a9e0aa06350c0954648fef9d9cd79db9.html">Hive</a></li><li class="navelem"><a class="el" href="_version_8pm.html">Version.pm</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>
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">1.9</span>
&#160;<span id="projectnumber">2.0</span>
</div>
</td>
</tr>
......@@ -130,7 +130,7 @@ Namespaces</h2></td></tr>
<!-- start footer part -->
<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
<ul>
<li class="navelem"><a class="el" href="dir_67a94abf6e99d454046c3675e3bd1175.html">modules</a></li><li class="navelem"><a class="el" href="dir_2fb356b2600b67fb4ecdf615049082a3.html">Bio</a></li><li class="navelem"><a class="el" href="dir_f09fa94c377b37d40ac85c9124ee4df7.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="dir_6043810977801faf48a2b9bf5611c94b.html">Hive</a></li><li class="navelem"><a class="el" href="_worker_8pm.html">Worker.pm</a></li>
<li class="navelem"><a class="el" href="dir_6ebb522408489b2f8d403221bdd352ef.html">modules</a></li><li class="navelem"><a class="el" href="dir_3f1a5943108f8f570f78b93dd62c0c7c.html">Bio</a></li><li class="navelem"><a class="el" href="dir_b054d96fb2e130911ab7d5638fe95547.html">EnsEMBL</a></li><li class="navelem"><a class="el" href="dir_a9e0aa06350c0954648fef9d9cd79db9.html">Hive</a></li><li class="navelem"><a class="el" href="_worker_8pm.html">Worker.pm</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>
......
This diff is collapsed.
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">1.9</span>
&#160;<span id="projectnumber">2.0</span>
</div>
</td>
</tr>
......@@ -190,7 +190,6 @@ Functions</h2></td></tr>
<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"> $| = 1;</div>
<div class="line"> Bio::EnsEMBL::Registry-&gt;no_version_check(1);</div>
<div class="line"></div>
<div class="line"><span class="preprocessor"> # ok this is a hack, but I&#39;m going to pretend I&#39;ve got an object here</span></div>
<div class="line"><span class="preprocessor"></span><span class="preprocessor"> # by creating a hash ref and passing it around like an object</span></div>
......@@ -496,6 +495,8 @@ Functions</h2></td></tr>
<div class="line"></div>
<div class="line"> } elsif($reg_alias) {</div>
<div class="line"> script_usage(1) if $url;</div>
<div class="line"></div>
<div class="line"> require Bio::EnsEMBL::Registry;</div>
<div class="line"> Bio::EnsEMBL::Registry-&gt;load_all($reg_conf);</div>
<div class="line"></div>
<div class="line"> my $species = Bio::EnsEMBL::Registry-&gt;get_alias($reg_alias)</div>
......@@ -1163,17 +1164,17 @@ Functions</h2></td></tr>
<div class="line"> warn <span class="stringliteral">&quot;Since -input_id has not been set, assuming input_id=&#39;$input_id&#39;\n&quot;</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>-&gt;<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 =&gt; undef, # <span class="keyword">this</span> job has been created by the initialization script, not by another job</div>
<div class="line"> -analysis_id =&gt; $analysis-&gt;dbID,</div>
<div class="line"> -input_id =&gt; destringify( $input_id ), # Make sure all job creations undergo re-stringification to avoid alternative <span class="stringliteral">&quot;spellings&quot;</span> of the same input_id hash</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>-&gt;<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html#a52efcf0d0755525a7bc059b68442c620">new</a>(</div>
<div class="line"> <span class="stringliteral">&#39;prev_job_id&#39;</span> =&gt; undef, # <span class="keyword">this</span> job has been created by the initialization script, not by another job</div>
<div class="line"> <span class="stringliteral">&#39;analysis_id&#39;</span> =&gt; $analysis-&gt;dbID,</div>
<div class="line"> <span class="stringliteral">&#39;input_id&#39;</span> =&gt; destringify( $input_id ), # Make sure all job creations undergo re-stringification to avoid alternative <span class="stringliteral">&quot;spellings&quot;</span> of the same input_id hash</div>
<div class="line"> );</div>
<div class="line"></div>
<div class="line"> my ($job_id) = @{ $hive_dba-&gt;get_AnalysisJobAdaptor-&gt;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">&quot;Job $job_id [ &quot;</span>.$analysis-&gt;logic_name.<span class="charliteral">&#39;(&#39;</span>.$analysis-&gt;dbID.<span class="stringliteral">&quot;)] : &#39;$input_id&#39;\n&quot;</span>;</div>
<div class="line"> print <span class="stringliteral">&quot;Job $job_id [ &quot;</span>.$analysis-&gt;logic_name.<span class="charliteral">&#39;(&#39;</span>.$analysis-&gt;<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html#a5e5743dee1414d2c0dec45b5a5d42216">dbID</a>.<span class="stringliteral">&quot;)] : &#39;$input_id&#39;\n&quot;</span>;</div>
<div class="line"></div>
<div class="line"> } <span class="keywordflow">else</span> {</div>
<div class="line"></div>
......@@ -1296,7 +1297,7 @@ Functions</h2></td></tr>
<!-- 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="navelem"><a class="el" href="dir_54316937a66070d9897b24579a7d39ac.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>
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">1.9</span>
&#160;<span id="projectnumber">2.0</span>
</div>
</td>
</tr>
......@@ -112,12 +112,13 @@ $(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1
<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 class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html#ae3ce63575f76820319b7eaf0d22659e0">adaptor</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html">Bio::EnsEMBL::Hive::Storable</a></td><td class="entry"></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>
<tr class="even"><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html#a5e5743dee1414d2c0dec45b5a5d42216">dbID</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html">Bio::EnsEMBL::Hive::Storable</a></td><td class="entry"></td></tr>
<tr><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html#a52efcf0d0755525a7bc059b68442c620">new</a>()</td><td class="entry"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html">Bio::EnsEMBL::Hive::Storable</a></td><td class="entry"></td></tr>
<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#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><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 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#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 -->
......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
&#160;<span id="projectnumber">1.9</span>
&#160;<span id="projectnumber">2.0</span>
</div>
</td>
</tr>
......@@ -112,13 +112,27 @@ $(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1
<div class="title">Bio::EnsEMBL::Hive::Accumulator 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::Accumulator:</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_accumulator__inherit__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator_inherit__map" alt="Inheritance graph"/></div>
<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator_inherit__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator_inherit__map">
<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html" title="Bio::EnsEMBL::Hive\l::Storable" alt="" coords="5,6,147,47"/></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::Accumulator:</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_accumulator__coll__graph.png" border="0" usemap="#_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator_coll__map" alt="Collaboration graph"/></div>
<map name="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator_coll__map" id="_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_accumulator_coll__map">
<area shape="rect" id="node2" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html" title="Bio::EnsEMBL::Hive\l::Storable" 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:ac035312016653df35c35398474835764"><td class="memItemLeft" align="right" valign="top">public&#160;</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">&#160;</td></tr>
<tr class="memitem:a7dd96c5cf6b8c8c4b4b1447923250373"><td class="memItemLeft" align="right" valign="top">public&#160;</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">&#160;</td></tr>
<tr class="memitem:a0a2118e2f81d95101bf4d0e69d90852a"><td class="memItemLeft" align="right" valign="top">public&#160;</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">&#160;</td></tr>
<tr class="memitem:a9348142e49053884868319ec512435cd"><td class="memItemLeft" align="right" valign="top">public&#160;</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>
......@@ -127,6 +141,14 @@ Public Member Functions</h2></td></tr>
<tr class="separator:af5ca59dde1b1f4f1dba1c9154490a23a"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a16b156d26595a7d16e0e04b60d5f6f36"><td class="memItemLeft" align="right" valign="top">public&#160;</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">&#160;</td></tr>
<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html">Bio::EnsEMBL::Hive::Storable</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_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html#ae3ce63575f76820319b7eaf0d22659e0">adaptor</a> ()</td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><h1><a class="anchor" id="Description"></a>
......@@ -136,37 +158,6 @@ Description</h1>
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-&gt;{<span class="stringliteral">&#39;_adaptor&#39;</span>} = shift @_;</div>
<div class="line"> weaken $self-&gt;{<span class="stringliteral">&#39;_adaptor&#39;</span>};</div>
<div class="line"> }</div>
<div class="line"></div>
<div class="line"> <span class="keywordflow">return</span> $self-&gt;{<span class="stringliteral">&#39;_adaptor&#39;</span>};</div>
<div class="line">}</div>
</div><!-- fragment --> </div>
</div>
</div>
<a class="anchor" id="a16b156d26595a7d16e0e04b60d5f6f36"></a>
<div class="memitem">
<div class="memproto">
......@@ -215,41 +206,6 @@ Description</h1>
</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"> $self-&gt;adaptor($adaptor) <span class="keywordflow">if</span>(defined($adaptor));</div>
<div class="line"> $self-&gt;struct_name($struct_name) <span class="keywordflow">if</span>(defined($struct_name));</div>
<div class="line"> $self-&gt;signature_template($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>
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<div class="memitem">
<div class="memproto">
......
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......
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......@@ -30,7 +30,7 @@
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......@@ -112,15 +112,17 @@ $(document).ready(function(){initNavTree('class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1
<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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......
......@@ -30,7 +30,7 @@
<tr style="height: 56px;">
<td style="padding-left: 0.5em;">
<div id="projectname">ensembl-hive
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</td>
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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::Analysis:</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:ad61a51a522d45f6a30e2a596b5165524"><td class="memItemLeft" align="right" valign="top">public&#160;</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#ad61a51a522d45f6a30e2a596b5165524">new</a> ()</td></tr>
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......@@ -166,6 +164,14 @@ Public Member Functions</h2></td></tr>
<tr class="separator:a6ff6efb50bd9f7dbb2d2b221920e73a1"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a19564942a29c32c01248d9b84bc15c83"><td class="memItemLeft" align="right" valign="top">public&#160;</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">&#160;</td></tr>
<tr class="inherit_header pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable')"><img src="closed.png" alt="-"/>&#160;Public Member Functions inherited from <a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html">Bio::EnsEMBL::Hive::Storable</a></td></tr>
<tr class="memitem:a52efcf0d0755525a7bc059b68442c620 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable"><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_storable.html">Bio::EnsEMBL::Hive::Storable</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html#a52efcf0d0755525a7bc059b68442c620">new</a> ()</td></tr>
<tr class="separator:a52efcf0d0755525a7bc059b68442c620 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:a5e5743dee1414d2c0dec45b5a5d42216 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable"><td class="memItemLeft" align="right" valign="top">public Int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html#a5e5743dee1414d2c0dec45b5a5d42216">dbID</a> ()</td></tr>
<tr class="separator:a5e5743dee1414d2c0dec45b5a5d42216 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable"><td class="memSeparator" colspan="2">&#160;</td></tr>
<tr class="memitem:ae3ce63575f76820319b7eaf0d22659e0 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable"><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_base_adaptor.html">Bio::EnsEMBL::Hive::DBSQL::BaseAdaptor</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html#ae3ce63575f76820319b7eaf0d22659e0">adaptor</a> ()</td></tr>
<tr class="separator:ae3ce63575f76820319b7eaf0d22659e0 inherit pub_methods_class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable"><td class="memSeparator" colspan="2">&#160;</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>
......@@ -398,48 +404,6 @@ Description</h1>
</div><!-- fragment --> </div>
</div>
</div>
<a class="anchor" id="ad61a51a522d45f6a30e2a596b5165524"></a>
<div class="memitem">
<div class="memproto">
<table class="memname">
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<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 = $class-&gt;SUPER::new( @_ ); # deal with Storable stuff</div>
<div class="line"></div>
<div class="line"> my ($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"> $self-&gt;logic_name($logic_name) <span class="keywordflow">if</span>($logic_name);</div>
<div class="line"> $self-&gt;module($module) <span class="keywordflow">if</span>($module);</div>
<div class="line"> $self-&gt;parameters($parameters) <span class="keywordflow">if</span>($parameters);</div>
<div class="line"> $self-&gt;resource_class_id($resource_class_id) <span class="keywordflow">if</span>($resource_class_id);</div>
<div class="line"> $self-&gt;failed_job_tolerance($failed_job_tolerance) <span class="keywordflow">if</span>($failed_job_tolerance);</div>
<div class="line"> $self-&gt;max_retry_count($max_retry_count) <span class="keywordflow">if</span>($max_retry_count);</div>
<div class="line"> $self-&gt;can_be_empty($can_be_empty) <span class="keywordflow">if</span>($can_be_empty);</div>
<div class="line"> $self-&gt;priority($priority) <span class="keywordflow">if</span>($priority);</div>
<div class="line"> $self-&gt;meadow_type($meadow_type) <span class="keywordflow">if</span>($meadow_type);</div>
<div class="line"> $self-&gt;analysis_capacity($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">
......@@ -522,7 +486,8 @@ Description</h1>
<div 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-&gt;get_compiled_module_name-&gt;<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>( -analysis =&gt; $self );</div>
<div class="line"> my $runnable_object = $self-&gt;get_compiled_module_name-&gt;<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_process.html#ae2f3da1c5a538fc990739595101bbfc5">new</a>();</div>
<div class="line"> $runnable_object-&gt;analysis( $self );</div>
<div class="line"></div>
<div class="line"> <span class="keywordflow">return</span> $runnable_object;</div>
<div class="line">}</div>
......@@ -586,7 +551,7 @@ Description</h1>
<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 &#39;sync&#39; calls.</span></div>
<div class="line"><span class="preprocessor"></span></div>
<div class="line"> my $stats = $self-&gt;adaptor-&gt;db-&gt;get_AnalysisStatsAdaptor-&gt;fetch_by_analysis_id($self-&gt;dbID);</div>
<div class="line"> my $stats = $self-&gt;<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html#ae3ce63575f76820319b7eaf0d22659e0">adaptor</a>-&gt;<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_d_b_s_q_l_1_1_base_adaptor.html#a020d1ee154f436e472e855e746b5467d">db</a>-&gt;get_AnalysisStatsAdaptor-&gt;fetch_by_analysis_id($self-&gt;dbID);</div>
<div class="line"> <span class="keywordflow">return</span> $stats;</div>
<div class="line">}</div>
</div><!-- fragment --> </div>
......@@ -613,7 +578,7 @@ Description</h1>
<div 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">&#39;: &#39;</span>.join(<span class="stringliteral">&#39;, &#39;</span>, map { $_.<span class="stringliteral">&#39;=&quot;&#39;</span>.$self-&gt;$_().<span class="charliteral">&#39;&quot;&#39;</span> } qw(dbID <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a6528be48120416c630abe32227e70bdb">logic_name</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac491521c673320cec2ce7cecf1d841cd">module</a> <a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#aa4d07a94412dd36e4dbb0d3db533c419">parameters</a>) ));</div>
<div class="line"> <span class="keywordflow">return</span> (ref($self).<span class="stringliteral">&#39;: &#39;</span>.join(<span class="stringliteral">&#39;, &#39;</span>, map { $_.<span class="stringliteral">&#39;=&quot;&#39;</span>.$self-&gt;$_().<span class="charliteral">&#39;&quot;&#39;</span> } qw(<a class="code" href="class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_storable.html#a5e5743dee1414d2c0dec45b5a5d42216">dbID</a> <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>
......
......@@ -8,7 +8,6 @@ var class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis =
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[ "meadow_type", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#ac41c5978a943fb1bf45a7c42507460ef", null ],
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[ "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 ],
[ "process", "class_bio_1_1_ens_e_m_b_l_1_1_hive_1_1_analysis.html#a45dd4f95b7b508ddf2ba2d620734d96c", null ],
......
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