website/tests/emailable-report.html

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   4 <title>TestNG:  Unit Test</title>
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  29 <body>
  30 <table cellspacing=0 cellpadding=0 class="param">
  31 <tr><th>Test</th><th class="numi">Methods<br/>Passed</th><th class="numi">Scenarios<br/>Passed</th><th class="numi"># skipped</th><th class="numi"># failed</th><th class="numi">Total<br/>Time</th><th class="numi">Included<br/>Groups</th><th class="numi">Excluded<br/>Groups</th></tr>
  32 <tr><td style="text-align:left;padding-right:2em">Ant test</td><td class="numi">205</td><td class="numi">216</td><td class="numi">0</td><td class="numi">0</td><td class="numi">453.9 seconds</td><td class="numi"></td><td class="numi">webservices performance </td></tr>
  33 </table>
  34 <a id="summary"></a>
  35 <table cellspacing=0 cellpadding=0 class="passed">
  36 <tr><th>Class</th><th>Method</th><th># of<br/>Scenarios</th><th>Time<br/>(Msecs)</th></tr>
  37 <tr><th colspan="4">Ant test &#8212; passed</th></tr>
  38 <tr class="passedodd"><td rowspan="3">compbio.data.sequence.ClustalAlignmentUtilTester<td><a href="#m1"><b>testReadClustalFile</b>  </a></td><td class="numi">1</td><td class="numi">12</td></tr><tr class="passedodd"><td><a href="#m2"><b>testReadClustalFileLongNames</b>  </a></td><td class="numi">1</td><td class="numi">19</td></tr><tr class="passedodd"><td><a href="#m3"><b>testReadClustalFileShortNames</b>  </a></td><td class="numi">1</td><td class="numi">14</td></tr>
  39 <tr class="passedeven"><td rowspan="1">compbio.data.sequence.FastaReaderTester<td><a href="#m4"><b>test</b>  </a></td><td class="numi">1</td><td class="numi">18</td></tr>
  40 <tr class="passedodd"><td rowspan="1">compbio.data.sequence.FastaSequenceGeneratorTester<td><a href="#m5"><b>testProteinSequenceGeneration</b>  </a></td><td class="numi">1</td><td class="numi">7</td></tr>
  41 <tr class="passedeven"><td rowspan="1">compbio.data.sequence.FastaSequenceTester<td><a href="#m6"><b>testGetFormattedFasta</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  42 <tr class="passedodd"><td rowspan="12">compbio.data.sequence.SequenceUtilTester<td><a href="#m7"><b>loadJronnFile</b>  </a></td><td class="numi">1</td><td class="numi">27</td></tr><tr class="passedodd"><td><a href="#m8"><b>testCleanProteinSequence</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedodd"><td><a href="#m9"><b>testCleanSequence</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m10"><b>testDeepCleanSequence</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m11"><b>testReadAAConResults</b>  </a></td><td class="numi">1</td><td class="numi">269</td></tr><tr class="passedodd"><td><a href="#m12"><b>testReadDisemblResults</b>  </a></td><td class="numi">1</td><td class="numi">125</td></tr><tr class="passedodd"><td><a href="#m13"><b>testReadGlobPlotResults</b>  </a></td><td class="numi">1</td><td class="numi">104</td></tr><tr class="passedodd"><td><a href="#m14"><b>testReadIUPredForGlobDomain</b>  </a></td><td class="numi">1</td><td class="numi">6</td></tr><tr class="passedodd"><td><a href="#m15"><b>testReadIUPredForShortAndLongDisorder</b>  </a></td><td class="numi">1</td><td class="numi">36</td></tr><tr class="passedodd"><td><a href="#m16"><b>testReadWriteFasta</b>  </a></td><td class="numi">1</td><td class="numi">8</td></tr><tr class="passedodd"><td><a href="#m17"><b>testisNonAmbNucleotideSequence</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedodd"><td><a href="#m18"><b>testisProteinSequence</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  43 <tr class="passedeven"><td rowspan="2">compbio.engine.EngineConfiguratorTester<td><a href="#m19"><b>testGetAsyncEngine</b>  </a></td><td class="numi">1</td><td class="numi">12</td></tr><tr class="passedeven"><td><a href="#m20"><b>testGetSyncEngine</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr>
  44 <tr class="passedodd"><td rowspan="4">compbio.engine.FilePullerTester<td><a href="#m21"><b>testCache</b> (engine) </a></td><td class="numi">1</td><td class="numi">6008</td></tr><tr class="passedodd"><td><a href="#m22"><b>testGet</b>  </a></td><td class="numi">1</td><td class="numi">2</td></tr><tr class="passedodd"><td><a href="#m23"><b>testGetDelay</b> (engine) </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m24"><b>testPull</b> (engine) </a></td><td class="numi">1</td><td class="numi">14</td></tr>
  45 <tr class="passedeven"><td rowspan="1">compbio.engine.LoadBalancerTester<td><a href="#m25"><b>testLoadBalance</b>  </a></td><td class="numi">1</td><td class="numi">57</td></tr>
  46 <tr class="passedodd"><td rowspan="1">compbio.engine.PulledFileCacheTester<td><a href="#m26"><b>test</b>  </a></td><td class="numi">1</td><td class="numi">5011</td></tr>
  47 <tr class="passedeven"><td rowspan="3">compbio.engine.client.CommandBuilderTester<td><a href="#m27"><b>testCommandBuilding</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedeven"><td><a href="#m28"><b>testOptionsToCommand</b>  </a></td><td class="numi">1</td><td class="numi">40</td></tr><tr class="passedeven"><td><a href="#m29"><b>testSpaceDelimiterExecutable</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  48 <tr class="passedodd"><td rowspan="2">compbio.engine.client.PathValidatorTester<td><a href="#m30"><b>testGetClassPath</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedodd"><td><a href="#m31"><b>testIsAbsolutePath</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  49 <tr class="passedeven"><td rowspan="1">compbio.engine.cluster.drmaa.ClusterSessionTester<td><a href="#m32"><b>testTaskList</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">3953</td></tr>
  50 <tr class="passedodd"><td rowspan="3">compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester<td><a href="#m33"><b>testCancel</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">1257</td></tr><tr class="passedodd"><td><a href="#m34"><b>testGetJobStatus</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">4765</td></tr><tr class="passedodd"><td><a href="#m35"><b>testSubmit</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">3976</td></tr>
  51 <tr class="passedeven"><td rowspan="2">compbio.engine.cluster.drmaa.DrmaaClusterEngineTester<td><a href="#m36"><b>testCancel</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">1538</td></tr><tr class="passedeven"><td><a href="#m37"><b>testSubmit</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">3508</td></tr>
  52 <tr class="passedodd"><td rowspan="1">compbio.engine.cluster.drmaa.UtilTester<td><a href="#m38"><b>testParser</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr>
  53 <tr class="passedeven"><td rowspan="1">compbio.engine.cluster.dundee._QueueTester<td><a href="#m39"><b>testQueue</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  54 <tr class="passedodd"><td rowspan="1">compbio.engine.conf.DirectoryManagerTester<td><a href="#m40"><b>testGetDirectory</b>  </a></td><td class="numi">4</td><td class="numi">105</td></tr>
  55 <tr class="passedeven"><td rowspan="5">compbio.engine.conf.PropertyHelperManagerTester<td><a href="#m41"><b>testClusterEngineConf</b> (cluster) </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedeven"><td><a href="#m42"><b>validateClustalConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m43"><b>validateMafftConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">2</td></tr><tr class="passedeven"><td><a href="#m44"><b>validateMuscleConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m45"><b>validateTcoffeeConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  56 <tr class="passedodd"><td rowspan="5">compbio.engine.conf.RunnerConfigMarshallerTester<td><a href="#m46"><b>testMarshalling</b>  </a></td><td class="numi">1</td><td class="numi">4</td></tr><tr class="passedodd"><td><a href="#m47"><b>testSchemaFromCodeGeneration</b>  </a></td><td class="numi">1</td><td class="numi">130</td></tr><tr class="passedodd"><td><a href="#m48"><b>testUnMarshalling</b>  </a></td><td class="numi">1</td><td class="numi">17</td></tr><tr class="passedodd"><td><a href="#m49"><b>testValidation</b>  </a></td><td class="numi">1</td><td class="numi">82</td></tr><tr class="passedodd"><td><a href="#m50"><b>testValidationOnMarshalling</b>  </a></td><td class="numi">1</td><td class="numi">10</td></tr>
  57 <tr class="passedeven"><td rowspan="7">compbio.engine.local.AsyncLocalRunnerTester<td><a href="#m51"><b>testAsyncCancelOperation</b> (engine) </a></td><td class="numi">1</td><td class="numi">17</td></tr><tr class="passedeven"><td><a href="#m52"><b>testAsyncRetrievOperation</b> (engine) </a></td><td class="numi">1</td><td class="numi">124</td></tr><tr class="passedeven"><td><a href="#m53"><b>testCancelCompletedTaskLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">3017</td></tr><tr class="passedeven"><td><a href="#m54"><b>testCancelLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">13</td></tr><tr class="passedeven"><td><a href="#m55"><b>testGetStatus</b> (engine) </a></td><td class="numi">5</td><td class="numi">38622</td></tr><tr class="passedeven"><td><a href="#m56"><b>testMultipleCancelLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">54</td></tr><tr class="passedeven"><td><a href="#m57"><b>testSubmitLocally</b> (engine) </a></td><td class="numi">5</td><td class="numi">229</td></tr>
  58 <tr class="passedodd"><td rowspan="3">compbio.engine.local.LocalRunnerTester<td><a href="#m58"><b>testCancelCompletedTaskLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">49</td></tr><tr class="passedodd"><td><a href="#m59"><b>testCancelLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">17</td></tr><tr class="passedodd"><td><a href="#m60"><b>testMultipleCancelLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">44</td></tr>
  59 <tr class="passedeven"><td rowspan="2">compbio.metadata.OptionCombinatorTester<td><a href="#m61"><b>testgetAllOptions</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedeven"><td><a href="#m62"><b>testgetAllParameters</b>  </a></td><td class="numi">1</td><td class="numi">3</td></tr>
  60 <tr class="passedodd"><td rowspan="2">compbio.metadata.OptionMarshallerTester<td><a href="#m63"><b>testMarshalling</b>  </a></td><td class="numi">1</td><td class="numi">33</td></tr><tr class="passedodd"><td><a href="#m64"><b>testUnMarshalling</b>  </a></td><td class="numi">1</td><td class="numi">65</td></tr>
  61 <tr class="passedeven"><td rowspan="3">compbio.metadata.PresetTester<td><a href="#m65"><b>marshallPreset</b>  </a></td><td class="numi">1</td><td class="numi">14</td></tr><tr class="passedeven"><td><a href="#m66"><b>testPresetWithMuptiOptions</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedeven"><td><a href="#m67"><b>validatePresets</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr>
  62 <tr class="passedodd"><td rowspan="12">compbio.metadata.RunnerConfigTester<td><a href="#m68"><b>testCreateNumParameterWithoutValidValue</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m69"><b>testCreateParameter</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m70"><b>testCreateParameterWithValidValueConstrain</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m71"><b>testOptionNoDefaultValidate</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m72"><b>testOptionSetInvalidValue</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m73"><b>testOptionToCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m74"><b>testParameterToCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m75"><b>testValidate</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m76"><b>testValidateBoundaryConstrainCheck</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m77"><b>testValidateLowerBoundaryConstrainCheck</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m78"><b>testValidateUpperBoundaryConstrainCheck</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedodd"><td><a href="#m79"><b>testValidateValueConstrain</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  63 <tr class="passedeven"><td rowspan="1">compbio.runner._impl.MclTester<td><a href="#m80"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  64 <tr class="passedodd"><td rowspan="1">compbio.runner._impl.NetNglycTester<td><a href="#m81"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr>
  65 <tr class="passedeven"><td rowspan="2">compbio.runner._impl.OBTester<td><a href="#m82"><b>testGetTestArgsCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m83"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  66 <tr class="passedodd"><td rowspan="2">compbio.runner._impl.RPSBlastTester<td><a href="#m84"><b>testGetTestArgsCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m85"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  67 <tr class="passedeven"><td rowspan="1">compbio.runner._impl.RonnTester<td><a href="#m86"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  68 <tr class="passedodd"><td rowspan="1">compbio.runner._impl.Tmhmm2Tester<td><a href="#m87"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  69 <tr class="passedeven"><td rowspan="8">compbio.runner.conservation.AAConTester<td><a href="#m88"><b>readStatistics</b> (runner) </a></td><td class="numi">1</td><td class="numi">1493</td></tr><tr class="passedeven"><td><a href="#m89"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">113</td></tr><tr class="passedeven"><td><a href="#m90"><b>testPersistance</b> (runner) </a></td><td class="numi">1</td><td class="numi">775</td></tr><tr class="passedeven"><td><a href="#m91"><b>testRunLocally</b> (runner) </a></td><td class="numi">1</td><td class="numi">827</td></tr><tr class="passedeven"><td><a href="#m92"><b>testRunLocallyOnTwoCpu</b> (runner) </a></td><td class="numi">1</td><td class="numi">289</td></tr><tr class="passedeven"><td><a href="#m93"><b>testRunLocallyWithPreset</b> (runner) </a></td><td class="numi">1</td><td class="numi">653</td></tr><tr class="passedeven"><td><a href="#m94"><b>testRunOnCluster</b> (runner) </a></td><td class="numi">1</td><td class="numi">3640</td></tr><tr class="passedeven"><td><a href="#m95"><b>testRunOnClusterAsync</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">5018</td></tr>
  70 <tr class="passedodd"><td rowspan="6">compbio.runner.disorder.DisemblTester<td><a href="#m96"><b>readStatistics</b> (runner) </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m97"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">44</td></tr><tr class="passedodd"><td><a href="#m98"><b>testPersistance</b> (runner) </a></td><td class="numi">1</td><td class="numi">1297</td></tr><tr class="passedodd"><td><a href="#m99"><b>testRunLocally</b> (runner) </a></td><td class="numi">1</td><td class="numi">579</td></tr><tr class="passedodd"><td><a href="#m100"><b>testRunOnCluster</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">2047</td></tr><tr class="passedodd"><td><a href="#m101"><b>testRunOnClusterAsync</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">6011</td></tr>
  71 <tr class="passedeven"><td rowspan="6">compbio.runner.disorder.GlobPlotTester<td><a href="#m102"><b>readStatistics</b> (runner) </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m103"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">43</td></tr><tr class="passedeven"><td><a href="#m104"><b>testPersistance</b> (runner) </a></td><td class="numi">1</td><td class="numi">980</td></tr><tr class="passedeven"><td><a href="#m105"><b>testRunLocally</b> (runner) </a></td><td class="numi">1</td><td class="numi">454</td></tr><tr class="passedeven"><td><a href="#m106"><b>testRunOnCluster</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">2503</td></tr><tr class="passedeven"><td><a href="#m107"><b>testRunOnClusterAsync</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">6021</td></tr>
  72 <tr class="passedodd"><td rowspan="8">compbio.runner.disorder.IUPredTester<td><a href="#m108"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">69</td></tr><tr class="passedodd"><td><a href="#m109"><b>testPersistance</b> (runner) </a></td><td class="numi">1</td><td class="numi">308</td></tr><tr class="passedodd"><td><a href="#m110"><b>testReadResults</b> (runner) </a></td><td class="numi">1</td><td class="numi">25</td></tr><tr class="passedodd"><td><a href="#m111"><b>testRunLocally</b> (runner) </a></td><td class="numi">1</td><td class="numi">196</td></tr><tr class="passedodd"><td><a href="#m112"><b>testRunLocallyWithParams</b> (runner) </a></td><td class="numi">1</td><td class="numi">71</td></tr><tr class="passedodd"><td><a href="#m113"><b>testRunOnCluster</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">3308</td></tr><tr class="passedodd"><td><a href="#m114"><b>testRunOnClusterAsync</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">6025</td></tr><tr class="passedodd"><td><a href="#m115"><b>testSetParameter</b> (runner) </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  73 <tr class="passedeven"><td rowspan="7">compbio.runner.disorder.JronnTester<td><a href="#m116"><b>readStatistics</b> (runner) </a></td><td class="numi">1</td><td class="numi">18639</td></tr><tr class="passedeven"><td><a href="#m117"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">45</td></tr><tr class="passedeven"><td><a href="#m118"><b>testPersistance</b> (runner) </a></td><td class="numi">1</td><td class="numi">18613</td></tr><tr class="passedeven"><td><a href="#m119"><b>testRunLocally</b> (runner) </a></td><td class="numi">1</td><td class="numi">18541</td></tr><tr class="passedeven"><td><a href="#m120"><b>testRunLocallyOnTwoCpu</b> (runner) </a></td><td class="numi">1</td><td class="numi">7131</td></tr><tr class="passedeven"><td><a href="#m121"><b>testRunOnCluster</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">13058</td></tr><tr class="passedeven"><td><a href="#m122"><b>testRunOnClusterAsync</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">11022</td></tr>
  74 <tr class="passedodd"><td rowspan="9">compbio.runner.msa.ClustalWParametersTester<td><a href="#m123"><b>testArguments</b> (runner) </a></td><td class="numi">1</td><td class="numi">1649</td></tr><tr class="passedodd"><td><a href="#m124"><b>testConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedodd"><td><a href="#m125"><b>testConstrainedParametersMaxValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">678</td></tr><tr class="passedodd"><td><a href="#m126"><b>testConstrainedParametersMinValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">682</td></tr><tr class="passedodd"><td><a href="#m127"><b>testConstrainedParametersRandomValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">672</td></tr><tr class="passedodd"><td><a href="#m128"><b>testDefaultParameters</b> (runner) </a></td><td class="numi">1</td><td class="numi">129</td></tr><tr class="passedodd"><td><a href="#m129"><b>testOptions</b> (runner) </a></td><td class="numi">1</td><td class="numi">396</td></tr><tr class="passedodd"><td><a href="#m130"><b>testParameters</b> (runner) </a></td><td class="numi">1</td><td class="numi">1074</td></tr><tr class="passedodd"><td><a href="#m131"><b>testPresets</b> (runner) </a></td><td class="numi">1</td><td class="numi">129</td></tr>
  75 <tr class="passedeven"><td rowspan="8">compbio.runner.msa.ClustalWTester<td><a href="#m132"><b>readStatistics</b> (runner) </a></td><td class="numi">1</td><td class="numi">518</td></tr><tr class="passedeven"><td><a href="#m133"><b>readStatisticsClusterExecution</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">1640</td></tr><tr class="passedeven"><td><a href="#m134"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">46</td></tr><tr class="passedeven"><td><a href="#m135"><b>testOptionsLocally</b> (runner) </a></td><td class="numi">1</td><td class="numi">429</td></tr><tr class="passedeven"><td><a href="#m136"><b>testPersistance</b> (runner) </a></td><td class="numi">1</td><td class="numi">303</td></tr><tr class="passedeven"><td><a href="#m137"><b>testRunLocally</b> (runner) </a></td><td class="numi">1</td><td class="numi">132</td></tr><tr class="passedeven"><td><a href="#m138"><b>testRunOnCluster</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">5003</td></tr><tr class="passedeven"><td><a href="#m139"><b>testRunWithMatrix</b> (runner) </a></td><td class="numi">1</td><td class="numi">130</td></tr>
  76 <tr class="passedodd"><td rowspan="2">compbio.runner.msa.LimitTester<td><a href="#m140"><b>testLimitExceeded</b>  </a></td><td class="numi">1</td><td class="numi">14</td></tr><tr class="passedodd"><td><a href="#m141"><b>testLoadLimits</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  77 <tr class="passedeven"><td rowspan="9">compbio.runner.msa.MafftParametersTester<td><a href="#m142"><b>testArguments</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">3027</td></tr><tr class="passedeven"><td><a href="#m143"><b>testConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m144"><b>testConstrainedParametersMaxValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">1461</td></tr><tr class="passedeven"><td><a href="#m145"><b>testConstrainedParametersMinValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">886</td></tr><tr class="passedeven"><td><a href="#m146"><b>testConstrainedParametersRandomValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">3530</td></tr><tr class="passedeven"><td><a href="#m147"><b>testDefaultParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">4507</td></tr><tr class="passedeven"><td><a href="#m148"><b>testOptions</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">971</td></tr><tr class="passedeven"><td><a href="#m149"><b>testParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">1179</td></tr><tr class="passedeven"><td><a href="#m150"><b>testPresets</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">965</td></tr>
  78 <tr class="passedodd"><td rowspan="7">compbio.runner.msa.MafftTester<td><a href="#m151"><b>readStatistics</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">516</td></tr><tr class="passedodd"><td><a href="#m152"><b>testClusterExecute</b> (cluster, runner, non_windows) </a></td><td class="numi">1</td><td class="numi">1264</td></tr><tr class="passedodd"><td><a href="#m153"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">62</td></tr><tr class="passedodd"><td><a href="#m154"><b>testExecute</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">162</td></tr><tr class="passedodd"><td><a href="#m155"><b>testPersistance</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">305</td></tr><tr class="passedodd"><td><a href="#m156"><b>testRunOnClusterAsyncCheckStatusLongPoolingTime</b> (cluster, runner, non_windows) </a></td><td class="numi">1</td><td class="numi">5535</td></tr><tr class="passedodd"><td><a href="#m157"><b>testSetInputTester</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  79 <tr class="passedeven"><td rowspan="9">compbio.runner.msa.MuscleParametersTester<td><a href="#m158"><b>testArguments</b> (runner) </a></td><td class="numi">1</td><td class="numi">4387</td></tr><tr class="passedeven"><td><a href="#m159"><b>testConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedeven"><td><a href="#m160"><b>testConstrainedParametersMaxValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">1977</td></tr><tr class="passedeven"><td><a href="#m161"><b>testConstrainedParametersMinValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">1112</td></tr><tr class="passedeven"><td><a href="#m162"><b>testConstrainedParametersRandomValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">2749</td></tr><tr class="passedeven"><td><a href="#m163"><b>testDefaultParameters</b> (runner) </a></td><td class="numi">1</td><td class="numi">100</td></tr><tr class="passedeven"><td><a href="#m164"><b>testOptions</b> (runner) </a></td><td class="numi">1</td><td class="numi">1360</td></tr><tr class="passedeven"><td><a href="#m165"><b>testParameters</b> (runner) </a></td><td class="numi">1</td><td class="numi">1919</td></tr><tr class="passedeven"><td><a href="#m166"><b>testPresets</b> (runner) </a></td><td class="numi">1</td><td class="numi">242</td></tr>
  80 <tr class="passedodd"><td rowspan="5">compbio.runner.msa.MuscleTester<td><a href="#m167"><b>readStatistics</b> (runner) </a></td><td class="numi">1</td><td class="numi">520</td></tr><tr class="passedodd"><td><a href="#m168"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">43</td></tr><tr class="passedodd"><td><a href="#m169"><b>testPersistance</b> (runner) </a></td><td class="numi">1</td><td class="numi">233</td></tr><tr class="passedodd"><td><a href="#m170"><b>testRunLocally</b> (runner) </a></td><td class="numi">1</td><td class="numi">100</td></tr><tr class="passedodd"><td><a href="#m171"><b>testRunOnCluster</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">3867</td></tr>
  81 <tr class="passedeven"><td rowspan="8">compbio.runner.msa.ProbconsParametersTester<td><a href="#m172"><b>testArguments</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">1819</td></tr><tr class="passedeven"><td><a href="#m173"><b>testConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m174"><b>testConstrainedParametersMaxValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">37102</td></tr><tr class="passedeven"><td><a href="#m175"><b>testConstrainedParametersMinValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">768</td></tr><tr class="passedeven"><td><a href="#m176"><b>testConstrainedParametersRandomValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">70319</td></tr><tr class="passedeven"><td><a href="#m177"><b>testDefaultParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">4845</td></tr><tr class="passedeven"><td><a href="#m178"><b>testOptions</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">443</td></tr><tr class="passedeven"><td><a href="#m179"><b>testParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">1344</td></tr>
  82 <tr class="passedodd"><td rowspan="6">compbio.runner.msa.ProbconsTester<td><a href="#m180"><b>readStatistics</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">455</td></tr><tr class="passedodd"><td><a href="#m181"><b>testClusterExecute</b> (cluster, runner, non_windows) </a></td><td class="numi">1</td><td class="numi">2710</td></tr><tr class="passedodd"><td><a href="#m182"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">89</td></tr><tr class="passedodd"><td><a href="#m183"><b>testExecute</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">455</td></tr><tr class="passedodd"><td><a href="#m184"><b>testPersistance</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">527</td></tr><tr class="passedodd"><td><a href="#m185"><b>testSetInputTester</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  83 <tr class="passedeven"><td rowspan="9">compbio.runner.msa.TcoffeeParametersTester<td><a href="#m186"><b>testArguments</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">4098</td></tr><tr class="passedeven"><td><a href="#m187"><b>testConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m188"><b>testConstrainedParametersMaxValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">4319</td></tr><tr class="passedeven"><td><a href="#m189"><b>testConstrainedParametersMinValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">2887</td></tr><tr class="passedeven"><td><a href="#m190"><b>testConstrainedParametersRandomValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">8762</td></tr><tr class="passedeven"><td><a href="#m191"><b>testDefaultParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">3850</td></tr><tr class="passedeven"><td><a href="#m192"><b>testOptions</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">377</td></tr><tr class="passedeven"><td><a href="#m193"><b>testParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">3800</td></tr><tr class="passedeven"><td><a href="#m194"><b>testPresets</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">214</td></tr>
  84 <tr class="passedodd"><td rowspan="6">compbio.runner.msa.TcoffeeTester<td><a href="#m195"><b>readStatistics</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">516</td></tr><tr class="passedodd"><td><a href="#m196"><b>testClusterExecute</b> (cluster, runner, non_windows) </a></td><td class="numi">1</td><td class="numi">5084</td></tr><tr class="passedodd"><td><a href="#m197"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">39</td></tr><tr class="passedodd"><td><a href="#m198"><b>testExecute</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">364</td></tr><tr class="passedodd"><td><a href="#m199"><b>testNcore</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m200"><b>testPersistance</b> (cluster, runner, non_windows) </a></td><td class="numi">1</td><td class="numi">769</td></tr>
  85 <tr class="passedeven"><td rowspan="3">compbio.stat.collector.ExecutionStatCollectorTester<td><a href="#m201"><b>testCollectStat</b>  </a></td><td class="numi">1</td><td class="numi">271</td></tr><tr class="passedeven"><td><a href="#m202"><b>testHasCompleted</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedeven"><td><a href="#m203"><b>testUpdateStatTester</b>  </a></td><td class="numi">1</td><td class="numi">35012</td></tr>
  86 <tr class="passedodd"><td rowspan="1">compbio.stat.collector.StatDBTester<td><a href="#m204"><b>testVerifyJobsCount</b>  </a></td><td class="numi">1</td><td class="numi">412</td></tr>
  87 <tr class="passedeven"><td rowspan="1">compbio.stat.servlet.util.StatCollectionTester<br>"Ant test"<td><a href="#m205"><b>testGetStats</b>  </a></td><td class="numi">1</td><td class="numi">22</td></tr>
  88 </table>
  89 <h1>Ant test</h1>
  90 <a id="m1"></a><h2>compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFile</h2>
  91 <p class="totop"><a href="#summary">back to summary</a></p>
  92 <a id="m2"></a><h2>compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileLongNames</h2>
  93 <p class="totop"><a href="#summary">back to summary</a></p>
  94 <a id="m3"></a><h2>compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileShortNames</h2>
  95 <p class="totop"><a href="#summary">back to summary</a></p>
  96 <a id="m4"></a><h2>compbio.data.sequence.FastaReaderTester:test</h2>
  97 <p class="totop"><a href="#summary">back to summary</a></p>
  98 <a id="m5"></a><h2>compbio.data.sequence.FastaSequenceGeneratorTester:testProteinSequenceGeneration</h2>
  99 <p class="totop"><a href="#summary">back to summary</a></p>
 100 <a id="m6"></a><h2>compbio.data.sequence.FastaSequenceTester:testGetFormattedFasta</h2>
 101 <p class="totop"><a href="#summary">back to summary</a></p>
 102 <a id="m7"></a><h2>compbio.data.sequence.SequenceUtilTester:loadJronnFile</h2>
 103 <p class="totop"><a href="#summary">back to summary</a></p>
 104 <a id="m8"></a><h2>compbio.data.sequence.SequenceUtilTester:testCleanProteinSequence</h2>
 105 <p class="totop"><a href="#summary">back to summary</a></p>
 106 <a id="m9"></a><h2>compbio.data.sequence.SequenceUtilTester:testCleanSequence</h2>
 107 <p class="totop"><a href="#summary">back to summary</a></p>
 108 <a id="m10"></a><h2>compbio.data.sequence.SequenceUtilTester:testDeepCleanSequence</h2>
 109 <p class="totop"><a href="#summary">back to summary</a></p>
 110 <a id="m11"></a><h2>compbio.data.sequence.SequenceUtilTester:testReadAAConResults</h2>
 111 <p class="totop"><a href="#summary">back to summary</a></p>
 112 <a id="m12"></a><h2>compbio.data.sequence.SequenceUtilTester:testReadDisemblResults</h2>
 113 <p class="totop"><a href="#summary">back to summary</a></p>
 114 <a id="m13"></a><h2>compbio.data.sequence.SequenceUtilTester:testReadGlobPlotResults</h2>
 115 <p class="totop"><a href="#summary">back to summary</a></p>
 116 <a id="m14"></a><h2>compbio.data.sequence.SequenceUtilTester:testReadIUPredForGlobDomain</h2>
 117 <p class="totop"><a href="#summary">back to summary</a></p>
 118 <a id="m15"></a><h2>compbio.data.sequence.SequenceUtilTester:testReadIUPredForShortAndLongDisorder</h2>
 119 <p class="totop"><a href="#summary">back to summary</a></p>
 120 <a id="m16"></a><h2>compbio.data.sequence.SequenceUtilTester:testReadWriteFasta</h2>
 121 <p class="totop"><a href="#summary">back to summary</a></p>
 122 <a id="m17"></a><h2>compbio.data.sequence.SequenceUtilTester:testisNonAmbNucleotideSequence</h2>
 123 <p class="totop"><a href="#summary">back to summary</a></p>
 124 <a id="m18"></a><h2>compbio.data.sequence.SequenceUtilTester:testisProteinSequence</h2>
 125 <p class="totop"><a href="#summary">back to summary</a></p>
 126 <a id="m19"></a><h2>compbio.engine.EngineConfiguratorTester:testGetAsyncEngine</h2>
 127 <p class="totop"><a href="#summary">back to summary</a></p>
 128 <a id="m20"></a><h2>compbio.engine.EngineConfiguratorTester:testGetSyncEngine</h2>
 129 <p class="totop"><a href="#summary">back to summary</a></p>
 130 <a id="m21"></a><h2>compbio.engine.FilePullerTester:testCache</h2>
 131 <p class="totop"><a href="#summary">back to summary</a></p>
 132 <a id="m22"></a><h2>compbio.engine.FilePullerTester:testGet</h2>
 133 <p class="totop"><a href="#summary">back to summary</a></p>
 134 <a id="m23"></a><h2>compbio.engine.FilePullerTester:testGetDelay</h2>
 135 <p class="totop"><a href="#summary">back to summary</a></p>
 136 <a id="m24"></a><h2>compbio.engine.FilePullerTester:testPull</h2>
 137 <p class="totop"><a href="#summary">back to summary</a></p>
 138 <a id="m25"></a><h2>compbio.engine.LoadBalancerTester:testLoadBalance</h2>
 139 <p class="totop"><a href="#summary">back to summary</a></p>
 140 <a id="m26"></a><h2>compbio.engine.PulledFileCacheTester:test</h2>
 141 <p class="totop"><a href="#summary">back to summary</a></p>
 142 <a id="m27"></a><h2>compbio.engine.client.CommandBuilderTester:testCommandBuilding</h2>
 143 <p class="totop"><a href="#summary">back to summary</a></p>
 144 <a id="m28"></a><h2>compbio.engine.client.CommandBuilderTester:testOptionsToCommand</h2>
 145 <p class="totop"><a href="#summary">back to summary</a></p>
 146 <a id="m29"></a><h2>compbio.engine.client.CommandBuilderTester:testSpaceDelimiterExecutable</h2>
 147 <p class="totop"><a href="#summary">back to summary</a></p>
 148 <a id="m30"></a><h2>compbio.engine.client.PathValidatorTester:testGetClassPath</h2>
 149 <p class="totop"><a href="#summary">back to summary</a></p>
 150 <a id="m31"></a><h2>compbio.engine.client.PathValidatorTester:testIsAbsolutePath</h2>
 151 <p class="totop"><a href="#summary">back to summary</a></p>
 152 <a id="m32"></a><h2>compbio.engine.cluster.drmaa.ClusterSessionTester:testTaskList</h2>
 153 <p class="totop"><a href="#summary">back to summary</a></p>
 154 <a id="m33"></a><h2>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testCancel</h2>
 155 <div style="padding-left:3em">
 156 <p>java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/jaba2/local_jobsout/ClustalW#6405924652151282 with file name TO1381.clustal.cluster.out is not found!</p>
 157 compbio.runner.msa.ClustalW.getResults(ClustalW.java:73)
 158 <br/>at compbio.runner.msa.ClustalW.getResults(ClustalW.java:34)
 159 <br/>at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:207)
 160 <br/>at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
 161 <br/>23 lines not shown
 162 <p>Caused by Result for the jobId /homes/pvtroshin/workspace/jaba2/local_jobsout/ClustalW#6405924652151282 with file name TO1381.clustal.cluster.out is not found!</p>
 163 compbio.runner.Util.readClustalFile(Util.java:93)
 164 <br/>at compbio.runner.msa.ClustalW.getResults(ClustalW.java:70)
 165 <br/>at compbio.runner.msa.ClustalW.getResults(ClustalW.java:34)
 166 <br/>at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:207)
 167 <br/>at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
 168 <br/>23 lines not shown
 169 </div>
 170 <p class="totop"><a href="#summary">back to summary</a></p>
 171 <a id="m34"></a><h2>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testGetJobStatus</h2>
 172 <p class="totop"><a href="#summary">back to summary</a></p>
 173 <a id="m35"></a><h2>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testSubmit</h2>
 174 <p class="totop"><a href="#summary">back to summary</a></p>
 175 <a id="m36"></a><h2>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testCancel</h2>
 176 <p class="totop"><a href="#summary">back to summary</a></p>
 177 <a id="m37"></a><h2>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testSubmit</h2>
 178 <p class="totop"><a href="#summary">back to summary</a></p>
 179 <a id="m38"></a><h2>compbio.engine.cluster.drmaa.UtilTester:testParser</h2>
 180 <p class="totop"><a href="#summary">back to summary</a></p>
 181 <a id="m39"></a><h2>compbio.engine.cluster.dundee._QueueTester:testQueue</h2>
 182 <p class="totop"><a href="#summary">back to summary</a></p>
 183 <a id="m40"></a><h2>compbio.engine.conf.DirectoryManagerTester:testGetDirectory</h2>
 184 <p class="totop"><a href="#summary">back to summary</a></p>
 185 <a id="m41"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:testClusterEngineConf</h2>
 186 <p class="totop"><a href="#summary">back to summary</a></p>
 187 <a id="m42"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateClustalConfiguration</h2>
 188 <p class="totop"><a href="#summary">back to summary</a></p>
 189 <a id="m43"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateMafftConfiguration</h2>
 190 <p class="totop"><a href="#summary">back to summary</a></p>
 191 <a id="m44"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateMuscleConfiguration</h2>
 192 <p class="totop"><a href="#summary">back to summary</a></p>
 193 <a id="m45"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateTcoffeeConfiguration</h2>
 194 <p class="totop"><a href="#summary">back to summary</a></p>
 195 <a id="m46"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testMarshalling</h2>
 196 <p class="totop"><a href="#summary">back to summary</a></p>
 197 <a id="m47"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testSchemaFromCodeGeneration</h2>
 198 <p class="totop"><a href="#summary">back to summary</a></p>
 199 <a id="m48"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testUnMarshalling</h2>
 200 <p class="totop"><a href="#summary">back to summary</a></p>
 201 <a id="m49"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testValidation</h2>
 202 <p class="totop"><a href="#summary">back to summary</a></p>
 203 <a id="m50"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testValidationOnMarshalling</h2>
 204 <div style="padding-left:3em">
 205 <p>null</p>
 206 com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:323)
 207 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
 208 <br/>at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
 209 <br/>at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
 210 <br/>at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:259)
 211 <br/>23 lines not shown
 212 <p>Caused by cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.</p>
 213 com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
 214 <br/>at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
 215 <br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
 216 <br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
 217 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
 218 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
 219 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
 220 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
 221 <br/>at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
 222 <br/>at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
 223 <br/>at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:128)
 224 <br/>at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:106)
 225 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:310)
 226 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:699)
 227 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:69)
 228 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:172)
 229 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:159)
 230 <br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:344)
 231 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:597)
 232 <br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:328)
 233 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:498)
 234 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:320)
 235 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
 236 <br/>at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
 237 <br/>at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
 238 <br/>at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:259)
 239 <br/>23 lines not shown
 240 </div>
 241 <p class="totop"><a href="#summary">back to summary</a></p>
 242 <a id="m51"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testAsyncCancelOperation</h2>
 243 <p class="totop"><a href="#summary">back to summary</a></p>
 244 <a id="m52"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testAsyncRetrievOperation</h2>
 245 <p class="totop"><a href="#summary">back to summary</a></p>
 246 <a id="m53"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testCancelCompletedTaskLocally</h2>
 247 <p class="totop"><a href="#summary">back to summary</a></p>
 248 <a id="m54"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testCancelLocally</h2>
 249 <div style="padding-left:3em">
 250 <p>null</p>
 251 java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 252 <br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 253 <br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 254 <br/>at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 255 <br/>at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
 256 <br/>23 lines not shown
 257 </div>
 258 <p class="totop"><a href="#summary">back to summary</a></p>
 259 <a id="m55"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testGetStatus</h2>
 260 <p class="totop"><a href="#summary">back to summary</a></p>
 261 <a id="m56"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testMultipleCancelLocally</h2>
 262 <div style="padding-left:3em">
 263 <p>null</p>
 264 java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 265 <br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 266 <br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 267 <br/>at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 268 <br/>at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
 269 <br/>23 lines not shown
 270 </div>
 271 <p class="totop"><a href="#summary">back to summary</a></p>
 272 <a id="m57"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testSubmitLocally</h2>
 273 <p class="totop"><a href="#summary">back to summary</a></p>
 274 <a id="m58"></a><h2>compbio.engine.local.LocalRunnerTester:testCancelCompletedTaskLocally</h2>
 275 <div style="padding-left:3em">
 276 <p>null</p>
 277 java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 278 <br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 279 <br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 280 <br/>at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 281 <br/>at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
 282 <br/>23 lines not shown
 283 </div>
 284 <p class="totop"><a href="#summary">back to summary</a></p>
 285 <a id="m59"></a><h2>compbio.engine.local.LocalRunnerTester:testCancelLocally</h2>
 286 <div style="padding-left:3em">
 287 <p>null</p>
 288 java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 289 <br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 290 <br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 291 <br/>at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 292 <br/>at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
 293 <br/>23 lines not shown
 294 </div>
 295 <p class="totop"><a href="#summary">back to summary</a></p>
 296 <a id="m60"></a><h2>compbio.engine.local.LocalRunnerTester:testMultipleCancelLocally</h2>
 297 <div style="padding-left:3em">
 298 <p>null</p>
 299 java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 300 <br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 301 <br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 302 <br/>at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 303 <br/>at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
 304 <br/>23 lines not shown
 305 </div>
 306 <p class="totop"><a href="#summary">back to summary</a></p>
 307 <a id="m61"></a><h2>compbio.metadata.OptionCombinatorTester:testgetAllOptions</h2>
 308 <p class="totop"><a href="#summary">back to summary</a></p>
 309 <a id="m62"></a><h2>compbio.metadata.OptionCombinatorTester:testgetAllParameters</h2>
 310 <p class="totop"><a href="#summary">back to summary</a></p>
 311 <a id="m63"></a><h2>compbio.metadata.OptionMarshallerTester:testMarshalling</h2>
 312 <div style="padding-left:3em">
 313 <p>null</p>
 314 com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:323)
 315 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
 316 <br/>at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
 317 <br/>at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
 318 <br/>at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
 319 <br/>23 lines not shown
 320 <p>Caused by cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.</p>
 321 com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
 322 <br/>at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
 323 <br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
 324 <br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
 325 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
 326 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
 327 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
 328 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
 329 <br/>at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
 330 <br/>at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
 331 <br/>at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:128)
 332 <br/>at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:106)
 333 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:310)
 334 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:699)
 335 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:69)
 336 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:172)
 337 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:159)
 338 <br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:344)
 339 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:597)
 340 <br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:328)
 341 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:498)
 342 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:320)
 343 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
 344 <br/>at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
 345 <br/>at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
 346 <br/>at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
 347 <br/>23 lines not shown
 348 </div>
 349 <p class="totop"><a href="#summary">back to summary</a></p>
 350 <a id="m64"></a><h2>compbio.metadata.OptionMarshallerTester:testUnMarshalling</h2>
 351 <p class="totop"><a href="#summary">back to summary</a></p>
 352 <a id="m65"></a><h2>compbio.metadata.PresetTester:marshallPreset</h2>
 353 <p class="totop"><a href="#summary">back to summary</a></p>
 354 <a id="m66"></a><h2>compbio.metadata.PresetTester:testPresetWithMuptiOptions</h2>
 355 <p class="totop"><a href="#summary">back to summary</a></p>
 356 <a id="m67"></a><h2>compbio.metadata.PresetTester:validatePresets</h2>
 357 <p class="totop"><a href="#summary">back to summary</a></p>
 358 <a id="m68"></a><h2>compbio.metadata.RunnerConfigTester:testCreateNumParameterWithoutValidValue</h2>
 359 <div style="padding-left:3em">
 360 <p>Attempting to set default value for parameter: Option name: Matrix
 361 Description: DNA weight matrix
 362 URL: null
 363 Is required: false
 364
 365  Without possible values! Please define possible value first!</p>
 366 compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
 367 <br/>at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
 368 <br/>23 lines not shown
 369 </div>
 370 <p class="totop"><a href="#summary">back to summary</a></p>
 371 <a id="m69"></a><h2>compbio.metadata.RunnerConfigTester:testCreateParameter</h2>
 372 <div style="padding-left:3em">
 373 <p>Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
 374 Description: Protein weight matrix
 375 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 376 Is required: true
 377 Option Names:
 378 --AAMATRIX
 379 POSSIBLE VALUES:
 380 BLOSUM
 381 GONNET
 382 ID
 383 PAM
 384
 385 </p>
 386 compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
 387 <br/>at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
 388 <br/>23 lines not shown
 389 </div>
 390 <p class="totop"><a href="#summary">back to summary</a></p>
 391 <a id="m70"></a><h2>compbio.metadata.RunnerConfigTester:testCreateParameterWithValidValueConstrain</h2>
 392 <p class="totop"><a href="#summary">back to summary</a></p>
 393 <a id="m71"></a><h2>compbio.metadata.RunnerConfigTester:testOptionNoDefaultValidate</h2>
 394 <div style="padding-left:3em">
 395 <p>Default value is required as multiple optionNames are defined for option: Option name: Matrix1
 396 Description: Protein weight matrix
 397 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 398 Is required: true
 399 Option Names:
 400 --AAMATRIX
 401 --ABMAT
 402 --BBBB
 403 </p>
 404 compbio.metadata.Option.validate(Option.java:317)
 405 <br/>at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
 406 <br/>23 lines not shown
 407 </div>
 408 <p class="totop"><a href="#summary">back to summary</a></p>
 409 <a id="m72"></a><h2>compbio.metadata.RunnerConfigTester:testOptionSetInvalidValue</h2>
 410 <div style="padding-left:3em">
 411 <p>Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
 412 Description: Protein weight matrix
 413 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 414 Is required: true
 415 Option Names:
 416 --AAMATRIX
 417 --ABMAT
 418 --BBBB
 419 </p>
 420 compbio.metadata.Option.setDefaultValue(Option.java:130)
 421 <br/>at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
 422 <br/>23 lines not shown
 423 </div>
 424 <p class="totop"><a href="#summary">back to summary</a></p>
 425 <a id="m73"></a><h2>compbio.metadata.RunnerConfigTester:testOptionToCommand</h2>
 426 <p class="totop"><a href="#summary">back to summary</a></p>
 427 <a id="m74"></a><h2>compbio.metadata.RunnerConfigTester:testParameterToCommand</h2>
 428 <p class="totop"><a href="#summary">back to summary</a></p>
 429 <a id="m75"></a><h2>compbio.metadata.RunnerConfigTester:testValidate</h2>
 430 <p class="totop"><a href="#summary">back to summary</a></p>
 431 <a id="m76"></a><h2>compbio.metadata.RunnerConfigTester:testValidateBoundaryConstrainCheck</h2>
 432 <p class="totop"><a href="#summary">back to summary</a></p>
 433 <a id="m77"></a><h2>compbio.metadata.RunnerConfigTester:testValidateLowerBoundaryConstrainCheck</h2>
 434 <div style="padding-left:3em">
 435 <p>Attempting to set default value outside boundaries defined by the constraint: Type: Float
 436 Min: -10.12
 437 Max: 0
 438
 439  For parameter: Option name: Matrix1
 440 Description: Protein weight matrix
 441 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 442 Is required: true
 443 Option Names:
 444 --AAMATRIX
 445 Type: Float
 446 Min: -10.12
 447 Max: 0
 448
 449 </p>
 450 compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
 451 <br/>at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
 452 <br/>23 lines not shown
 453 </div>
 454 <p class="totop"><a href="#summary">back to summary</a></p>
 455 <a id="m78"></a><h2>compbio.metadata.RunnerConfigTester:testValidateUpperBoundaryConstrainCheck</h2>
 456 <div style="padding-left:3em">
 457 <p>Attempting to set default value outside boundaries defined by the constraint: Type: Float
 458 Min: -10.12
 459 Max: 0
 460
 461  For parameter: Option name: Matrix1
 462 Description: Protein weight matrix
 463 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 464 Is required: true
 465 Option Names:
 466 --AAMATRIX
 467 Type: Float
 468 Min: -10.12
 469 Max: 0
 470
 471 </p>
 472 compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
 473 <br/>at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
 474 <br/>23 lines not shown
 475 </div>
 476 <p class="totop"><a href="#summary">back to summary</a></p>
 477 <a id="m79"></a><h2>compbio.metadata.RunnerConfigTester:testValidateValueConstrain</h2>
 478 <div style="padding-left:3em">
 479 <p>Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
 480 </p>
 481 compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
 482 <br/>at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
 483 <br/>23 lines not shown
 484 </div>
 485 <p class="totop"><a href="#summary">back to summary</a></p>
 486 <a id="m80"></a><h2>compbio.runner._impl.MclTester:testGetTestCommand</h2>
 487 <p class="totop"><a href="#summary">back to summary</a></p>
 488 <a id="m81"></a><h2>compbio.runner._impl.NetNglycTester:testGetTestCommand</h2>
 489 <p class="totop"><a href="#summary">back to summary</a></p>
 490 <a id="m82"></a><h2>compbio.runner._impl.OBTester:testGetTestArgsCommand</h2>
 491 <p class="totop"><a href="#summary">back to summary</a></p>
 492 <a id="m83"></a><h2>compbio.runner._impl.OBTester:testGetTestCommand</h2>
 493 <p class="totop"><a href="#summary">back to summary</a></p>
 494 <a id="m84"></a><h2>compbio.runner._impl.RPSBlastTester:testGetTestArgsCommand</h2>
 495 <p class="totop"><a href="#summary">back to summary</a></p>
 496 <a id="m85"></a><h2>compbio.runner._impl.RPSBlastTester:testGetTestCommand</h2>
 497 <p class="totop"><a href="#summary">back to summary</a></p>
 498 <a id="m86"></a><h2>compbio.runner._impl.RonnTester:testGetTestCommand</h2>
 499 <p class="totop"><a href="#summary">back to summary</a></p>
 500 <a id="m87"></a><h2>compbio.runner._impl.Tmhmm2Tester:testGetTestCommand</h2>
 501 <p class="totop"><a href="#summary">back to summary</a></p>
 502 <a id="m88"></a><h2>compbio.runner.conservation.AAConTester:readStatistics</h2>
 503 <p class="totop"><a href="#summary">back to summary</a></p>
 504 <a id="m89"></a><h2>compbio.runner.conservation.AAConTester:testConfigurationLoading</h2>
 505 <p class="totop"><a href="#summary">back to summary</a></p>
 506 <a id="m90"></a><h2>compbio.runner.conservation.AAConTester:testPersistance</h2>
 507 <p class="totop"><a href="#summary">back to summary</a></p>
 508 <a id="m91"></a><h2>compbio.runner.conservation.AAConTester:testRunLocally</h2>
 509 <p class="totop"><a href="#summary">back to summary</a></p>
 510 <a id="m92"></a><h2>compbio.runner.conservation.AAConTester:testRunLocallyOnTwoCpu</h2>
 511 <p class="totop"><a href="#summary">back to summary</a></p>
 512 <a id="m93"></a><h2>compbio.runner.conservation.AAConTester:testRunLocallyWithPreset</h2>
 513 <p class="totop"><a href="#summary">back to summary</a></p>
 514 <a id="m94"></a><h2>compbio.runner.conservation.AAConTester:testRunOnCluster</h2>
 515 <p class="totop"><a href="#summary">back to summary</a></p>
 516 <a id="m95"></a><h2>compbio.runner.conservation.AAConTester:testRunOnClusterAsync</h2>
 517 <p class="totop"><a href="#summary">back to summary</a></p>
 518 <a id="m96"></a><h2>compbio.runner.disorder.DisemblTester:readStatistics</h2>
 519 <p class="totop"><a href="#summary">back to summary</a></p>
 520 <a id="m97"></a><h2>compbio.runner.disorder.DisemblTester:testConfigurationLoading</h2>
 521 <p class="totop"><a href="#summary">back to summary</a></p>
 522 <a id="m98"></a><h2>compbio.runner.disorder.DisemblTester:testPersistance</h2>
 523 <p class="totop"><a href="#summary">back to summary</a></p>
 524 <a id="m99"></a><h2>compbio.runner.disorder.DisemblTester:testRunLocally</h2>
 525 <p class="totop"><a href="#summary">back to summary</a></p>
 526 <a id="m100"></a><h2>compbio.runner.disorder.DisemblTester:testRunOnCluster</h2>
 527 <p class="totop"><a href="#summary">back to summary</a></p>
 528 <a id="m101"></a><h2>compbio.runner.disorder.DisemblTester:testRunOnClusterAsync</h2>
 529 <p class="totop"><a href="#summary">back to summary</a></p>
 530 <a id="m102"></a><h2>compbio.runner.disorder.GlobPlotTester:readStatistics</h2>
 531 <p class="totop"><a href="#summary">back to summary</a></p>
 532 <a id="m103"></a><h2>compbio.runner.disorder.GlobPlotTester:testConfigurationLoading</h2>
 533 <p class="totop"><a href="#summary">back to summary</a></p>
 534 <a id="m104"></a><h2>compbio.runner.disorder.GlobPlotTester:testPersistance</h2>
 535 <p class="totop"><a href="#summary">back to summary</a></p>
 536 <a id="m105"></a><h2>compbio.runner.disorder.GlobPlotTester:testRunLocally</h2>
 537 <p class="totop"><a href="#summary">back to summary</a></p>
 538 <a id="m106"></a><h2>compbio.runner.disorder.GlobPlotTester:testRunOnCluster</h2>
 539 <p class="totop"><a href="#summary">back to summary</a></p>
 540 <a id="m107"></a><h2>compbio.runner.disorder.GlobPlotTester:testRunOnClusterAsync</h2>
 541 <p class="totop"><a href="#summary">back to summary</a></p>
 542 <a id="m108"></a><h2>compbio.runner.disorder.IUPredTester:testConfigurationLoading</h2>
 543 <p class="totop"><a href="#summary">back to summary</a></p>
 544 <a id="m109"></a><h2>compbio.runner.disorder.IUPredTester:testPersistance</h2>
 545 <p class="totop"><a href="#summary">back to summary</a></p>
 546 <a id="m110"></a><h2>compbio.runner.disorder.IUPredTester:testReadResults</h2>
 547 <p class="totop"><a href="#summary">back to summary</a></p>
 548 <a id="m111"></a><h2>compbio.runner.disorder.IUPredTester:testRunLocally</h2>
 549 <p class="totop"><a href="#summary">back to summary</a></p>
 550 <a id="m112"></a><h2>compbio.runner.disorder.IUPredTester:testRunLocallyWithParams</h2>
 551 <p class="totop"><a href="#summary">back to summary</a></p>
 552 <a id="m113"></a><h2>compbio.runner.disorder.IUPredTester:testRunOnCluster</h2>
 553 <p class="totop"><a href="#summary">back to summary</a></p>
 554 <a id="m114"></a><h2>compbio.runner.disorder.IUPredTester:testRunOnClusterAsync</h2>
 555 <p class="totop"><a href="#summary">back to summary</a></p>
 556 <a id="m115"></a><h2>compbio.runner.disorder.IUPredTester:testSetParameter</h2>
 557 <p class="totop"><a href="#summary">back to summary</a></p>
 558 <a id="m116"></a><h2>compbio.runner.disorder.JronnTester:readStatistics</h2>
 559 <p class="totop"><a href="#summary">back to summary</a></p>
 560 <a id="m117"></a><h2>compbio.runner.disorder.JronnTester:testConfigurationLoading</h2>
 561 <p class="totop"><a href="#summary">back to summary</a></p>
 562 <a id="m118"></a><h2>compbio.runner.disorder.JronnTester:testPersistance</h2>
 563 <p class="totop"><a href="#summary">back to summary</a></p>
 564 <a id="m119"></a><h2>compbio.runner.disorder.JronnTester:testRunLocally</h2>
 565 <p class="totop"><a href="#summary">back to summary</a></p>
 566 <a id="m120"></a><h2>compbio.runner.disorder.JronnTester:testRunLocallyOnTwoCpu</h2>
 567 <p class="totop"><a href="#summary">back to summary</a></p>
 568 <a id="m121"></a><h2>compbio.runner.disorder.JronnTester:testRunOnCluster</h2>
 569 <p class="totop"><a href="#summary">back to summary</a></p>
 570 <a id="m122"></a><h2>compbio.runner.disorder.JronnTester:testRunOnClusterAsync</h2>
 571 <p class="totop"><a href="#summary">back to summary</a></p>
 572 <a id="m123"></a><h2>compbio.runner.msa.ClustalWParametersTester:testArguments</h2>
 573 <p class="totop"><a href="#summary">back to summary</a></p>
 574 <a id="m124"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConfiguration</h2>
 575 <p class="totop"><a href="#summary">back to summary</a></p>
 576 <a id="m125"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersMaxValues</h2>
 577 <p class="totop"><a href="#summary">back to summary</a></p>
 578 <a id="m126"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersMinValues</h2>
 579 <p class="totop"><a href="#summary">back to summary</a></p>
 580 <a id="m127"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersRandomValues</h2>
 581 <p class="totop"><a href="#summary">back to summary</a></p>
 582 <a id="m128"></a><h2>compbio.runner.msa.ClustalWParametersTester:testDefaultParameters</h2>
 583 <p class="totop"><a href="#summary">back to summary</a></p>
 584 <a id="m129"></a><h2>compbio.runner.msa.ClustalWParametersTester:testOptions</h2>
 585 <p class="totop"><a href="#summary">back to summary</a></p>
 586 <a id="m130"></a><h2>compbio.runner.msa.ClustalWParametersTester:testParameters</h2>
 587 <p class="totop"><a href="#summary">back to summary</a></p>
 588 <a id="m131"></a><h2>compbio.runner.msa.ClustalWParametersTester:testPresets</h2>
 589 <p class="totop"><a href="#summary">back to summary</a></p>
 590 <a id="m132"></a><h2>compbio.runner.msa.ClustalWTester:readStatistics</h2>
 591 <p class="totop"><a href="#summary">back to summary</a></p>
 592 <a id="m133"></a><h2>compbio.runner.msa.ClustalWTester:readStatisticsClusterExecution</h2>
 593 <p class="totop"><a href="#summary">back to summary</a></p>
 594 <a id="m134"></a><h2>compbio.runner.msa.ClustalWTester:testConfigurationLoading</h2>
 595 <p class="totop"><a href="#summary">back to summary</a></p>
 596 <a id="m135"></a><h2>compbio.runner.msa.ClustalWTester:testOptionsLocally</h2>
 597 <p class="totop"><a href="#summary">back to summary</a></p>
 598 <a id="m136"></a><h2>compbio.runner.msa.ClustalWTester:testPersistance</h2>
 599 <p class="totop"><a href="#summary">back to summary</a></p>
 600 <a id="m137"></a><h2>compbio.runner.msa.ClustalWTester:testRunLocally</h2>
 601 <p class="totop"><a href="#summary">back to summary</a></p>
 602 <a id="m138"></a><h2>compbio.runner.msa.ClustalWTester:testRunOnCluster</h2>
 603 <p class="totop"><a href="#summary">back to summary</a></p>
 604 <a id="m139"></a><h2>compbio.runner.msa.ClustalWTester:testRunWithMatrix</h2>
 605 <p class="totop"><a href="#summary">back to summary</a></p>
 606 <a id="m140"></a><h2>compbio.runner.msa.LimitTester:testLimitExceeded</h2>
 607 <p class="totop"><a href="#summary">back to summary</a></p>
 608 <a id="m141"></a><h2>compbio.runner.msa.LimitTester:testLoadLimits</h2>
 609 <p class="totop"><a href="#summary">back to summary</a></p>
 610 <a id="m142"></a><h2>compbio.runner.msa.MafftParametersTester:testArguments</h2>
 611 <p class="totop"><a href="#summary">back to summary</a></p>
 612 <a id="m143"></a><h2>compbio.runner.msa.MafftParametersTester:testConfiguration</h2>
 613 <p class="totop"><a href="#summary">back to summary</a></p>
 614 <a id="m144"></a><h2>compbio.runner.msa.MafftParametersTester:testConstrainedParametersMaxValues</h2>
 615 <p class="totop"><a href="#summary">back to summary</a></p>
 616 <a id="m145"></a><h2>compbio.runner.msa.MafftParametersTester:testConstrainedParametersMinValues</h2>
 617 <p class="totop"><a href="#summary">back to summary</a></p>
 618 <a id="m146"></a><h2>compbio.runner.msa.MafftParametersTester:testConstrainedParametersRandomValues</h2>
 619 <p class="totop"><a href="#summary">back to summary</a></p>
 620 <a id="m147"></a><h2>compbio.runner.msa.MafftParametersTester:testDefaultParameters</h2>
 621 <p class="totop"><a href="#summary">back to summary</a></p>
 622 <a id="m148"></a><h2>compbio.runner.msa.MafftParametersTester:testOptions</h2>
 623 <p class="totop"><a href="#summary">back to summary</a></p>
 624 <a id="m149"></a><h2>compbio.runner.msa.MafftParametersTester:testParameters</h2>
 625 <p class="totop"><a href="#summary">back to summary</a></p>
 626 <a id="m150"></a><h2>compbio.runner.msa.MafftParametersTester:testPresets</h2>
 627 <p class="totop"><a href="#summary">back to summary</a></p>
 628 <a id="m151"></a><h2>compbio.runner.msa.MafftTester:readStatistics</h2>
 629 <p class="totop"><a href="#summary">back to summary</a></p>
 630 <a id="m152"></a><h2>compbio.runner.msa.MafftTester:testClusterExecute</h2>
 631 <p class="totop"><a href="#summary">back to summary</a></p>
 632 <a id="m153"></a><h2>compbio.runner.msa.MafftTester:testConfigurationLoading</h2>
 633 <p class="totop"><a href="#summary">back to summary</a></p>
 634 <a id="m154"></a><h2>compbio.runner.msa.MafftTester:testExecute</h2>
 635 <p class="totop"><a href="#summary">back to summary</a></p>
 636 <a id="m155"></a><h2>compbio.runner.msa.MafftTester:testPersistance</h2>
 637 <p class="totop"><a href="#summary">back to summary</a></p>
 638 <a id="m156"></a><h2>compbio.runner.msa.MafftTester:testRunOnClusterAsyncCheckStatusLongPoolingTime</h2>
 639 <p class="totop"><a href="#summary">back to summary</a></p>
 640 <a id="m157"></a><h2>compbio.runner.msa.MafftTester:testSetInputTester</h2>
 641 <p class="totop"><a href="#summary">back to summary</a></p>
 642 <a id="m158"></a><h2>compbio.runner.msa.MuscleParametersTester:testArguments</h2>
 643 <p class="totop"><a href="#summary">back to summary</a></p>
 644 <a id="m159"></a><h2>compbio.runner.msa.MuscleParametersTester:testConfiguration</h2>
 645 <p class="totop"><a href="#summary">back to summary</a></p>
 646 <a id="m160"></a><h2>compbio.runner.msa.MuscleParametersTester:testConstrainedParametersMaxValues</h2>
 647 <p class="totop"><a href="#summary">back to summary</a></p>
 648 <a id="m161"></a><h2>compbio.runner.msa.MuscleParametersTester:testConstrainedParametersMinValues</h2>
 649 <p class="totop"><a href="#summary">back to summary</a></p>
 650 <a id="m162"></a><h2>compbio.runner.msa.MuscleParametersTester:testConstrainedParametersRandomValues</h2>
 651 <p class="totop"><a href="#summary">back to summary</a></p>
 652 <a id="m163"></a><h2>compbio.runner.msa.MuscleParametersTester:testDefaultParameters</h2>
 653 <p class="totop"><a href="#summary">back to summary</a></p>
 654 <a id="m164"></a><h2>compbio.runner.msa.MuscleParametersTester:testOptions</h2>
 655 <p class="totop"><a href="#summary">back to summary</a></p>
 656 <a id="m165"></a><h2>compbio.runner.msa.MuscleParametersTester:testParameters</h2>
 657 <p class="totop"><a href="#summary">back to summary</a></p>
 658 <a id="m166"></a><h2>compbio.runner.msa.MuscleParametersTester:testPresets</h2>
 659 <p class="totop"><a href="#summary">back to summary</a></p>
 660 <a id="m167"></a><h2>compbio.runner.msa.MuscleTester:readStatistics</h2>
 661 <p class="totop"><a href="#summary">back to summary</a></p>
 662 <a id="m168"></a><h2>compbio.runner.msa.MuscleTester:testConfigurationLoading</h2>
 663 <p class="totop"><a href="#summary">back to summary</a></p>
 664 <a id="m169"></a><h2>compbio.runner.msa.MuscleTester:testPersistance</h2>
 665 <p class="totop"><a href="#summary">back to summary</a></p>
 666 <a id="m170"></a><h2>compbio.runner.msa.MuscleTester:testRunLocally</h2>
 667 <p class="totop"><a href="#summary">back to summary</a></p>
 668 <a id="m171"></a><h2>compbio.runner.msa.MuscleTester:testRunOnCluster</h2>
 669 <p class="totop"><a href="#summary">back to summary</a></p>
 670 <a id="m172"></a><h2>compbio.runner.msa.ProbconsParametersTester:testArguments</h2>
 671 <p class="totop"><a href="#summary">back to summary</a></p>
 672 <a id="m173"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConfiguration</h2>
 673 <p class="totop"><a href="#summary">back to summary</a></p>
 674 <a id="m174"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersMaxValues</h2>
 675 <p class="totop"><a href="#summary">back to summary</a></p>
 676 <a id="m175"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersMinValues</h2>
 677 <p class="totop"><a href="#summary">back to summary</a></p>
 678 <a id="m176"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersRandomValues</h2>
 679 <p class="totop"><a href="#summary">back to summary</a></p>
 680 <a id="m177"></a><h2>compbio.runner.msa.ProbconsParametersTester:testDefaultParameters</h2>
 681 <p class="totop"><a href="#summary">back to summary</a></p>
 682 <a id="m178"></a><h2>compbio.runner.msa.ProbconsParametersTester:testOptions</h2>
 683 <p class="totop"><a href="#summary">back to summary</a></p>
 684 <a id="m179"></a><h2>compbio.runner.msa.ProbconsParametersTester:testParameters</h2>
 685 <p class="totop"><a href="#summary">back to summary</a></p>
 686 <a id="m180"></a><h2>compbio.runner.msa.ProbconsTester:readStatistics</h2>
 687 <p class="totop"><a href="#summary">back to summary</a></p>
 688 <a id="m181"></a><h2>compbio.runner.msa.ProbconsTester:testClusterExecute</h2>
 689 <p class="totop"><a href="#summary">back to summary</a></p>
 690 <a id="m182"></a><h2>compbio.runner.msa.ProbconsTester:testConfigurationLoading</h2>
 691 <p class="totop"><a href="#summary">back to summary</a></p>
 692 <a id="m183"></a><h2>compbio.runner.msa.ProbconsTester:testExecute</h2>
 693 <p class="totop"><a href="#summary">back to summary</a></p>
 694 <a id="m184"></a><h2>compbio.runner.msa.ProbconsTester:testPersistance</h2>
 695 <p class="totop"><a href="#summary">back to summary</a></p>
 696 <a id="m185"></a><h2>compbio.runner.msa.ProbconsTester:testSetInputTester</h2>
 697 <p class="totop"><a href="#summary">back to summary</a></p>
 698 <a id="m186"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testArguments</h2>
 699 <p class="totop"><a href="#summary">back to summary</a></p>
 700 <a id="m187"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConfiguration</h2>
 701 <p class="totop"><a href="#summary">back to summary</a></p>
 702 <a id="m188"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersMaxValues</h2>
 703 <p class="totop"><a href="#summary">back to summary</a></p>
 704 <a id="m189"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersMinValues</h2>
 705 <p class="totop"><a href="#summary">back to summary</a></p>
 706 <a id="m190"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersRandomValues</h2>
 707 <p class="totop"><a href="#summary">back to summary</a></p>
 708 <a id="m191"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testDefaultParameters</h2>
 709 <p class="totop"><a href="#summary">back to summary</a></p>
 710 <a id="m192"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testOptions</h2>
 711 <p class="totop"><a href="#summary">back to summary</a></p>
 712 <a id="m193"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testParameters</h2>
 713 <p class="totop"><a href="#summary">back to summary</a></p>
 714 <a id="m194"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testPresets</h2>
 715 <p class="totop"><a href="#summary">back to summary</a></p>
 716 <a id="m195"></a><h2>compbio.runner.msa.TcoffeeTester:readStatistics</h2>
 717 <p class="totop"><a href="#summary">back to summary</a></p>
 718 <a id="m196"></a><h2>compbio.runner.msa.TcoffeeTester:testClusterExecute</h2>
 719 <p class="totop"><a href="#summary">back to summary</a></p>
 720 <a id="m197"></a><h2>compbio.runner.msa.TcoffeeTester:testConfigurationLoading</h2>
 721 <p class="totop"><a href="#summary">back to summary</a></p>
 722 <a id="m198"></a><h2>compbio.runner.msa.TcoffeeTester:testExecute</h2>
 723 <p class="totop"><a href="#summary">back to summary</a></p>
 724 <a id="m199"></a><h2>compbio.runner.msa.TcoffeeTester:testNcore</h2>
 725 <p class="totop"><a href="#summary">back to summary</a></p>
 726 <a id="m200"></a><h2>compbio.runner.msa.TcoffeeTester:testPersistance</h2>
 727 <p class="totop"><a href="#summary">back to summary</a></p>
 728 <a id="m201"></a><h2>compbio.stat.collector.ExecutionStatCollectorTester:testCollectStat</h2>
 729 <p class="totop"><a href="#summary">back to summary</a></p>
 730 <a id="m202"></a><h2>compbio.stat.collector.ExecutionStatCollectorTester:testHasCompleted</h2>
 731 <p class="totop"><a href="#summary">back to summary</a></p>
 732 <a id="m203"></a><h2>compbio.stat.collector.ExecutionStatCollectorTester:testUpdateStatTester</h2>
 733 <p class="totop"><a href="#summary">back to summary</a></p>
 734 <a id="m204"></a><h2>compbio.stat.collector.StatDBTester:testVerifyJobsCount</h2>
 735 <p class="totop"><a href="#summary">back to summary</a></p>
 736 <a id="m205"></a><h2>compbio.stat.servlet.util.StatCollectionTester:testGetStats</h2>
 737 <p class="totop"><a href="#summary">back to summary</a></p>
 738 </body></html>