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">154</td><td class="numi">165</td><td class="numi">0</td><td class="numi">0</td><td class="numi">524.4 seconds</td><td class="numi"></td><td class="numi">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">22</td></tr><tr class="passedodd"><td><a href="#m2"><b>testReadClustalFileLongNames</b>  </a></td><td class="numi">1</td><td class="numi">52</td></tr><tr class="passedodd"><td><a href="#m3"><b>testReadClustalFileShortNames</b>  </a></td><td class="numi">1</td><td class="numi">54</td></tr>
  39 <tr class="passedeven"><td rowspan="1">compbio.data.sequence.FastaSequenceGeneratorTester<td><a href="#m4"><b>testProteinSequenceGeneration</b>  </a></td><td class="numi">1</td><td class="numi">8</td></tr>
  40 <tr class="passedodd"><td rowspan="1">compbio.data.sequence.FastaSequenceTester<td><a href="#m5"><b>testGetFormattedFasta</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  41 <tr class="passedeven"><td rowspan="5">compbio.data.sequence.SequenceUtilTester<td><a href="#m6"><b>testCleanSequence</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m7"><b>testDeepCleanSequence</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m8"><b>testReadWriteFasta</b>  </a></td><td class="numi">1</td><td class="numi">16</td></tr><tr class="passedeven"><td><a href="#m9"><b>testisNonAmbNucleotideSequence</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m10"><b>testisProteinSequence</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  42 <tr class="passedodd"><td rowspan="2">compbio.engine.EngineConfiguratorTester<td><a href="#m11"><b>testGetAsyncEngine</b>  </a></td><td class="numi">1</td><td class="numi">296</td></tr><tr class="passedodd"><td><a href="#m12"><b>testGetSyncEngine</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  43 <tr class="passedeven"><td rowspan="4">compbio.engine.FilePullerTester<td><a href="#m13"><b>testCache</b> (engine) </a></td><td class="numi">1</td><td class="numi">6006</td></tr><tr class="passedeven"><td><a href="#m14"><b>testGet</b>  </a></td><td class="numi">1</td><td class="numi">46</td></tr><tr class="passedeven"><td><a href="#m15"><b>testGetDelay</b> (engine) </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m16"><b>testPull</b> (engine) </a></td><td class="numi">1</td><td class="numi">450</td></tr>
  44 <tr class="passedodd"><td rowspan="1">compbio.engine.PulledFileCacheTester<td><a href="#m17"><b>test</b>  </a></td><td class="numi">1</td><td class="numi">5187</td></tr>
  45 <tr class="passedeven"><td rowspan="3">compbio.engine.client.CommandBuilderTester<td><a href="#m18"><b>testCommandBuilding</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedeven"><td><a href="#m19"><b>testOptionsToCommand</b>  </a></td><td class="numi">1</td><td class="numi">567</td></tr><tr class="passedeven"><td><a href="#m20"><b>testSpaceDelimiterExecutable</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  46 <tr class="passedodd"><td rowspan="2">compbio.engine.client.PathValidatorTester<td><a href="#m21"><b>testGetClassPath</b>  </a></td><td class="numi">1</td><td class="numi">234</td></tr><tr class="passedodd"><td><a href="#m22"><b>testIsAbsolutePath</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  47 <tr class="passedeven"><td rowspan="1">compbio.engine.cluster.drmaa.ClusterSessionTester<td><a href="#m23"><b>testTaskList</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">8964</td></tr>
  48 <tr class="passedodd"><td rowspan="3">compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester<td><a href="#m24"><b>testCancel</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">1273</td></tr><tr class="passedodd"><td><a href="#m25"><b>testGetJobStatus</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">20778</td></tr><tr class="passedodd"><td><a href="#m26"><b>testSubmit</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">18714</td></tr>
  49 <tr class="passedeven"><td rowspan="2">compbio.engine.cluster.drmaa.DrmaaClusterEngineTester<td><a href="#m27"><b>testCancel</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">1587</td></tr><tr class="passedeven"><td><a href="#m28"><b>testSubmit</b> (engine, cluster) </a></td><td class="numi">1</td><td class="numi">17835</td></tr>
  50 <tr class="passedodd"><td rowspan="1">compbio.engine.cluster.drmaa.UtilTester<td><a href="#m29"><b>testParser</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  51 <tr class="passedeven"><td rowspan="1">compbio.engine.cluster.dundee._QueueTester<td><a href="#m30"><b>testQueue</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  52 <tr class="passedodd"><td rowspan="1">compbio.engine.conf.DirectoryManagerTester<td><a href="#m31"><b>testGetDirectory</b>  </a></td><td class="numi">4</td><td class="numi">111</td></tr>
  53 <tr class="passedeven"><td rowspan="5">compbio.engine.conf.PropertyHelperManagerTester<td><a href="#m32"><b>testClusterEngineConf</b> (cluster) </a></td><td class="numi">1</td><td class="numi">104</td></tr><tr class="passedeven"><td><a href="#m33"><b>validateClustalConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">43</td></tr><tr class="passedeven"><td><a href="#m34"><b>validateMafftConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedeven"><td><a href="#m35"><b>validateMuscleConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">4</td></tr><tr class="passedeven"><td><a href="#m36"><b>validateTcoffeeConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">4</td></tr>
  54 <tr class="passedodd"><td rowspan="5">compbio.engine.conf.RunnerConfigMarshallerTester<td><a href="#m37"><b>testMarshalling</b>  </a></td><td class="numi">1</td><td class="numi">20</td></tr><tr class="passedodd"><td><a href="#m38"><b>testSchemaFromCodeGeneration</b>  </a></td><td class="numi">1</td><td class="numi">504</td></tr><tr class="passedodd"><td><a href="#m39"><b>testUnMarshalling</b>  </a></td><td class="numi">1</td><td class="numi">580</td></tr><tr class="passedodd"><td><a href="#m40"><b>testValidation</b>  </a></td><td class="numi">1</td><td class="numi">636</td></tr><tr class="passedodd"><td><a href="#m41"><b>testValidationOnMarshalling</b>  </a></td><td class="numi">1</td><td class="numi">11</td></tr>
  55 <tr class="passedeven"><td rowspan="7">compbio.engine.local.AsyncLocalRunnerTester<td><a href="#m42"><b>testAsyncCancelOperation</b> (engine) </a></td><td class="numi">1</td><td class="numi">48</td></tr><tr class="passedeven"><td><a href="#m43"><b>testAsyncRetrievOperation</b> (engine) </a></td><td class="numi">1</td><td class="numi">560</td></tr><tr class="passedeven"><td><a href="#m44"><b>testCancelCompletedTaskLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">3053</td></tr><tr class="passedeven"><td><a href="#m45"><b>testCancelLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">27</td></tr><tr class="passedeven"><td><a href="#m46"><b>testGetStatus</b> (engine) </a></td><td class="numi">5</td><td class="numi">41735</td></tr><tr class="passedeven"><td><a href="#m47"><b>testMultipleCancelLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">267</td></tr><tr class="passedeven"><td><a href="#m48"><b>testSubmitLocally</b> (engine) </a></td><td class="numi">5</td><td class="numi">634</td></tr>
  56 <tr class="passedodd"><td rowspan="3">compbio.engine.local.LocalRunnerTester<td><a href="#m49"><b>testCancelCompletedTaskLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">336</td></tr><tr class="passedodd"><td><a href="#m50"><b>testCancelLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">20</td></tr><tr class="passedodd"><td><a href="#m51"><b>testMultipleCancelLocally</b> (engine) </a></td><td class="numi">1</td><td class="numi">58</td></tr>
  57 <tr class="passedeven"><td rowspan="2">compbio.metadata.OptionCombinatorTester<td><a href="#m52"><b>testgetAllOptions</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedeven"><td><a href="#m53"><b>testgetAllParameters</b>  </a></td><td class="numi">1</td><td class="numi">3</td></tr>
  58 <tr class="passedodd"><td rowspan="2">compbio.metadata.OptionMarshallerTester<td><a href="#m54"><b>testMarshalling</b>  </a></td><td class="numi">1</td><td class="numi">58</td></tr><tr class="passedodd"><td><a href="#m55"><b>testUnMarshalling</b>  </a></td><td class="numi">1</td><td class="numi">386</td></tr>
  59 <tr class="passedeven"><td rowspan="2">compbio.metadata.PresetTester<td><a href="#m56"><b>marshallPreset</b>  </a></td><td class="numi">1</td><td class="numi">899</td></tr><tr class="passedeven"><td><a href="#m57"><b>validatePresets</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr>
  60 <tr class="passedodd"><td rowspan="12">compbio.metadata.RunnerConfigTester<td><a href="#m58"><b>testCreateNumParameterWithoutValidValue</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedodd"><td><a href="#m59"><b>testCreateParameter</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m60"><b>testCreateParameterWithValidValueConstrain</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m61"><b>testOptionNoDefaultValidate</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m62"><b>testOptionSetInvalidValue</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedodd"><td><a href="#m63"><b>testOptionToCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m64"><b>testParameterToCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m65"><b>testValidate</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m66"><b>testValidateBoundaryConstrainCheck</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedodd"><td><a href="#m67"><b>testValidateLowerBoundaryConstrainCheck</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m68"><b>testValidateUpperBoundaryConstrainCheck</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m69"><b>testValidateValueConstrain</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  61 <tr class="passedeven"><td rowspan="1">compbio.runner._impl.MclTester<td><a href="#m70"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr>
  62 <tr class="passedodd"><td rowspan="1">compbio.runner._impl.NetNglycTester<td><a href="#m71"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  63 <tr class="passedeven"><td rowspan="2">compbio.runner._impl.OBTester<td><a href="#m72"><b>testGetTestArgsCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedeven"><td><a href="#m73"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  64 <tr class="passedodd"><td rowspan="2">compbio.runner._impl.RPSBlastTester<td><a href="#m74"><b>testGetTestArgsCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m75"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  65 <tr class="passedeven"><td rowspan="1">compbio.runner._impl.RonnTester<td><a href="#m76"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  66 <tr class="passedodd"><td rowspan="1">compbio.runner._impl.Tmhmm2Tester<td><a href="#m77"><b>testGetTestCommand</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  67 <tr class="passedeven"><td rowspan="9">compbio.runner.msa.ClustalWParametersTester<td><a href="#m78"><b>testArguments</b> (runner) </a></td><td class="numi">1</td><td class="numi">3518</td></tr><tr class="passedeven"><td><a href="#m79"><b>testConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedeven"><td><a href="#m80"><b>testConstrainedParametersMaxValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">1835</td></tr><tr class="passedeven"><td><a href="#m81"><b>testConstrainedParametersMinValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">1232</td></tr><tr class="passedeven"><td><a href="#m82"><b>testConstrainedParametersRandomValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">3105</td></tr><tr class="passedeven"><td><a href="#m83"><b>testDefaultParameters</b> (runner) </a></td><td class="numi">1</td><td class="numi">502</td></tr><tr class="passedeven"><td><a href="#m84"><b>testOptions</b> (runner) </a></td><td class="numi">1</td><td class="numi">2109</td></tr><tr class="passedeven"><td><a href="#m85"><b>testParameters</b> (runner) </a></td><td class="numi">1</td><td class="numi">2680</td></tr><tr class="passedeven"><td><a href="#m86"><b>testPresets</b> (runner) </a></td><td class="numi">1</td><td class="numi">177</td></tr>
  68 <tr class="passedodd"><td rowspan="8">compbio.runner.msa.ClustalWTester<td><a href="#m87"><b>readStatistics</b> (runner) </a></td><td class="numi">1</td><td class="numi">1178</td></tr><tr class="passedodd"><td><a href="#m88"><b>readStatisticsClusterExecution</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">8121</td></tr><tr class="passedodd"><td><a href="#m89"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">688</td></tr><tr class="passedodd"><td><a href="#m90"><b>testOptionsLocally</b> (runner) </a></td><td class="numi">1</td><td class="numi">1932</td></tr><tr class="passedodd"><td><a href="#m91"><b>testPersistance</b> (runner) </a></td><td class="numi">1</td><td class="numi">431</td></tr><tr class="passedodd"><td><a href="#m92"><b>testRunLocally</b> (runner) </a></td><td class="numi">1</td><td class="numi">171</td></tr><tr class="passedodd"><td><a href="#m93"><b>testRunOnCluster</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">15937</td></tr><tr class="passedodd"><td><a href="#m94"><b>testRunWithMatrix</b> (runner) </a></td><td class="numi">1</td><td class="numi">824</td></tr>
  69 <tr class="passedeven"><td rowspan="1">compbio.runner.msa.LimitTester<td><a href="#m95"><b>testLoadLimits</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  70 <tr class="passedodd"><td rowspan="9">compbio.runner.msa.MafftParametersTester<td><a href="#m96"><b>testArguments</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">6103</td></tr><tr class="passedodd"><td><a href="#m97"><b>testConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedodd"><td><a href="#m98"><b>testConstrainedParametersMaxValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">3235</td></tr><tr class="passedodd"><td><a href="#m99"><b>testConstrainedParametersMinValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">1326</td></tr><tr class="passedodd"><td><a href="#m100"><b>testConstrainedParametersRandomValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">7672</td></tr><tr class="passedodd"><td><a href="#m101"><b>testDefaultParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">20463</td></tr><tr class="passedodd"><td><a href="#m102"><b>testOptions</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">4449</td></tr><tr class="passedodd"><td><a href="#m103"><b>testParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">2422</td></tr><tr class="passedodd"><td><a href="#m104"><b>testPresets</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">2136</td></tr>
  71 <tr class="passedeven"><td rowspan="7">compbio.runner.msa.MafftTester<td><a href="#m105"><b>readStatistics</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">639</td></tr><tr class="passedeven"><td><a href="#m106"><b>testClusterExecute</b> (cluster, runner, non_windows) </a></td><td class="numi">1</td><td class="numi">11340</td></tr><tr class="passedeven"><td><a href="#m107"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">435</td></tr><tr class="passedeven"><td><a href="#m108"><b>testExecute</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">428</td></tr><tr class="passedeven"><td><a href="#m109"><b>testPersistance</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">1033</td></tr><tr class="passedeven"><td><a href="#m110"><b>testRunOnClusterAsyncCheckStatusLongPoolingTime</b> (cluster, runner, non_windows) </a></td><td class="numi">1</td><td class="numi">21418</td></tr><tr class="passedeven"><td><a href="#m111"><b>testSetInputTester</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  72 <tr class="passedodd"><td rowspan="9">compbio.runner.msa.MuscleParametersTester<td><a href="#m112"><b>testArguments</b> (runner) </a></td><td class="numi">1</td><td class="numi">7798</td></tr><tr class="passedodd"><td><a href="#m113"><b>testConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m114"><b>testConstrainedParametersMaxValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">1534</td></tr><tr class="passedodd"><td><a href="#m115"><b>testConstrainedParametersMinValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">845</td></tr><tr class="passedodd"><td><a href="#m116"><b>testConstrainedParametersRandomValues</b> (runner) </a></td><td class="numi">1</td><td class="numi">7603</td></tr><tr class="passedodd"><td><a href="#m117"><b>testDefaultParameters</b> (runner) </a></td><td class="numi">1</td><td class="numi">622</td></tr><tr class="passedodd"><td><a href="#m118"><b>testOptions</b> (runner) </a></td><td class="numi">1</td><td class="numi">2481</td></tr><tr class="passedodd"><td><a href="#m119"><b>testParameters</b> (runner) </a></td><td class="numi">1</td><td class="numi">4773</td></tr><tr class="passedodd"><td><a href="#m120"><b>testPresets</b> (runner) </a></td><td class="numi">1</td><td class="numi">856</td></tr>
  73 <tr class="passedeven"><td rowspan="5">compbio.runner.msa.MuscleTester<td><a href="#m121"><b>readStatistics</b> (runner) </a></td><td class="numi">1</td><td class="numi">932</td></tr><tr class="passedeven"><td><a href="#m122"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">313</td></tr><tr class="passedeven"><td><a href="#m123"><b>testPersistance</b> (runner) </a></td><td class="numi">1</td><td class="numi">241</td></tr><tr class="passedeven"><td><a href="#m124"><b>testRunLocally</b> (runner) </a></td><td class="numi">1</td><td class="numi">101</td></tr><tr class="passedeven"><td><a href="#m125"><b>testRunOnCluster</b> (cluster, runner) </a></td><td class="numi">1</td><td class="numi">8142</td></tr>
  74 <tr class="passedodd"><td rowspan="8">compbio.runner.msa.ProbconsParametersTester<td><a href="#m126"><b>testArguments</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">2874</td></tr><tr class="passedodd"><td><a href="#m127"><b>testConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedodd"><td><a href="#m128"><b>testConstrainedParametersMaxValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">38416</td></tr><tr class="passedodd"><td><a href="#m129"><b>testConstrainedParametersMinValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">768</td></tr><tr class="passedodd"><td><a href="#m130"><b>testConstrainedParametersRandomValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">61881</td></tr><tr class="passedodd"><td><a href="#m131"><b>testDefaultParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">14704</td></tr><tr class="passedodd"><td><a href="#m132"><b>testOptions</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">433</td></tr><tr class="passedodd"><td><a href="#m133"><b>testParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">1321</td></tr>
  75 <tr class="passedeven"><td rowspan="6">compbio.runner.msa.ProbconsTester<td><a href="#m134"><b>readStatistics</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">441</td></tr><tr class="passedeven"><td><a href="#m135"><b>testClusterExecute</b> (cluster, runner, non_windows) </a></td><td class="numi">1</td><td class="numi">19326</td></tr><tr class="passedeven"><td><a href="#m136"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">107</td></tr><tr class="passedeven"><td><a href="#m137"><b>testExecute</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">436</td></tr><tr class="passedeven"><td><a href="#m138"><b>testPersistance</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">509</td></tr><tr class="passedeven"><td><a href="#m139"><b>testSetInputTester</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">0</td></tr>
  76 <tr class="passedodd"><td rowspan="9">compbio.runner.msa.TcoffeeParametersTester<td><a href="#m140"><b>testArguments</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">8765</td></tr><tr class="passedodd"><td><a href="#m141"><b>testConfiguration</b>  </a></td><td class="numi">1</td><td class="numi">0</td></tr><tr class="passedodd"><td><a href="#m142"><b>testConstrainedParametersMaxValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">11166</td></tr><tr class="passedodd"><td><a href="#m143"><b>testConstrainedParametersMinValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">5507</td></tr><tr class="passedodd"><td><a href="#m144"><b>testConstrainedParametersRandomValues</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">21942</td></tr><tr class="passedodd"><td><a href="#m145"><b>testDefaultParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">10988</td></tr><tr class="passedodd"><td><a href="#m146"><b>testOptions</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">891</td></tr><tr class="passedodd"><td><a href="#m147"><b>testParameters</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">12717</td></tr><tr class="passedodd"><td><a href="#m148"><b>testPresets</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">1094</td></tr>
  77 <tr class="passedeven"><td rowspan="6">compbio.runner.msa.TcoffeeTester<br>"Ant test"<td><a href="#m149"><b>readStatistics</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">876</td></tr><tr class="passedeven"><td><a href="#m150"><b>testClusterExecute</b> (cluster, runner, non_windows) </a></td><td class="numi">1</td><td class="numi">5526</td></tr><tr class="passedeven"><td><a href="#m151"><b>testConfigurationLoading</b> (runner) </a></td><td class="numi">1</td><td class="numi">99</td></tr><tr class="passedeven"><td><a href="#m152"><b>testExecute</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">868</td></tr><tr class="passedeven"><td><a href="#m153"><b>testNcore</b> (runner, non_windows) </a></td><td class="numi">1</td><td class="numi">1</td></tr><tr class="passedeven"><td><a href="#m154"><b>testPersistance</b> (cluster, runner, non_windows) </a></td><td class="numi">1</td><td class="numi">1771</td></tr>
  78 </table>
  79 <h1>Ant test</h1>
  80 <a id="m1"></a><h2>compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFile</h2>
  81 <p class="totop"><a href="#summary">back to summary</a></p>
  82 <a id="m2"></a><h2>compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileLongNames</h2>
  83 <p class="totop"><a href="#summary">back to summary</a></p>
  84 <a id="m3"></a><h2>compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileShortNames</h2>
  85 <p class="totop"><a href="#summary">back to summary</a></p>
  86 <a id="m4"></a><h2>compbio.data.sequence.FastaSequenceGeneratorTester:testProteinSequenceGeneration</h2>
  87 <p class="totop"><a href="#summary">back to summary</a></p>
  88 <a id="m5"></a><h2>compbio.data.sequence.FastaSequenceTester:testGetFormattedFasta</h2>
  89 <p class="totop"><a href="#summary">back to summary</a></p>
  90 <a id="m6"></a><h2>compbio.data.sequence.SequenceUtilTester:testCleanSequence</h2>
  91 <p class="totop"><a href="#summary">back to summary</a></p>
  92 <a id="m7"></a><h2>compbio.data.sequence.SequenceUtilTester:testDeepCleanSequence</h2>
  93 <p class="totop"><a href="#summary">back to summary</a></p>
  94 <a id="m8"></a><h2>compbio.data.sequence.SequenceUtilTester:testReadWriteFasta</h2>
  95 <p class="totop"><a href="#summary">back to summary</a></p>
  96 <a id="m9"></a><h2>compbio.data.sequence.SequenceUtilTester:testisNonAmbNucleotideSequence</h2>
  97 <p class="totop"><a href="#summary">back to summary</a></p>
  98 <a id="m10"></a><h2>compbio.data.sequence.SequenceUtilTester:testisProteinSequence</h2>
  99 <p class="totop"><a href="#summary">back to summary</a></p>
 100 <a id="m11"></a><h2>compbio.engine.EngineConfiguratorTester:testGetAsyncEngine</h2>
 101 <p class="totop"><a href="#summary">back to summary</a></p>
 102 <a id="m12"></a><h2>compbio.engine.EngineConfiguratorTester:testGetSyncEngine</h2>
 103 <p class="totop"><a href="#summary">back to summary</a></p>
 104 <a id="m13"></a><h2>compbio.engine.FilePullerTester:testCache</h2>
 105 <p class="totop"><a href="#summary">back to summary</a></p>
 106 <a id="m14"></a><h2>compbio.engine.FilePullerTester:testGet</h2>
 107 <p class="totop"><a href="#summary">back to summary</a></p>
 108 <a id="m15"></a><h2>compbio.engine.FilePullerTester:testGetDelay</h2>
 109 <p class="totop"><a href="#summary">back to summary</a></p>
 110 <a id="m16"></a><h2>compbio.engine.FilePullerTester:testPull</h2>
 111 <p class="totop"><a href="#summary">back to summary</a></p>
 112 <a id="m17"></a><h2>compbio.engine.PulledFileCacheTester:test</h2>
 113 <p class="totop"><a href="#summary">back to summary</a></p>
 114 <a id="m18"></a><h2>compbio.engine.client.CommandBuilderTester:testCommandBuilding</h2>
 115 <p class="totop"><a href="#summary">back to summary</a></p>
 116 <a id="m19"></a><h2>compbio.engine.client.CommandBuilderTester:testOptionsToCommand</h2>
 117 <p class="totop"><a href="#summary">back to summary</a></p>
 118 <a id="m20"></a><h2>compbio.engine.client.CommandBuilderTester:testSpaceDelimiterExecutable</h2>
 119 <p class="totop"><a href="#summary">back to summary</a></p>
 120 <a id="m21"></a><h2>compbio.engine.client.PathValidatorTester:testGetClassPath</h2>
 121 <p class="totop"><a href="#summary">back to summary</a></p>
 122 <a id="m22"></a><h2>compbio.engine.client.PathValidatorTester:testIsAbsolutePath</h2>
 123 <p class="totop"><a href="#summary">back to summary</a></p>
 124 <a id="m23"></a><h2>compbio.engine.cluster.drmaa.ClusterSessionTester:testTaskList</h2>
 125 <p class="totop"><a href="#summary">back to summary</a></p>
 126 <a id="m24"></a><h2>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testCancel</h2>
 127 <div style="padding-left:3em">
 128 <p>java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!</p>
 129 compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
 130 <br/>at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
 131 <br/>at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
 132 <br/>at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
 133 <br/>23 lines not shown
 134 <p>Caused by Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!</p>
 135 compbio.runner.Util.readClustalFile(Util.java:126)
 136 <br/>at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
 137 <br/>at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
 138 <br/>at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
 139 <br/>at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
 140 <br/>23 lines not shown
 141 </div>
 142 <p class="totop"><a href="#summary">back to summary</a></p>
 143 <a id="m25"></a><h2>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testGetJobStatus</h2>
 144 <p class="totop"><a href="#summary">back to summary</a></p>
 145 <a id="m26"></a><h2>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testSubmit</h2>
 146 <p class="totop"><a href="#summary">back to summary</a></p>
 147 <a id="m27"></a><h2>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testCancel</h2>
 148 <p class="totop"><a href="#summary">back to summary</a></p>
 149 <a id="m28"></a><h2>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testSubmit</h2>
 150 <p class="totop"><a href="#summary">back to summary</a></p>
 151 <a id="m29"></a><h2>compbio.engine.cluster.drmaa.UtilTester:testParser</h2>
 152 <p class="totop"><a href="#summary">back to summary</a></p>
 153 <a id="m30"></a><h2>compbio.engine.cluster.dundee._QueueTester:testQueue</h2>
 154 <p class="totop"><a href="#summary">back to summary</a></p>
 155 <a id="m31"></a><h2>compbio.engine.conf.DirectoryManagerTester:testGetDirectory</h2>
 156 <p class="totop"><a href="#summary">back to summary</a></p>
 157 <a id="m32"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:testClusterEngineConf</h2>
 158 <p class="totop"><a href="#summary">back to summary</a></p>
 159 <a id="m33"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateClustalConfiguration</h2>
 160 <p class="totop"><a href="#summary">back to summary</a></p>
 161 <a id="m34"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateMafftConfiguration</h2>
 162 <p class="totop"><a href="#summary">back to summary</a></p>
 163 <a id="m35"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateMuscleConfiguration</h2>
 164 <p class="totop"><a href="#summary">back to summary</a></p>
 165 <a id="m36"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateTcoffeeConfiguration</h2>
 166 <p class="totop"><a href="#summary">back to summary</a></p>
 167 <a id="m37"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testMarshalling</h2>
 168 <p class="totop"><a href="#summary">back to summary</a></p>
 169 <a id="m38"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testSchemaFromCodeGeneration</h2>
 170 <p class="totop"><a href="#summary">back to summary</a></p>
 171 <a id="m39"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testUnMarshalling</h2>
 172 <p class="totop"><a href="#summary">back to summary</a></p>
 173 <a id="m40"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testValidation</h2>
 174 <p class="totop"><a href="#summary">back to summary</a></p>
 175 <a id="m41"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testValidationOnMarshalling</h2>
 176 <div style="padding-left:3em">
 177 <p>null</p>
 178 com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
 179 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
 180 <br/>at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
 181 <br/>at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
 182 <br/>at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
 183 <br/>23 lines not shown
 184 <p>Caused by cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.</p>
 185 com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
 186 <br/>at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
 187 <br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
 188 <br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
 189 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
 190 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
 191 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
 192 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
 193 <br/>at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
 194 <br/>at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
 195 <br/>at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
 196 <br/>at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
 197 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
 198 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
 199 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
 200 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
 201 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
 202 <br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
 203 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
 204 <br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
 205 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
 206 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
 207 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
 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:258)
 211 <br/>23 lines not shown
 212 </div>
 213 <p class="totop"><a href="#summary">back to summary</a></p>
 214 <a id="m42"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testAsyncCancelOperation</h2>
 215 <p class="totop"><a href="#summary">back to summary</a></p>
 216 <a id="m43"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testAsyncRetrievOperation</h2>
 217 <p class="totop"><a href="#summary">back to summary</a></p>
 218 <a id="m44"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testCancelCompletedTaskLocally</h2>
 219 <p class="totop"><a href="#summary">back to summary</a></p>
 220 <a id="m45"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testCancelLocally</h2>
 221 <div style="padding-left:3em">
 222 <p>null</p>
 223 java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 224 <br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 225 <br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 226 <br/>at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 227 <br/>at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
 228 <br/>23 lines not shown
 229 </div>
 230 <p class="totop"><a href="#summary">back to summary</a></p>
 231 <a id="m46"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testGetStatus</h2>
 232 <p class="totop"><a href="#summary">back to summary</a></p>
 233 <a id="m47"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testMultipleCancelLocally</h2>
 234 <div style="padding-left:3em">
 235 <p>null</p>
 236 java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 237 <br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 238 <br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 239 <br/>at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 240 <br/>at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
 241 <br/>23 lines not shown
 242 </div>
 243 <p class="totop"><a href="#summary">back to summary</a></p>
 244 <a id="m48"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testSubmitLocally</h2>
 245 <p class="totop"><a href="#summary">back to summary</a></p>
 246 <a id="m49"></a><h2>compbio.engine.local.LocalRunnerTester:testCancelCompletedTaskLocally</h2>
 247 <div style="padding-left:3em">
 248 <p>null</p>
 249 java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 250 <br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 251 <br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 252 <br/>at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 253 <br/>at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
 254 <br/>23 lines not shown
 255 </div>
 256 <p class="totop"><a href="#summary">back to summary</a></p>
 257 <a id="m50"></a><h2>compbio.engine.local.LocalRunnerTester:testCancelLocally</h2>
 258 <div style="padding-left:3em">
 259 <p>null</p>
 260 java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 261 <br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 262 <br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 263 <br/>at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 264 <br/>at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
 265 <br/>23 lines not shown
 266 </div>
 267 <p class="totop"><a href="#summary">back to summary</a></p>
 268 <a id="m51"></a><h2>compbio.engine.local.LocalRunnerTester:testMultipleCancelLocally</h2>
 269 <div style="padding-left:3em">
 270 <p>null</p>
 271 java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 272 <br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 273 <br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 274 <br/>at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 275 <br/>at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
 276 <br/>23 lines not shown
 277 </div>
 278 <p class="totop"><a href="#summary">back to summary</a></p>
 279 <a id="m52"></a><h2>compbio.metadata.OptionCombinatorTester:testgetAllOptions</h2>
 280 <p class="totop"><a href="#summary">back to summary</a></p>
 281 <a id="m53"></a><h2>compbio.metadata.OptionCombinatorTester:testgetAllParameters</h2>
 282 <p class="totop"><a href="#summary">back to summary</a></p>
 283 <a id="m54"></a><h2>compbio.metadata.OptionMarshallerTester:testMarshalling</h2>
 284 <div style="padding-left:3em">
 285 <p>null</p>
 286 com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
 287 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
 288 <br/>at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
 289 <br/>at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
 290 <br/>at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
 291 <br/>23 lines not shown
 292 <p>Caused by cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.</p>
 293 com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
 294 <br/>at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
 295 <br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
 296 <br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
 297 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
 298 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
 299 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
 300 <br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
 301 <br/>at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
 302 <br/>at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
 303 <br/>at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
 304 <br/>at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
 305 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
 306 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
 307 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
 308 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
 309 <br/>at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
 310 <br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
 311 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
 312 <br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
 313 <br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
 314 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
 315 <br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
 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 </div>
 321 <p class="totop"><a href="#summary">back to summary</a></p>
 322 <a id="m55"></a><h2>compbio.metadata.OptionMarshallerTester:testUnMarshalling</h2>
 323 <p class="totop"><a href="#summary">back to summary</a></p>
 324 <a id="m56"></a><h2>compbio.metadata.PresetTester:marshallPreset</h2>
 325 <p class="totop"><a href="#summary">back to summary</a></p>
 326 <a id="m57"></a><h2>compbio.metadata.PresetTester:validatePresets</h2>
 327 <p class="totop"><a href="#summary">back to summary</a></p>
 328 <a id="m58"></a><h2>compbio.metadata.RunnerConfigTester:testCreateNumParameterWithoutValidValue</h2>
 329 <div style="padding-left:3em">
 330 <p>Attempting to set default value for parameter: Option name: Matrix
 331 Description: DNA weight matrix
 332 URL: null
 333 Is required: false
 334
 335  Without possible values! Please define possible value first!</p>
 336 compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
 337 <br/>at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
 338 <br/>23 lines not shown
 339 </div>
 340 <p class="totop"><a href="#summary">back to summary</a></p>
 341 <a id="m59"></a><h2>compbio.metadata.RunnerConfigTester:testCreateParameter</h2>
 342 <div style="padding-left:3em">
 343 <p>Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
 344 Description: Protein weight matrix
 345 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 346 Is required: true
 347 Option Names:
 348 --AAMATRIX
 349 POSSIBLE VALUES:
 350 BLOSUM
 351 GONNET
 352 ID
 353 PAM
 354
 355 </p>
 356 compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
 357 <br/>at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
 358 <br/>23 lines not shown
 359 </div>
 360 <p class="totop"><a href="#summary">back to summary</a></p>
 361 <a id="m60"></a><h2>compbio.metadata.RunnerConfigTester:testCreateParameterWithValidValueConstrain</h2>
 362 <p class="totop"><a href="#summary">back to summary</a></p>
 363 <a id="m61"></a><h2>compbio.metadata.RunnerConfigTester:testOptionNoDefaultValidate</h2>
 364 <div style="padding-left:3em">
 365 <p>Default value is required as multiple optionNames are defined for option: Option name: Matrix1
 366 Description: Protein weight matrix
 367 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 368 Is required: true
 369 Option Names:
 370 --AAMATRIX
 371 --ABMAT
 372 --BBBB
 373 </p>
 374 compbio.metadata.Option.validate(Option.java:317)
 375 <br/>at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
 376 <br/>23 lines not shown
 377 </div>
 378 <p class="totop"><a href="#summary">back to summary</a></p>
 379 <a id="m62"></a><h2>compbio.metadata.RunnerConfigTester:testOptionSetInvalidValue</h2>
 380 <div style="padding-left:3em">
 381 <p>Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
 382 Description: Protein weight matrix
 383 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 384 Is required: true
 385 Option Names:
 386 --AAMATRIX
 387 --ABMAT
 388 --BBBB
 389 </p>
 390 compbio.metadata.Option.setDefaultValue(Option.java:130)
 391 <br/>at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
 392 <br/>23 lines not shown
 393 </div>
 394 <p class="totop"><a href="#summary">back to summary</a></p>
 395 <a id="m63"></a><h2>compbio.metadata.RunnerConfigTester:testOptionToCommand</h2>
 396 <p class="totop"><a href="#summary">back to summary</a></p>
 397 <a id="m64"></a><h2>compbio.metadata.RunnerConfigTester:testParameterToCommand</h2>
 398 <p class="totop"><a href="#summary">back to summary</a></p>
 399 <a id="m65"></a><h2>compbio.metadata.RunnerConfigTester:testValidate</h2>
 400 <p class="totop"><a href="#summary">back to summary</a></p>
 401 <a id="m66"></a><h2>compbio.metadata.RunnerConfigTester:testValidateBoundaryConstrainCheck</h2>
 402 <p class="totop"><a href="#summary">back to summary</a></p>
 403 <a id="m67"></a><h2>compbio.metadata.RunnerConfigTester:testValidateLowerBoundaryConstrainCheck</h2>
 404 <div style="padding-left:3em">
 405 <p>Attempting to set default value outside boundaries defined by the constraint: Type: Float
 406 Min: -10.12
 407 Max: 0
 408
 409  For parameter: Option name: Matrix1
 410 Description: Protein weight matrix
 411 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 412 Is required: true
 413 Option Names:
 414 --AAMATRIX
 415 Type: Float
 416 Min: -10.12
 417 Max: 0
 418
 419 </p>
 420 compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
 421 <br/>at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
 422 <br/>23 lines not shown
 423 </div>
 424 <p class="totop"><a href="#summary">back to summary</a></p>
 425 <a id="m68"></a><h2>compbio.metadata.RunnerConfigTester:testValidateUpperBoundaryConstrainCheck</h2>
 426 <div style="padding-left:3em">
 427 <p>Attempting to set default value outside boundaries defined by the constraint: Type: Float
 428 Min: -10.12
 429 Max: 0
 430
 431  For parameter: Option name: Matrix1
 432 Description: Protein weight matrix
 433 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 434 Is required: true
 435 Option Names:
 436 --AAMATRIX
 437 Type: Float
 438 Min: -10.12
 439 Max: 0
 440
 441 </p>
 442 compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
 443 <br/>at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
 444 <br/>23 lines not shown
 445 </div>
 446 <p class="totop"><a href="#summary">back to summary</a></p>
 447 <a id="m69"></a><h2>compbio.metadata.RunnerConfigTester:testValidateValueConstrain</h2>
 448 <div style="padding-left:3em">
 449 <p>Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
 450 </p>
 451 compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
 452 <br/>at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
 453 <br/>23 lines not shown
 454 </div>
 455 <p class="totop"><a href="#summary">back to summary</a></p>
 456 <a id="m70"></a><h2>compbio.runner._impl.MclTester:testGetTestCommand</h2>
 457 <p class="totop"><a href="#summary">back to summary</a></p>
 458 <a id="m71"></a><h2>compbio.runner._impl.NetNglycTester:testGetTestCommand</h2>
 459 <p class="totop"><a href="#summary">back to summary</a></p>
 460 <a id="m72"></a><h2>compbio.runner._impl.OBTester:testGetTestArgsCommand</h2>
 461 <p class="totop"><a href="#summary">back to summary</a></p>
 462 <a id="m73"></a><h2>compbio.runner._impl.OBTester:testGetTestCommand</h2>
 463 <p class="totop"><a href="#summary">back to summary</a></p>
 464 <a id="m74"></a><h2>compbio.runner._impl.RPSBlastTester:testGetTestArgsCommand</h2>
 465 <p class="totop"><a href="#summary">back to summary</a></p>
 466 <a id="m75"></a><h2>compbio.runner._impl.RPSBlastTester:testGetTestCommand</h2>
 467 <p class="totop"><a href="#summary">back to summary</a></p>
 468 <a id="m76"></a><h2>compbio.runner._impl.RonnTester:testGetTestCommand</h2>
 469 <p class="totop"><a href="#summary">back to summary</a></p>
 470 <a id="m77"></a><h2>compbio.runner._impl.Tmhmm2Tester:testGetTestCommand</h2>
 471 <p class="totop"><a href="#summary">back to summary</a></p>
 472 <a id="m78"></a><h2>compbio.runner.msa.ClustalWParametersTester:testArguments</h2>
 473 <p class="totop"><a href="#summary">back to summary</a></p>
 474 <a id="m79"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConfiguration</h2>
 475 <p class="totop"><a href="#summary">back to summary</a></p>
 476 <a id="m80"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersMaxValues</h2>
 477 <p class="totop"><a href="#summary">back to summary</a></p>
 478 <a id="m81"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersMinValues</h2>
 479 <p class="totop"><a href="#summary">back to summary</a></p>
 480 <a id="m82"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersRandomValues</h2>
 481 <p class="totop"><a href="#summary">back to summary</a></p>
 482 <a id="m83"></a><h2>compbio.runner.msa.ClustalWParametersTester:testDefaultParameters</h2>
 483 <p class="totop"><a href="#summary">back to summary</a></p>
 484 <a id="m84"></a><h2>compbio.runner.msa.ClustalWParametersTester:testOptions</h2>
 485 <p class="totop"><a href="#summary">back to summary</a></p>
 486 <a id="m85"></a><h2>compbio.runner.msa.ClustalWParametersTester:testParameters</h2>
 487 <p class="totop"><a href="#summary">back to summary</a></p>
 488 <a id="m86"></a><h2>compbio.runner.msa.ClustalWParametersTester:testPresets</h2>
 489 <p class="totop"><a href="#summary">back to summary</a></p>
 490 <a id="m87"></a><h2>compbio.runner.msa.ClustalWTester:readStatistics</h2>
 491 <p class="totop"><a href="#summary">back to summary</a></p>
 492 <a id="m88"></a><h2>compbio.runner.msa.ClustalWTester:readStatisticsClusterExecution</h2>
 493 <p class="totop"><a href="#summary">back to summary</a></p>
 494 <a id="m89"></a><h2>compbio.runner.msa.ClustalWTester:testConfigurationLoading</h2>
 495 <p class="totop"><a href="#summary">back to summary</a></p>
 496 <a id="m90"></a><h2>compbio.runner.msa.ClustalWTester:testOptionsLocally</h2>
 497 <p class="totop"><a href="#summary">back to summary</a></p>
 498 <a id="m91"></a><h2>compbio.runner.msa.ClustalWTester:testPersistance</h2>
 499 <p class="totop"><a href="#summary">back to summary</a></p>
 500 <a id="m92"></a><h2>compbio.runner.msa.ClustalWTester:testRunLocally</h2>
 501 <p class="totop"><a href="#summary">back to summary</a></p>
 502 <a id="m93"></a><h2>compbio.runner.msa.ClustalWTester:testRunOnCluster</h2>
 503 <p class="totop"><a href="#summary">back to summary</a></p>
 504 <a id="m94"></a><h2>compbio.runner.msa.ClustalWTester:testRunWithMatrix</h2>
 505 <p class="totop"><a href="#summary">back to summary</a></p>
 506 <a id="m95"></a><h2>compbio.runner.msa.LimitTester:testLoadLimits</h2>
 507 <p class="totop"><a href="#summary">back to summary</a></p>
 508 <a id="m96"></a><h2>compbio.runner.msa.MafftParametersTester:testArguments</h2>
 509 <p class="totop"><a href="#summary">back to summary</a></p>
 510 <a id="m97"></a><h2>compbio.runner.msa.MafftParametersTester:testConfiguration</h2>
 511 <p class="totop"><a href="#summary">back to summary</a></p>
 512 <a id="m98"></a><h2>compbio.runner.msa.MafftParametersTester:testConstrainedParametersMaxValues</h2>
 513 <p class="totop"><a href="#summary">back to summary</a></p>
 514 <a id="m99"></a><h2>compbio.runner.msa.MafftParametersTester:testConstrainedParametersMinValues</h2>
 515 <p class="totop"><a href="#summary">back to summary</a></p>
 516 <a id="m100"></a><h2>compbio.runner.msa.MafftParametersTester:testConstrainedParametersRandomValues</h2>
 517 <p class="totop"><a href="#summary">back to summary</a></p>
 518 <a id="m101"></a><h2>compbio.runner.msa.MafftParametersTester:testDefaultParameters</h2>
 519 <p class="totop"><a href="#summary">back to summary</a></p>
 520 <a id="m102"></a><h2>compbio.runner.msa.MafftParametersTester:testOptions</h2>
 521 <p class="totop"><a href="#summary">back to summary</a></p>
 522 <a id="m103"></a><h2>compbio.runner.msa.MafftParametersTester:testParameters</h2>
 523 <p class="totop"><a href="#summary">back to summary</a></p>
 524 <a id="m104"></a><h2>compbio.runner.msa.MafftParametersTester:testPresets</h2>
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 526 <a id="m105"></a><h2>compbio.runner.msa.MafftTester:readStatistics</h2>
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 528 <a id="m106"></a><h2>compbio.runner.msa.MafftTester:testClusterExecute</h2>
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 530 <a id="m107"></a><h2>compbio.runner.msa.MafftTester:testConfigurationLoading</h2>
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 532 <a id="m108"></a><h2>compbio.runner.msa.MafftTester:testExecute</h2>
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 534 <a id="m109"></a><h2>compbio.runner.msa.MafftTester:testPersistance</h2>
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 536 <a id="m110"></a><h2>compbio.runner.msa.MafftTester:testRunOnClusterAsyncCheckStatusLongPoolingTime</h2>
 537 <p class="totop"><a href="#summary">back to summary</a></p>
 538 <a id="m111"></a><h2>compbio.runner.msa.MafftTester:testSetInputTester</h2>
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 540 <a id="m112"></a><h2>compbio.runner.msa.MuscleParametersTester:testArguments</h2>
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 542 <a id="m113"></a><h2>compbio.runner.msa.MuscleParametersTester:testConfiguration</h2>
 543 <p class="totop"><a href="#summary">back to summary</a></p>
 544 <a id="m114"></a><h2>compbio.runner.msa.MuscleParametersTester:testConstrainedParametersMaxValues</h2>
 545 <p class="totop"><a href="#summary">back to summary</a></p>
 546 <a id="m115"></a><h2>compbio.runner.msa.MuscleParametersTester:testConstrainedParametersMinValues</h2>
 547 <p class="totop"><a href="#summary">back to summary</a></p>
 548 <a id="m116"></a><h2>compbio.runner.msa.MuscleParametersTester:testConstrainedParametersRandomValues</h2>
 549 <p class="totop"><a href="#summary">back to summary</a></p>
 550 <a id="m117"></a><h2>compbio.runner.msa.MuscleParametersTester:testDefaultParameters</h2>
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 552 <a id="m118"></a><h2>compbio.runner.msa.MuscleParametersTester:testOptions</h2>
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 554 <a id="m119"></a><h2>compbio.runner.msa.MuscleParametersTester:testParameters</h2>
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 556 <a id="m120"></a><h2>compbio.runner.msa.MuscleParametersTester:testPresets</h2>
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 558 <a id="m121"></a><h2>compbio.runner.msa.MuscleTester:readStatistics</h2>
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 560 <a id="m122"></a><h2>compbio.runner.msa.MuscleTester:testConfigurationLoading</h2>
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 562 <a id="m123"></a><h2>compbio.runner.msa.MuscleTester:testPersistance</h2>
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 564 <a id="m124"></a><h2>compbio.runner.msa.MuscleTester:testRunLocally</h2>
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 566 <a id="m125"></a><h2>compbio.runner.msa.MuscleTester:testRunOnCluster</h2>
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 568 <a id="m126"></a><h2>compbio.runner.msa.ProbconsParametersTester:testArguments</h2>
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 570 <a id="m127"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConfiguration</h2>
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 572 <a id="m128"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersMaxValues</h2>
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 574 <a id="m129"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersMinValues</h2>
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 576 <a id="m130"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersRandomValues</h2>
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 578 <a id="m131"></a><h2>compbio.runner.msa.ProbconsParametersTester:testDefaultParameters</h2>
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 580 <a id="m132"></a><h2>compbio.runner.msa.ProbconsParametersTester:testOptions</h2>
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 582 <a id="m133"></a><h2>compbio.runner.msa.ProbconsParametersTester:testParameters</h2>
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 584 <a id="m134"></a><h2>compbio.runner.msa.ProbconsTester:readStatistics</h2>
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 586 <a id="m135"></a><h2>compbio.runner.msa.ProbconsTester:testClusterExecute</h2>
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 588 <a id="m136"></a><h2>compbio.runner.msa.ProbconsTester:testConfigurationLoading</h2>
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 590 <a id="m137"></a><h2>compbio.runner.msa.ProbconsTester:testExecute</h2>
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 592 <a id="m138"></a><h2>compbio.runner.msa.ProbconsTester:testPersistance</h2>
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 594 <a id="m139"></a><h2>compbio.runner.msa.ProbconsTester:testSetInputTester</h2>
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 596 <a id="m140"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testArguments</h2>
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 598 <a id="m141"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConfiguration</h2>
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 600 <a id="m142"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersMaxValues</h2>
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 602 <a id="m143"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersMinValues</h2>
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 604 <a id="m144"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersRandomValues</h2>
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 606 <a id="m145"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testDefaultParameters</h2>
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 608 <a id="m146"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testOptions</h2>
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 610 <a id="m147"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testParameters</h2>
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 612 <a id="m148"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testPresets</h2>
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 614 <a id="m149"></a><h2>compbio.runner.msa.TcoffeeTester:readStatistics</h2>
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 616 <a id="m150"></a><h2>compbio.runner.msa.TcoffeeTester:testClusterExecute</h2>
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 618 <a id="m151"></a><h2>compbio.runner.msa.TcoffeeTester:testConfigurationLoading</h2>
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 620 <a id="m152"></a><h2>compbio.runner.msa.TcoffeeTester:testExecute</h2>
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 622 <a id="m153"></a><h2>compbio.runner.msa.TcoffeeTester:testNcore</h2>
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 624 <a id="m154"></a><h2>compbio.runner.msa.TcoffeeTester:testPersistance</h2>
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 626 </body></html>