Remove old versions of web site

[jabaws.git] / website / tests / Ant suite / classes.html

diff --git a/website/tests/Ant suite/classes.html b/website/tests/Ant suite/classes.html
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-<table border='1'>
-<tr>
-<th>Class name</th>
-<th>Method name</th>
-<th>Groups</th>
-</tr><tr>
-<td>compbio.engine.client.CommandBuilderTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testOptionsToCommand</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testSpaceDelimiterExecutable</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCommandBuilding</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.metadata.RunnerConfigTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testValidateUpperBoundaryConstrainCheck</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testOptionSetInvalidValue</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testValidateBoundaryConstrainCheck</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testValidateValueConstrain</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCreateParameterWithValidValueConstrain</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testValidateLowerBoundaryConstrainCheck</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testOptionNoDefaultValidate</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCreateParameter</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testOptionToCommand</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testParameterToCommand</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCreateNumParameterWithoutValidValue</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testValidate</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>setup</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner._impl.NetNglycTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetTestCommand</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testBuildCommand</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner.msa.MafftParametersTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersMaxValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testArguments</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testOptions</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testDefaultParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testPresets</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConfiguration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>setup</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.EngineConfiguratorTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetAsyncEngine</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetSyncEngine</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner._impl.RonnTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetTestCommand</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testBuildCommand</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner.msa.ProbconsTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testExecute</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testPersistance</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testClusterExecute</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testSetInputTester</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>readStatistics</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>init</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.conf.PropertyHelperManagerTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testClusterEngineConf</td>
-<td>cluster </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>validateClustalConfiguration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>validateTcoffeeConfiguration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>validateMuscleConfiguration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>validateMafftConfiguration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testLoadResources</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.FilePullerTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGet</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCache</td>
-<td>engine </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetDelay</td>
-<td>engine </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testPull</td>
-<td>engine </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.metadata.OptionCombinatorTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testgetAllParameters</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testgetAllOptions</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>setup</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner.msa.MuscleTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testRunOnCluster</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testRunOnClusterAsync</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testPersistance</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>readStatistics</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testRunLocally</td>
-<td>runner </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>init</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner.msa.TcoffeeTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testExecute</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testPersistance</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testNcore</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testClusterExecute</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>readStatistics</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>init</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner.msa.LimitTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testLoadLimits</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>setup</td>
-<td>runner </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner._impl.OBTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetTestCommand</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testBuildCommand</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetTestArgsCommand</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.local.AsyncLocalRunnerTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCancelLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testMultipleCancelLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testAsyncCancelOperation</td>
-<td>engine </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testAsyncRetrievOperation</td>
-<td>engine </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testSubmitLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCancelCompletedTaskLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetStatus</td>
-<td>engine </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.local.LocalRunnerTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCancelLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testMultipleCancelLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCancelCompletedTaskLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner._impl.Tmhmm2Tester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetTestCommand</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testBuildCommand</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner.msa.MafftTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testExecute</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testRunOnClusterAsyncCheckStatusShortPoolingTime</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testPersistance</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testClusterExecute</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testSetInputTester</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>readStatistics</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testRunOnClusterAsyncCheckStatusLongPoolingTime</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>init</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.data.sequence.ClustalAlignmentUtilTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testReadClustalFile</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testReadClustalFileLongNames</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testReadClustalFileShortNames</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner.msa.MuscleParametersTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersMaxValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testArguments</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testOptions</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testDefaultParameters</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testParameters</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testPresets</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConfiguration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>setup</td>
-<td>runner </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.data.sequence.FastaSequenceGeneratorTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testProteinSequenceGeneration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.cluster.drmaa.ClusterSessionTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testTaskList</td>
-<td>engine cluster </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.data.sequence.FastaSequenceTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetFormattedFasta</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.client.PathValidatorTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testIsAbsolutePath</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetClassPath</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.data.sequence.SequenceUtilTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testDeepCleanSequence</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testReadWriteFasta</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testisNonAmbNucleotideSequence</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testisProteinSequence</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCleanSequence</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner.msa.TcoffeeParametersTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersMaxValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testArguments</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testOptions</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testDefaultParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testPresets</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConfiguration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>setup</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner.msa.ClustalWTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testRunOnCluster</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testPersistance</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testAddParameters</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testOptionsLocally</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>readStatisticsClusterExecution</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testRunWithMatrix</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>readStatistics</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testRunLocally</td>
-<td>runner </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.cluster.drmaa.UtilTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testParser</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.conf.DirectoryManagerTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetDirectory</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testNanoTime</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testSubmit</td>
-<td>engine cluster </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCancel</td>
-<td>engine cluster </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testSubmit</td>
-<td>engine cluster </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testCancel</td>
-<td>engine cluster </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetJobStatus</td>
-<td>engine cluster </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.metadata.PresetTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>marshallPreset</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>validatePresets</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.metadata.OptionMarshallerTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testUnMarshalling</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testMarshalling</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>setup</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner.msa.ClustalWParametersTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersMaxValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testArguments</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testOptions</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testDefaultParameters</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testParameters</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testPresets</td>
-<td>runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConfiguration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>setup</td>
-<td>runner </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner._impl.RPSBlastTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetTestCommand</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testBuildCommand</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetTestArgsCommand</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.PulledFileCacheTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>test</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner._impl.MclTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testGetTestCommand</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testBuildCommand</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.cluster.dundee._QueueTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testQueue</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.runner.msa.ProbconsParametersTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersMaxValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testArguments</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testOptions</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testDefaultParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testConfiguration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>setup</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-<tr>
-<td>compbio.engine.conf.RunnerConfigMarshallerTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>testValidationOnMarshalling</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testUnMarshalling</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testValidation</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testSchemaFromCodeGeneration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testMarshalling</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td>&nbsp;</td>
-<td>setup</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-</table>