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Re-formatting the file
[jabaws.git] / website / tests / Ant suite / classes.html
diff --git a/website/tests/Ant suite/classes.html b/website/tests/Ant suite/classes.html
index 34aa37e..2ff1808 100644 (file)
--- a/website/tests/Ant suite/classes.html
+++ b/website/tests/Ant suite/classes.html
@@ -34,58 +34,19 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.metadata.RunnerConfigTester</td>
+<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>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>
+<td>testBuildCommand</td>
+<td>cluster runner </td>
+</tr>
 <tr>
 <td>&nbsp;</td>
-<td>testValidate</td>
+<td>testGetTestCommand</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -94,30 +55,25 @@
 <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>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>testGetTestCommand</td>
+<td>testGetAsyncEngine</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testBuildCommand</td>
-<td>cluster runner </td>
-</tr>
+<td>testGetSyncEngine</td>
+<td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
 </tr>
@@ -131,56 +87,42 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.runner.msa.MafftParametersTester</td>
+<td>compbio.runner.disorder.GlobPlotTester</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>
+<td>testRunOnCluster</td>
+<td>cluster runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testArguments</td>
-<td>runner non_windows </td>
+<td>testPersistance</td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testOptions</td>
-<td>runner non_windows </td>
+<td>testRunOnClusterAsync</td>
+<td>cluster runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testDefaultParameters</td>
-<td>runner non_windows </td>
+<td>testConfigurationLoading</td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testParameters</td>
-<td>runner non_windows </td>
+<td>readStatistics</td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testPresets</td>
-<td>runner non_windows </td>
+<td>testRunLocally</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>
@@ -188,9 +130,8 @@
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>setup</td>
-<td>runner non_windows </td>
-</tr>
+<td>init</td>
+<td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@AfterMethod</td>
 </tr>
@@ -198,18 +139,26 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.engine.EngineConfiguratorTester</td>
+<td>compbio.stat.collector.ExecutionStatCollectorTester</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>testHasCompleted</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testGetSyncEngine</td>
+<td>testHasTimedOut</td>
+<td>&nbsp;</td></tr>
+<tr>
+<td>&nbsp;</td>
+<td>testCollectStat</td>
+<td>&nbsp;</td></tr>
+<tr>
+<td>&nbsp;</td>
+<td>testUpdateStatTester</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -224,19 +173,45 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.runner._impl.RonnTester</td>
+<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>testGetTestCommand</td>
-<td>&nbsp;</td></tr>
+<td>testCancelLocally</td>
+<td>engine </td>
+</tr>
 <tr>
 <td>&nbsp;</td>
-<td>testBuildCommand</td>
-<td>cluster runner </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>
@@ -251,7 +226,7 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.runner.msa.ProbconsTester</td>
+<td>compbio.runner.msa.MafftTester</td>
 <td>&nbsp;</td><td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@Test</td>
@@ -263,6 +238,11 @@
 </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>
@@ -287,6 +267,11 @@
 <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>
@@ -304,40 +289,27 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.engine.conf.PropertyHelperManagerTester</td>
+<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>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>testReadClustalFile</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>validateMuscleConfiguration</td>
+<td>testReadClustalFileLongNames</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>validateMafftConfiguration</td>
+<td>testReadClustalFileShortNames</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>
@@ -347,29 +319,50 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.engine.FilePullerTester</td>
+<td>compbio.runner.disorder.IUPredTester</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>
+<td>testRunOnCluster</td>
+<td>cluster runner </td>
+</tr>
 <tr>
 <td>&nbsp;</td>
-<td>testCache</td>
-<td>engine </td>
+<td>testReadResults</td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testGetDelay</td>
-<td>engine </td>
+<td>testPersistance</td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testPull</td>
-<td>engine </td>
+<td>testRunOnClusterAsync</td>
+<td>cluster runner </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>testSetParameter</td>
+<td>runner </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>testConfigurationLoading</td>
+<td>runner </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>testRunLocally</td>
+<td>runner </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>testRunLocallyWithParams</td>
+<td>runner </td>
 </tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -378,24 +371,28 @@
 <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.metadata.OptionCombinatorTester</td>
+<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>testgetAllParameters</td>
+<td>testIsAbsolutePath</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testgetAllOptions</td>
+<td>testGetClassPath</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -404,61 +401,98 @@
 <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>compbio.stat.collector.StatDBTester</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>
+<td>testReadOneMonthData</td>
+<td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testRunOnClusterAsync</td>
-<td>cluster runner </td>
-</tr>
+<td>testVerifyJobsCount</td>
+<td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testPersistance</td>
-<td>runner </td>
-</tr>
+<td>testReadYearData</td>
+<td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
+<td>testGetEarliestRecord</td>
+<td>&nbsp;</td></tr>
 <tr>
-<td>&nbsp;</td>
-<td>readStatistics</td>
-<td>runner </td>
+<td align='center' colspan='3'>@BeforeClass</td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testRunLocally</td>
-<td>runner </td>
+<td>init</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.stat.servlet.util.StatCollectionTester</td>
+<td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr>
+<td align='center' colspan='3'>@Test</td>
 </tr>
 <tr>
+<td>&nbsp;</td>
+<td>testGetStats</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.DrmaaAsyncClusterEngineTester</td>
+<td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr>
+<td align='center' colspan='3'>@Test</td>
+</tr>
+<tr>
 <td>&nbsp;</td>
-<td>init</td>
-<td>&nbsp;</td></tr>
+<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>
@@ -466,30 +500,63 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.runner.msa.TcoffeeTester</td>
+<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>testExecute</td>
-<td>runner non_windows </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.runner.conservation.AAConTester</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>runner </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>testRunLocallyWithPreset</td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testPersistance</td>
-<td>cluster runner non_windows </td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testNcore</td>
-<td>runner non_windows </td>
+<td>testRunOnClusterAsync</td>
+<td>cluster runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testClusterExecute</td>
-<td>cluster runner non_windows </td>
+<td>testRunLocallyOnTwoCpu</td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
@@ -499,7 +566,12 @@
 <tr>
 <td>&nbsp;</td>
 <td>readStatistics</td>
-<td>runner non_windows </td>
+<td>runner </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>testRunLocally</td>
+<td>runner </td>
 </tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -510,7 +582,37 @@
 <tr>
 <td>&nbsp;</td>
 <td>init</td>
-<td>cluster runner non_windows </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.RPSBlastTester</td>
+<td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr>
+<td align='center' colspan='3'>@Test</td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>testBuildCommand</td>
+<td>cluster runner </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>testGetTestCommand</td>
+<td>&nbsp;</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>
@@ -519,14 +621,14 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.runner.msa.LimitTester</td>
+<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>testLoadLimits</td>
+<td>test</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -535,34 +637,121 @@
 <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.disorder.DisemblTester</td>
+<td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr>
+<td align='center' colspan='3'>@Test</td>
+</tr>
+<tr>
 <td>&nbsp;</td>
-<td>setup</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>testRunOnClusterAsync</td>
+<td>cluster 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._impl.OBTester</td>
+<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>testBuildCommand</td>
+<td>cluster runner </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
 <td>testGetTestCommand</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.dundee._QueueTester</td>
+<td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr>
+<td align='center' colspan='3'>@Test</td>
+</tr>
+<tr>
 <td>&nbsp;</td>
-<td>testBuildCommand</td>
-<td>cluster runner </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.engine.LoadBalancerTester</td>
+<td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr>
+<td align='center' colspan='3'>@Test</td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testGetTestArgsCommand</td>
+<td>testLoadBalance</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -577,78 +766,177 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.engine.local.AsyncLocalRunnerTester</td>
+<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>testCancelLocally</td>
-<td>engine </td>
+<td>testConstrainedParametersMaxValues</td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testMultipleCancelLocally</td>
-<td>engine </td>
+<td>testConstrainedParametersRandomValues</td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testAsyncCancelOperation</td>
-<td>engine </td>
+<td>testConstrainedParametersMinValues</td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testAsyncRetrievOperation</td>
-<td>engine </td>
+<td>testArguments</td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testSubmitLocally</td>
-<td>engine </td>
+<td>testOptions</td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testCancelCompletedTaskLocally</td>
-<td>engine </td>
+<td>testDefaultParameters</td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testGetStatus</td>
-<td>engine </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.local.LocalRunnerTester</td>
+<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>testCancelLocally</td>
-<td>engine </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>testMultipleCancelLocally</td>
-<td>engine </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.disorder.JronnTester</td>
+<td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr>
+<td align='center' colspan='3'>@Test</td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testCancelCompletedTaskLocally</td>
-<td>engine </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>testRunOnClusterAsync</td>
+<td>cluster runner </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>testRunLocallyOnTwoCpu</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>
@@ -657,27 +945,98 @@
 <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._impl.Tmhmm2Tester</td>
+<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>testGetTestCommand</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._impl.RonnTester</td>
+<td>&nbsp;</td><td>&nbsp;</td></tr>
+<tr>
+<td align='center' colspan='3'>@Test</td>
+</tr>
+<tr>
 <td>&nbsp;</td>
 <td>testBuildCommand</td>
 <td>cluster runner </td>
 </tr>
 <tr>
+<td>&nbsp;</td>
+<td>testGetTestCommand</td>
+<td>&nbsp;</td></tr>
+<tr>
 <td align='center' colspan='3'>@BeforeClass</td>
 </tr>
 <tr>
@@ -690,7 +1049,7 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.runner.msa.MafftTester</td>
+<td>compbio.runner.msa.ProbconsTester</td>
 <td>&nbsp;</td><td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@Test</td>
@@ -702,11 +1061,6 @@
 </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>
@@ -731,11 +1085,6 @@
 <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>
@@ -753,27 +1102,40 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.data.sequence.ClustalAlignmentUtilTester</td>
+<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>testReadClustalFile</td>
+<td>testClusterEngineConf</td>
+<td>cluster </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>validateClustalConfiguration</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testReadClustalFileLongNames</td>
+<td>validateTcoffeeConfiguration</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testReadClustalFileShortNames</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>
@@ -783,55 +1145,60 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.runner.msa.MuscleParametersTester</td>
+<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>testConstrainedParametersMaxValues</td>
-<td>runner </td>
-</tr>
+<td>testgetAllParameters</td>
+<td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner </td>
+<td>testgetAllOptions</td>
+<td>&nbsp;</td></tr>
+<tr>
+<td align='center' colspan='3'>@BeforeClass</td>
 </tr>
 <tr>
-<td>&nbsp;</td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner </td>
+<td align='center' colspan='3'>@BeforeMethod</td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testArguments</td>
-<td>runner </td>
+<td>setup</td>
+<td>&nbsp;</td></tr>
+<tr>
+<td align='center' colspan='3'>@AfterMethod</td>
 </tr>
 <tr>
-<td>&nbsp;</td>
-<td>testOptions</td>
-<td>runner </td>
+<td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>&nbsp;</td>
-<td>testDefaultParameters</td>
-<td>runner </td>
+<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>testParameters</td>
-<td>runner </td>
+<td>testGet</td>
+<td>&nbsp;</td></tr>
+<tr>
+<td>&nbsp;</td>
+<td>testCache</td>
+<td>engine </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testPresets</td>
-<td>runner </td>
+<td>testGetDelay</td>
+<td>engine </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testConfiguration</td>
-<td>&nbsp;</td></tr>
+<td>testPull</td>
+<td>engine </td>
+</tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
 </tr>
@@ -839,48 +1206,46 @@
 <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>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>testProteinSequenceGeneration</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
+<td>testRunOnCluster</td>
+<td>cluster runner </td>
 </tr>
 <tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
+<td>&nbsp;</td>
+<td>testPersistance</td>
+<td>runner </td>
 </tr>
 <tr>
-<td align='center' colspan='3'>@AfterMethod</td>
+<td>&nbsp;</td>
+<td>testRunOnClusterAsync</td>
+<td>cluster runner </td>
 </tr>
 <tr>
-<td align='center' colspan='3'>@AfterClass</td>
+<td>&nbsp;</td>
+<td>testConfigurationLoading</td>
+<td>runner </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>
+<td>&nbsp;</td>
+<td>readStatistics</td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testTaskList</td>
-<td>engine cluster </td>
+<td>testRunLocally</td>
+<td>runner </td>
 </tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -889,21 +1254,51 @@
 <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.data.sequence.FastaSequenceTester</td>
+<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>testGetFormattedFasta</td>
-<td>&nbsp;</td></tr>
+<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>
@@ -911,24 +1306,34 @@
 <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.client.PathValidatorTester</td>
+<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>testIsAbsolutePath</td>
+<td>testBuildCommand</td>
+<td>cluster runner </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>testGetTestCommand</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testGetClassPath</td>
+<td>testGetTestArgsCommand</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -943,30 +1348,18 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.data.sequence.SequenceUtilTester</td>
+<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>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>testLimitExceeded</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testCleanSequence</td>
+<td>testLoadLimits</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -975,60 +1368,63 @@
 <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.msa.TcoffeeParametersTester</td>
+<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>testConstrainedParametersMaxValues</td>
-<td>runner non_windows </td>
+<td>testCancelLocally</td>
+<td>engine </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner non_windows </td>
+<td>testMultipleCancelLocally</td>
+<td>engine </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner non_windows </td>
+<td>testCancelCompletedTaskLocally</td>
+<td>engine </td>
 </tr>
 <tr>
-<td>&nbsp;</td>
-<td>testArguments</td>
-<td>runner non_windows </td>
+<td align='center' colspan='3'>@BeforeClass</td>
 </tr>
 <tr>
-<td>&nbsp;</td>
-<td>testOptions</td>
-<td>runner non_windows </td>
+<td align='center' colspan='3'>@BeforeMethod</td>
 </tr>
 <tr>
-<td>&nbsp;</td>
-<td>testDefaultParameters</td>
-<td>runner non_windows </td>
+<td align='center' colspan='3'>@AfterMethod</td>
 </tr>
 <tr>
-<td>&nbsp;</td>
-<td>testParameters</td>
-<td>runner non_windows </td>
+<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>testPresets</td>
-<td>runner non_windows </td>
+<td>testBuildCommand</td>
+<td>cluster runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testConfiguration</td>
+<td>testGetTestCommand</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -1037,87 +1433,87 @@
 <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>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>testRunOnCluster</td>
-<td>cluster runner </td>
+<tr>
+<td align='center' colspan='3'>@Test</td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testPersistance</td>
+<td>testConstrainedParametersMaxValues</td>
 <td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testAddParameters</td>
-<td>&nbsp;</td></tr>
+<td>testConstrainedParametersRandomValues</td>
+<td>runner </td>
+</tr>
 <tr>
 <td>&nbsp;</td>
-<td>testOptionsLocally</td>
+<td>testConstrainedParametersMinValues</td>
 <td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>readStatisticsClusterExecution</td>
-<td>cluster runner </td>
+<td>testArguments</td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testConfigurationLoading</td>
+<td>testOptions</td>
 <td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testRunWithMatrix</td>
+<td>testDefaultParameters</td>
 <td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>readStatistics</td>
+<td>testParameters</td>
 <td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testRunLocally</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.engine.cluster.drmaa.UtilTester</td>
+<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>testParser</td>
+<td>testProteinSequenceGeneration</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
@@ -1132,19 +1528,16 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.engine.conf.DirectoryManagerTester</td>
+<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>testGetDirectory</td>
-<td>&nbsp;</td></tr>
-<tr>
-<td>&nbsp;</td>
-<td>testNanoTime</td>
-<td>&nbsp;</td></tr>
+<td>testTaskList</td>
+<td>engine cluster </td>
+</tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
 </tr>
@@ -1158,21 +1551,15 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester</td>
+<td>compbio.data.sequence.FastaReaderTester</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>
+<td>test</td>
+<td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
 </tr>
@@ -1186,26 +1573,15 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester</td>
+<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>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>
+<td>testGetFormattedFasta</td>
+<td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@BeforeClass</td>
 </tr>
@@ -1219,44 +1595,58 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.metadata.PresetTester</td>
+<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>marshallPreset</td>
+<td>testReadIUPredForGlobDomain</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>validatePresets</td>
+<td>testDeepCleanSequence</td>
 <td>&nbsp;</td></tr>
 <tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
+<td>&nbsp;</td>
+<td>testReadIUPredForShortAndLongDisorder</td>
+<td>&nbsp;</td></tr>
 <tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
+<td>&nbsp;</td>
+<td>testCleanProteinSequence</td>
+<td>&nbsp;</td></tr>
 <tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
+<td>&nbsp;</td>
+<td>testReadWriteFasta</td>
+<td>&nbsp;</td></tr>
 <tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
+<td>&nbsp;</td>
+<td>testReadAAConResults</td>
+<td>&nbsp;</td></tr>
 <tr>
-<td>compbio.metadata.OptionMarshallerTester</td>
-<td>&nbsp;</td><td>&nbsp;</td></tr>
+<td>&nbsp;</td>
+<td>testReadGlobPlotResults</td>
+<td>&nbsp;</td></tr>
 <tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
+<td>&nbsp;</td>
+<td>testReadDisemblResults</td>
+<td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testUnMarshalling</td>
+<td>loadJronnFile</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testMarshalling</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>
@@ -1265,17 +1655,13 @@
 <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>compbio.runner.msa.TcoffeeParametersTester</td>
 <td>&nbsp;</td><td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@Test</td>
@@ -1283,42 +1669,42 @@
 <tr>
 <td>&nbsp;</td>
 <td>testConstrainedParametersMaxValues</td>
-<td>runner </td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testConstrainedParametersRandomValues</td>
-<td>runner </td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testConstrainedParametersMinValues</td>
-<td>runner </td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testArguments</td>
-<td>runner </td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testOptions</td>
-<td>runner </td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testDefaultParameters</td>
-<td>runner </td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testParameters</td>
-<td>runner </td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testPresets</td>
-<td>runner </td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
@@ -1333,7 +1719,7 @@
 <tr>
 <td>&nbsp;</td>
 <td>setup</td>
-<td>runner </td>
+<td>runner non_windows </td>
 </tr>
 <tr>
 <td align='center' colspan='3'>@AfterMethod</td>
@@ -1342,25 +1728,78 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.runner._impl.RPSBlastTester</td>
+<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>testGetTestCommand</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.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>testBuildCommand</td>
+<td>testRunOnCluster</td>
 <td>cluster runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
-<td>testGetTestArgsCommand</td>
+<td>testAddParameters</td>
 <td>&nbsp;</td></tr>
 <tr>
+<td>&nbsp;</td>
+<td>testPersistance</td>
+<td>runner </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>testRunWithMatrix</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>
@@ -1373,14 +1812,18 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.engine.PulledFileCacheTester</td>
+<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>test</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>
@@ -1395,20 +1838,23 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.runner._impl.MclTester</td>
+<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>testGetTestCommand</td>
+<td>testPresetWithMuptiOptions</td>
 <td>&nbsp;</td></tr>
 <tr>
 <td>&nbsp;</td>
-<td>testBuildCommand</td>
-<td>cluster runner </td>
-</tr>
+<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>
@@ -1422,14 +1868,18 @@
 <td align='center' colspan='3'>@AfterClass</td>
 </tr>
 <tr>
-<td>compbio.engine.cluster.dundee._QueueTester</td>
+<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>testQueue</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>
@@ -1438,13 +1888,17 @@
 <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.ProbconsParametersTester</td>
+<td>compbio.runner.msa.ClustalWParametersTester</td>
 <td>&nbsp;</td><td>&nbsp;</td></tr>
 <tr>
 <td align='center' colspan='3'>@Test</td>
@@ -1452,37 +1906,42 @@
 <tr>
 <td>&nbsp;</td>
 <td>testConstrainedParametersMaxValues</td>
-<td>runner non_windows </td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testConstrainedParametersRandomValues</td>
-<td>runner non_windows </td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testConstrainedParametersMinValues</td>
-<td>runner non_windows </td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testArguments</td>
-<td>runner non_windows </td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testOptions</td>
-<td>runner non_windows </td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testDefaultParameters</td>
-<td>runner non_windows </td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
 <td>testParameters</td>
-<td>runner non_windows </td>
+<td>runner </td>
+</tr>
+<tr>
+<td>&nbsp;</td>
+<td>testPresets</td>
+<td>runner </td>
 </tr>
 <tr>
 <td>&nbsp;</td>
@@ -1497,7 +1956,7 @@
 <tr>
 <td>&nbsp;</td>
 <td>setup</td>
-<td>runner non_windows </td>
+<td>runner </td>
 </tr>
 <tr>
 <td align='center' colspan='3'>@AfterMethod</td>