+++ /dev/null
-<html>
-<head>
-<title>TestNG: Ant test</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-
-<style type="text/css">
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-.stack-trace { display: none;}
-</style>
-<script type="text/javascript">
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-
-</head>
-<body>
-<h2 align='center'>Ant test</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>165/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Wed Feb 17 15:34:08 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>524 seconds (524407 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td>performance </td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-passed'>
-<tr><td colspan='4' align='center'><b>PASSED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.metadata.PresetTester.marshallPreset()'><b>marshallPreset</b><br>Test class:Ant test</td>
-<td>compbio.metadata.PresetTester@50009f0d</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()'><b>readStatisticsClusterExecution</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>8</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.PulledFileCacheTester.test()'><b>test</b><br>Test class:Ant test</td>
-<td>compbio.engine.PulledFileCacheTester@1164b9b6</td><td>5</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>3</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>6</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>7</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>2</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>8</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation()'><b>testAsyncCancelOperation</b><br>Test class:Ant test</td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation()'><b>testAsyncRetrievOperation</b><br>Test class:Ant test</td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.FilePullerTester.testCache()'><b>testCache</b><br>Test class:Ant test</td>
-<td>compbio.engine.FilePullerTester@5fa80aea</td><td>6</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()'><b>testCancel</b><br>Test class:Ant test</td>
-<td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18</td><td>1</td>
-<td><div><pre>compbio.metadata.ResultNotAvailableException: 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!
- at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
- at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
- at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
- at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
-Caused by: 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!
- at compbio.runner.Util.readClustalFile(Util.java:126)
- at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
- ... 25 more
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1915626539", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1915626539'><pre>compbio.metadata.ResultNotAvailableException: 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!
- at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
- at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
- at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
- at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-Caused by: 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!
- at compbio.runner.Util.readClustalFile(Util.java:126)
- at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
- ... 25 more
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()'><b>testCancel</b><br>Test class:Ant test</td>
-<td>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@4301ac93</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally()'><b>testCancelCompletedTaskLocally</b><br>Test class:Ant test</td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>3</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally()'><b>testCancelCompletedTaskLocally</b><br>Test class:Ant test</td>
-<td>compbio.engine.local.LocalRunnerTester@4b2922f6</td><td>0</td>
-<td><div><pre>java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
- at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1132612908", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1132612908'><pre>java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
- at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally()'><b>testCancelLocally</b><br>Test class:Ant test</td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
-<td><div><pre>java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
- at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1931494437", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1931494437'><pre>java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
- at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.LocalRunnerTester.testCancelLocally()'><b>testCancelLocally</b><br>Test class:Ant test</td>
-<td>compbio.engine.local.LocalRunnerTester@4b2922f6</td><td>0</td>
-<td><div><pre>java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
- at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1100010806", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1100010806'><pre>java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
- at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.data.sequence.SequenceUtilTester.testCleanSequence()'><b>testCleanSequence</b><br>Test class:Ant test</td>
-<td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()'><b>testClusterEngineConf</b><br>Test class:Ant test</td>
-<td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftTester@259a8416</td><td>11</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>19</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>5</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.client.CommandBuilderTester.testCommandBuilding()'><b>testCommandBuilding</b><br>Test class:Ant test</td>
-<td>compbio.engine.client.CommandBuilderTester@6bdc64a5</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>3</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>38</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>11</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>5</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>3</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>7</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>7</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>61</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>21</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue()'><b>testCreateNumParameterWithoutValidValue</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td><div><pre>java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
-Description: DNA weight matrix
-URL: null
-Is required: false
-
- Without possible values! Please define possible value first!
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
- at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace713889609", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace713889609'><pre>java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
-Description: DNA weight matrix
-URL: null
-Is required: false
-
- Without possible values! Please define possible value first!
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
- at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testCreateParameter()'><b>testCreateParameter</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td><div><pre>compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-POSSIBLE VALUES:
-BLOSUM
-GONNET
-ID
-PAM
-
-
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
- at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace321958204", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace321958204'><pre>compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-POSSIBLE VALUES:
-BLOSUM
-GONNET
-ID
-PAM
-
-
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
- at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testCreateParameterWithValidValueConstrain()'><b>testCreateParameterWithValidValueConstrain</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.data.sequence.SequenceUtilTester.testDeepCleanSequence()'><b>testDeepCleanSequence</b><br>Test class:Ant test</td>
-<td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>20</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>14</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>10</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.FilePullerTester.testGet()'><b>testGet</b><br>Test class:Ant test</td>
-<td>compbio.engine.FilePullerTester@5fa80aea</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.EngineConfiguratorTester.testGetAsyncEngine()'><b>testGetAsyncEngine</b><br>Test class:Ant test</td>
-<td>compbio.engine.EngineConfiguratorTester@31f9338f</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.client.PathValidatorTester.testGetClassPath()'><b>testGetClassPath</b><br>Test class:Ant test</td>
-<td>compbio.engine.client.PathValidatorTester@5253c3f5</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.FilePullerTester.testGetDelay()'><b>testGetDelay</b><br>Test class:Ant test</td>
-<td>compbio.engine.FilePullerTester@5fa80aea</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
-<td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
-<td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
-<td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
-<td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.data.sequence.FastaSequenceTester.testGetFormattedFasta()'><b>testGetFormattedFasta</b><br>Test class:Ant test</td>
-<td>compbio.data.sequence.FastaSequenceTester@ec0a9f9</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()'><b>testGetJobStatus</b><br>Test class:Ant test</td>
-<td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18</td><td>20</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>20</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>20</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>21</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>40</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>20</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.EngineConfiguratorTester.testGetSyncEngine()'><b>testGetSyncEngine</b><br>Test class:Ant test</td>
-<td>compbio.engine.EngineConfiguratorTester@31f9338f</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner._impl.OBTester.testGetTestArgsCommand()'><b>testGetTestArgsCommand</b><br>Test class:Ant test</td>
-<td>compbio.runner._impl.OBTester@327124af</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner._impl.RPSBlastTester.testGetTestArgsCommand()'><b>testGetTestArgsCommand</b><br>Test class:Ant test</td>
-<td>compbio.runner._impl.RPSBlastTester@221f7708</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner._impl.MclTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
-<td>compbio.runner._impl.MclTester@4402a6ff</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner._impl.NetNglycTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
-<td>compbio.runner._impl.NetNglycTester@a21d23b</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner._impl.OBTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
-<td>compbio.runner._impl.OBTester@327124af</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner._impl.RPSBlastTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
-<td>compbio.runner._impl.RPSBlastTester@221f7708</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner._impl.RonnTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
-<td>compbio.runner._impl.RonnTester@3fbfbfb8</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner._impl.Tmhmm2Tester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
-<td>compbio.runner._impl.Tmhmm2Tester@45c3e9ba</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.client.PathValidatorTester.testIsAbsolutePath()'><b>testIsAbsolutePath</b><br>Test class:Ant test</td>
-<td>compbio.engine.client.PathValidatorTester@5253c3f5</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.LimitTester.testLoadLimits()'><b>testLoadLimits</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.LimitTester@1b0c6cfc</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.RunnerConfigMarshallerTester.testMarshalling()'><b>testMarshalling</b><br>Test class:Ant test</td>
-<td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.metadata.OptionMarshallerTester.testMarshalling()'><b>testMarshalling</b><br>Test class:Ant test</td>
-<td>compbio.metadata.OptionMarshallerTester@372c9557</td><td>0</td>
-<td><div><pre>javax.xml.bind.MarshalException
- - with linked exception:
-[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
- at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
- at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
- at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
-Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
- at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
- at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
- at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
- at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
- at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
- ... 26 more
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1691463635", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1691463635'><pre>javax.xml.bind.MarshalException
- - with linked exception:
-[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
- at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
- at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
- at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
- at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
- at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
- at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
- at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
- at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
- ... 26 more
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally()'><b>testMultipleCancelLocally</b><br>Test class:Ant test</td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
-<td><div><pre>java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
- at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1281054121", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1281054121'><pre>java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
- at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally()'><b>testMultipleCancelLocally</b><br>Test class:Ant test</td>
-<td>compbio.engine.local.LocalRunnerTester@4b2922f6</td><td>0</td>
-<td><div><pre>java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
- at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace764924063", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace764924063'><pre>java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
- at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeTester.testNcore()'><b>testNcore</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate()'><b>testOptionNoDefaultValidate</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td><div><pre>javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
---ABMAT
---BBBB
-
- at compbio.metadata.Option.validate(Option.java:317)
- at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace283755922", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace283755922'><pre>javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
---ABMAT
---BBBB
-
- at compbio.metadata.Option.validate(Option.java:317)
- at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue()'><b>testOptionSetInvalidValue</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td><div><pre>compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
---ABMAT
---BBBB
-
- at compbio.metadata.Option.setDefaultValue(Option.java:130)
- at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1260681385", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1260681385'><pre>compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
---ABMAT
---BBBB
-
- at compbio.metadata.Option.setDefaultValue(Option.java:130)
- at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testOptionToCommand()'><b>testOptionToCommand</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>2</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>4</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>2</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWTester.testOptionsLocally()'><b>testOptionsLocally</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.client.CommandBuilderTester.testOptionsToCommand()'><b>testOptionsToCommand</b><br>Test class:Ant test</td>
-<td>compbio.engine.client.CommandBuilderTester@6bdc64a5</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testParameterToCommand()'><b>testParameterToCommand</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>2</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>2</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>4</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>12</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.cluster.drmaa.UtilTester.testParser()'><b>testParser</b><br>Test class:Ant test</td>
-<td>compbio.engine.cluster.drmaa.UtilTester@22e90943</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftTester@259a8416</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>2</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.TcoffeeParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.data.sequence.FastaSequenceGeneratorTester.testProteinSequenceGeneration()'><b>testProteinSequenceGeneration</b><br>Test class:Ant test</td>
-<td>compbio.data.sequence.FastaSequenceGeneratorTester@163b4b1e</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.FilePullerTester.testPull()'><b>testPull</b><br>Test class:Ant test</td>
-<td>compbio.engine.FilePullerTester@5fa80aea</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.cluster.dundee._QueueTester.testQueue()'><b>testQueue</b><br>Test class:Ant test</td>
-<td>compbio.engine.cluster.dundee._QueueTester@715f1f9c</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFile()'><b>testReadClustalFile</b><br>Test class:Ant test</td>
-<td>compbio.data.sequence.ClustalAlignmentUtilTester@38c52200</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileLongNames()'><b>testReadClustalFileLongNames</b><br>Test class:Ant test</td>
-<td>compbio.data.sequence.ClustalAlignmentUtilTester@38c52200</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileShortNames()'><b>testReadClustalFileShortNames</b><br>Test class:Ant test</td>
-<td>compbio.data.sequence.ClustalAlignmentUtilTester@38c52200</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.data.sequence.SequenceUtilTester.testReadWriteFasta()'><b>testReadWriteFasta</b><br>Test class:Ant test</td>
-<td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>15</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MuscleTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MuscleTester@37b994de</td><td>8</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()'><b>testRunOnClusterAsyncCheckStatusLongPoolingTime</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftTester@259a8416</td><td>21</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ClustalWTester.testRunWithMatrix()'><b>testRunWithMatrix</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.RunnerConfigMarshallerTester.testSchemaFromCodeGeneration()'><b>testSchemaFromCodeGeneration</b><br>Test class:Ant test</td>
-<td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.MafftTester.testSetInputTester()'><b>testSetInputTester</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsTester.testSetInputTester()'><b>testSetInputTester</b><br>Test class:Ant test</td>
-<td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.client.CommandBuilderTester.testSpaceDelimiterExecutable()'><b>testSpaceDelimiterExecutable</b><br>Test class:Ant test</td>
-<td>compbio.engine.client.CommandBuilderTester@6bdc64a5</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()'><b>testSubmit</b><br>Test class:Ant test</td>
-<td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18</td><td>18</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()'><b>testSubmit</b><br>Test class:Ant test</td>
-<td>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@4301ac93</td><td>17</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
-<td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()'><b>testTaskList</b><br>Test class:Ant test</td>
-<td>compbio.engine.cluster.drmaa.ClusterSessionTester@7966340c</td><td>8</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.RunnerConfigMarshallerTester.testUnMarshalling()'><b>testUnMarshalling</b><br>Test class:Ant test</td>
-<td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.metadata.OptionMarshallerTester.testUnMarshalling()'><b>testUnMarshalling</b><br>Test class:Ant test</td>
-<td>compbio.metadata.OptionMarshallerTester@372c9557</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testValidate()'><b>testValidate</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testValidateBoundaryConstrainCheck()'><b>testValidateBoundaryConstrainCheck</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck()'><b>testValidateLowerBoundaryConstrainCheck</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td><div><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
-Min: -10.12
-Max: 0
-
- For parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-Type: Float
-Min: -10.12
-Max: 0
-
-
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
- at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1790017034", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1790017034'><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
-Min: -10.12
-Max: 0
-
- For parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-Type: Float
-Min: -10.12
-Max: 0
-
-
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
- at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck()'><b>testValidateUpperBoundaryConstrainCheck</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td><div><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
-Min: -10.12
-Max: 0
-
- For parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-Type: Float
-Min: -10.12
-Max: 0
-
-
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
- at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace603950563", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace603950563'><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
-Min: -10.12
-Max: 0
-
- For parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-Type: Float
-Min: -10.12
-Max: 0
-
-
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
- at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.metadata.RunnerConfigTester.testValidateValueConstrain()'><b>testValidateValueConstrain</b><br>Test class:Ant test</td>
-<td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
-<td><div><pre>javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
-
- at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
- at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1313551855", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1313551855'><pre>javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
-
- at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
- at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.RunnerConfigMarshallerTester.testValidation()'><b>testValidation</b><br>Test class:Ant test</td>
-<td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling()'><b>testValidationOnMarshalling</b><br>Test class:Ant test</td>
-<td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
-<td><div><pre>javax.xml.bind.MarshalException
- - with linked exception:
-[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
- at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
- at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
- at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
-Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
- at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
- at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
- at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
- at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
- at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
- ... 26 more
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace831577209", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace831577209'><pre>javax.xml.bind.MarshalException
- - with linked exception:
-[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
- at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
- at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
- at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
- at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
- at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
- at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
- at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
- at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
- ... 26 more
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.metadata.OptionCombinatorTester.testgetAllOptions()'><b>testgetAllOptions</b><br>Test class:Ant test</td>
-<td>compbio.metadata.OptionCombinatorTester@79b66b06</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.metadata.OptionCombinatorTester.testgetAllParameters()'><b>testgetAllParameters</b><br>Test class:Ant test</td>
-<td>compbio.metadata.OptionCombinatorTester@79b66b06</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.data.sequence.SequenceUtilTester.testisNonAmbNucleotideSequence()'><b>testisNonAmbNucleotideSequence</b><br>Test class:Ant test</td>
-<td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.data.sequence.SequenceUtilTester.testisProteinSequence()'><b>testisProteinSequence</b><br>Test class:Ant test</td>
-<td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration()'><b>validateClustalConfiguration</b><br>Test class:Ant test</td>
-<td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration()'><b>validateMafftConfiguration</b><br>Test class:Ant test</td>
-<td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration()'><b>validateMuscleConfiguration</b><br>Test class:Ant test</td>
-<td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.metadata.PresetTester.validatePresets()'><b>validatePresets</b><br>Test class:Ant test</td>
-<td>compbio.metadata.PresetTester@50009f0d</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration()'><b>validateTcoffeeConfiguration</b><br>Test class:Ant test</td>
-<td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult Ant test]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="Ant test" failures="0" tests="165" time="524.407" errors="0">
- <properties/>
- <testcase name="testPull" time="0.45" classname="compbio.engine.FilePullerTester"/>
- <testcase name="testCache" time="6.006" classname="compbio.engine.FilePullerTester"/>
- <testcase name="testArguments" time="3.518" classname="compbio.runner.msa.ClustalWParametersTester"/>
- <testcase name="testConfiguration" time="0.0010" classname="compbio.runner.msa.ClustalWParametersTester"/>
- <testcase name="testConstrainedParametersMaxValues" time="1.835" classname="compbio.runner.msa.ClustalWParametersTester"/>
- <testcase name="testConstrainedParametersMinValues" time="1.232" classname="compbio.runner.msa.ClustalWParametersTester"/>
- <testcase name="testConstrainedParametersRandomValues" time="3.105" classname="compbio.runner.msa.ClustalWParametersTester"/>
- <testcase name="testDefaultParameters" time="0.502" classname="compbio.runner.msa.ClustalWParametersTester"/>
- <testcase name="testOptions" time="2.109" classname="compbio.runner.msa.ClustalWParametersTester"/>
- <testcase name="testParameters" time="2.68" classname="compbio.runner.msa.ClustalWParametersTester"/>
- <testcase name="testPresets" time="0.177" classname="compbio.runner.msa.ClustalWParametersTester"/>
- <testcase name="testReadClustalFile" time="0.022" classname="compbio.data.sequence.ClustalAlignmentUtilTester"/>
- <testcase name="testReadClustalFileLongNames" time="0.052" classname="compbio.data.sequence.ClustalAlignmentUtilTester"/>
- <testcase name="testReadClustalFileShortNames" time="0.054" classname="compbio.data.sequence.ClustalAlignmentUtilTester"/>
- <testcase name="testProteinSequenceGeneration" time="0.0080" classname="compbio.data.sequence.FastaSequenceGeneratorTester"/>
- <testcase name="testGetFormattedFasta" time="0.0" classname="compbio.data.sequence.FastaSequenceTester"/>
- <testcase name="testCleanSequence" time="0.0" classname="compbio.data.sequence.SequenceUtilTester"/>
- <testcase name="testDeepCleanSequence" time="0.0" classname="compbio.data.sequence.SequenceUtilTester"/>
- <testcase name="testReadWriteFasta" time="0.016" classname="compbio.data.sequence.SequenceUtilTester"/>
- <testcase name="testisNonAmbNucleotideSequence" time="0.0" classname="compbio.data.sequence.SequenceUtilTester"/>
- <testcase name="testisProteinSequence" time="0.0" classname="compbio.data.sequence.SequenceUtilTester"/>
- <testcase name="testGetAsyncEngine" time="0.296" classname="compbio.engine.EngineConfiguratorTester"/>
- <testcase name="testGetSyncEngine" time="0.0" classname="compbio.engine.EngineConfiguratorTester"/>
- <testcase name="testGetDelay" time="0.0" classname="compbio.engine.FilePullerTester"/>
- <testcase name="testGet" time="0.046" classname="compbio.engine.FilePullerTester"/>
- <testcase name="test" time="5.187" classname="compbio.engine.PulledFileCacheTester"/>
- <testcase name="testCommandBuilding" time="0.0010" classname="compbio.engine.client.CommandBuilderTester"/>
- <testcase name="testOptionsToCommand" time="0.567" classname="compbio.engine.client.CommandBuilderTester"/>
- <testcase name="testSpaceDelimiterExecutable" time="0.0" classname="compbio.engine.client.CommandBuilderTester"/>
- <testcase name="testGetClassPath" time="0.234" classname="compbio.engine.client.PathValidatorTester"/>
- <testcase name="testIsAbsolutePath" time="0.0" classname="compbio.engine.client.PathValidatorTester"/>
- <testcase name="testTaskList" time="8.964" classname="compbio.engine.cluster.drmaa.ClusterSessionTester"/>
- <testcase name="testCancel" time="1.273" classname="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
- <testcase name="testGetJobStatus" time="20.778" classname="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
- <testcase name="testSubmit" time="18.714" classname="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
- <testcase name="testCancel" time="1.587" classname="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
- <testcase name="testSubmit" time="17.835" classname="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
- <testcase name="testParser" time="0.0" classname="compbio.engine.cluster.drmaa.UtilTester"/>
- <testcase name="testQueue" time="0.0" classname="compbio.engine.cluster.dundee._QueueTester"/>
- <testcase name="testGetDirectory" time="0.1" classname="compbio.engine.conf.DirectoryManagerTester"/>
- <testcase name="testGetDirectory" time="0.104" classname="compbio.engine.conf.DirectoryManagerTester"/>
- <testcase name="testGetDirectory" time="0.11" classname="compbio.engine.conf.DirectoryManagerTester"/>
- <testcase name="testGetDirectory" time="0.103" classname="compbio.engine.conf.DirectoryManagerTester"/>
- <testcase name="testClusterEngineConf" time="0.104" classname="compbio.engine.conf.PropertyHelperManagerTester"/>
- <testcase name="validateClustalConfiguration" time="0.043" classname="compbio.engine.conf.PropertyHelperManagerTester"/>
- <testcase name="validateMafftConfiguration" time="0.0010" classname="compbio.engine.conf.PropertyHelperManagerTester"/>
- <testcase name="validateMuscleConfiguration" time="0.0040" classname="compbio.engine.conf.PropertyHelperManagerTester"/>
- <testcase name="validateTcoffeeConfiguration" time="0.0040" classname="compbio.engine.conf.PropertyHelperManagerTester"/>
- <testcase name="testMarshalling" time="0.02" classname="compbio.engine.conf.RunnerConfigMarshallerTester"/>
- <testcase name="testSchemaFromCodeGeneration" time="0.504" classname="compbio.engine.conf.RunnerConfigMarshallerTester"/>
- <testcase name="testUnMarshalling" time="0.58" classname="compbio.engine.conf.RunnerConfigMarshallerTester"/>
- <testcase name="testValidation" time="0.636" classname="compbio.engine.conf.RunnerConfigMarshallerTester"/>
- <testcase name="testValidationOnMarshalling" time="0.011" classname="compbio.engine.conf.RunnerConfigMarshallerTester"/>
- <testcase name="testAsyncCancelOperation" time="0.048" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testAsyncRetrievOperation" time="0.56" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testCancelCompletedTaskLocally" time="3.053" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testCancelLocally" time="0.027" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testGetStatus" time="20.872" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testGetStatus" time="20.915" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testGetStatus" time="21.332" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testGetStatus" time="40.987" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testGetStatus" time="20.863" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testMultipleCancelLocally" time="0.267" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testSubmitLocally" time="0.125" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testSubmitLocally" time="0.22" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testSubmitLocally" time="0.176" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testSubmitLocally" time="0.482" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testSubmitLocally" time="0.634" classname="compbio.engine.local.AsyncLocalRunnerTester"/>
- <testcase name="testCancelCompletedTaskLocally" time="0.336" classname="compbio.engine.local.LocalRunnerTester"/>
- <testcase name="testCancelLocally" time="0.02" classname="compbio.engine.local.LocalRunnerTester"/>
- <testcase name="testMultipleCancelLocally" time="0.058" classname="compbio.engine.local.LocalRunnerTester"/>
- <testcase name="testgetAllOptions" time="0.0010" classname="compbio.metadata.OptionCombinatorTester"/>
- <testcase name="testgetAllParameters" time="0.0030" classname="compbio.metadata.OptionCombinatorTester"/>
- <testcase name="testMarshalling" time="0.058" classname="compbio.metadata.OptionMarshallerTester"/>
- <testcase name="testUnMarshalling" time="0.386" classname="compbio.metadata.OptionMarshallerTester"/>
- <testcase name="marshallPreset" time="0.899" classname="compbio.metadata.PresetTester"/>
- <testcase name="validatePresets" time="0.0010" classname="compbio.metadata.PresetTester"/>
- <testcase name="testCreateNumParameterWithoutValidValue" time="0.0010" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testCreateParameter" time="0.0" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testCreateParameterWithValidValueConstrain" time="0.0" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testOptionNoDefaultValidate" time="0.0" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testOptionSetInvalidValue" time="0.0010" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testOptionToCommand" time="0.0" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testParameterToCommand" time="0.0" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testValidate" time="0.0" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testValidateBoundaryConstrainCheck" time="0.0010" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testValidateLowerBoundaryConstrainCheck" time="0.0" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testValidateUpperBoundaryConstrainCheck" time="0.0" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testValidateValueConstrain" time="0.0" classname="compbio.metadata.RunnerConfigTester"/>
- <testcase name="testGetTestCommand" time="0.0010" classname="compbio.runner._impl.MclTester"/>
- <testcase name="testGetTestCommand" time="0.0" classname="compbio.runner._impl.NetNglycTester"/>
- <testcase name="testGetTestArgsCommand" time="0.0" classname="compbio.runner._impl.OBTester"/>
- <testcase name="testGetTestCommand" time="0.0" classname="compbio.runner._impl.OBTester"/>
- <testcase name="testGetTestArgsCommand" time="0.0" classname="compbio.runner._impl.RPSBlastTester"/>
- <testcase name="testGetTestCommand" time="0.0" classname="compbio.runner._impl.RPSBlastTester"/>
- <testcase name="testGetTestCommand" time="0.0" classname="compbio.runner._impl.RonnTester"/>
- <testcase name="testGetTestCommand" time="0.0" classname="compbio.runner._impl.Tmhmm2Tester"/>
- <testcase name="readStatistics" time="1.178" classname="compbio.runner.msa.ClustalWTester"/>
- <testcase name="readStatisticsClusterExecution" time="8.121" classname="compbio.runner.msa.ClustalWTester"/>
- <testcase name="testConfigurationLoading" time="0.688" classname="compbio.runner.msa.ClustalWTester"/>
- <testcase name="testOptionsLocally" time="1.932" classname="compbio.runner.msa.ClustalWTester"/>
- <testcase name="testPersistance" time="0.431" classname="compbio.runner.msa.ClustalWTester"/>
- <testcase name="testRunLocally" time="0.171" classname="compbio.runner.msa.ClustalWTester"/>
- <testcase name="testRunOnCluster" time="15.937" classname="compbio.runner.msa.ClustalWTester"/>
- <testcase name="testRunWithMatrix" time="0.824" classname="compbio.runner.msa.ClustalWTester"/>
- <testcase name="testLoadLimits" time="0.0" classname="compbio.runner.msa.LimitTester"/>
- <testcase name="testArguments" time="6.103" classname="compbio.runner.msa.MafftParametersTester"/>
- <testcase name="testConfiguration" time="0.0010" classname="compbio.runner.msa.MafftParametersTester"/>
- <testcase name="testConstrainedParametersMaxValues" time="3.235" classname="compbio.runner.msa.MafftParametersTester"/>
- <testcase name="testConstrainedParametersMinValues" time="1.326" classname="compbio.runner.msa.MafftParametersTester"/>
- <testcase name="testConstrainedParametersRandomValues" time="7.672" classname="compbio.runner.msa.MafftParametersTester"/>
- <testcase name="testDefaultParameters" time="20.463" classname="compbio.runner.msa.MafftParametersTester"/>
- <testcase name="testOptions" time="4.449" classname="compbio.runner.msa.MafftParametersTester"/>
- <testcase name="testParameters" time="2.422" classname="compbio.runner.msa.MafftParametersTester"/>
- <testcase name="testPresets" time="2.136" classname="compbio.runner.msa.MafftParametersTester"/>
- <testcase name="readStatistics" time="0.639" classname="compbio.runner.msa.MafftTester"/>
- <testcase name="testClusterExecute" time="11.34" classname="compbio.runner.msa.MafftTester"/>
- <testcase name="testConfigurationLoading" time="0.435" classname="compbio.runner.msa.MafftTester"/>
- <testcase name="testExecute" time="0.428" classname="compbio.runner.msa.MafftTester"/>
- <testcase name="testPersistance" time="1.033" classname="compbio.runner.msa.MafftTester"/>
- <testcase name="testRunOnClusterAsyncCheckStatusLongPoolingTime" time="21.418" classname="compbio.runner.msa.MafftTester"/>
- <testcase name="testSetInputTester" time="0.0" classname="compbio.runner.msa.MafftTester"/>
- <testcase name="testArguments" time="7.798" classname="compbio.runner.msa.MuscleParametersTester"/>
- <testcase name="testConfiguration" time="0.0" classname="compbio.runner.msa.MuscleParametersTester"/>
- <testcase name="testConstrainedParametersMaxValues" time="1.534" classname="compbio.runner.msa.MuscleParametersTester"/>
- <testcase name="testConstrainedParametersMinValues" time="0.845" classname="compbio.runner.msa.MuscleParametersTester"/>
- <testcase name="testConstrainedParametersRandomValues" time="7.603" classname="compbio.runner.msa.MuscleParametersTester"/>
- <testcase name="testDefaultParameters" time="0.622" classname="compbio.runner.msa.MuscleParametersTester"/>
- <testcase name="testOptions" time="2.481" classname="compbio.runner.msa.MuscleParametersTester"/>
- <testcase name="testParameters" time="4.773" classname="compbio.runner.msa.MuscleParametersTester"/>
- <testcase name="testPresets" time="0.856" classname="compbio.runner.msa.MuscleParametersTester"/>
- <testcase name="readStatistics" time="0.932" classname="compbio.runner.msa.MuscleTester"/>
- <testcase name="testConfigurationLoading" time="0.313" classname="compbio.runner.msa.MuscleTester"/>
- <testcase name="testPersistance" time="0.241" classname="compbio.runner.msa.MuscleTester"/>
- <testcase name="testRunLocally" time="0.101" classname="compbio.runner.msa.MuscleTester"/>
- <testcase name="testRunOnCluster" time="8.142" classname="compbio.runner.msa.MuscleTester"/>
- <testcase name="testArguments" time="2.874" classname="compbio.runner.msa.ProbconsParametersTester"/>
- <testcase name="testConfiguration" time="0.0010" classname="compbio.runner.msa.ProbconsParametersTester"/>
- <testcase name="testConstrainedParametersMaxValues" time="38.416" classname="compbio.runner.msa.ProbconsParametersTester"/>
- <testcase name="testConstrainedParametersMinValues" time="0.768" classname="compbio.runner.msa.ProbconsParametersTester"/>
- <testcase name="testConstrainedParametersRandomValues" time="61.881" classname="compbio.runner.msa.ProbconsParametersTester"/>
- <testcase name="testDefaultParameters" time="14.704" classname="compbio.runner.msa.ProbconsParametersTester"/>
- <testcase name="testOptions" time="0.433" classname="compbio.runner.msa.ProbconsParametersTester"/>
- <testcase name="testParameters" time="1.321" classname="compbio.runner.msa.ProbconsParametersTester"/>
- <testcase name="readStatistics" time="0.441" classname="compbio.runner.msa.ProbconsTester"/>
- <testcase name="testClusterExecute" time="19.326" classname="compbio.runner.msa.ProbconsTester"/>
- <testcase name="testConfigurationLoading" time="0.107" classname="compbio.runner.msa.ProbconsTester"/>
- <testcase name="testExecute" time="0.436" classname="compbio.runner.msa.ProbconsTester"/>
- <testcase name="testPersistance" time="0.509" classname="compbio.runner.msa.ProbconsTester"/>
- <testcase name="testSetInputTester" time="0.0" classname="compbio.runner.msa.ProbconsTester"/>
- <testcase name="testArguments" time="8.765" classname="compbio.runner.msa.TcoffeeParametersTester"/>
- <testcase name="testConfiguration" time="0.0" classname="compbio.runner.msa.TcoffeeParametersTester"/>
- <testcase name="testConstrainedParametersMaxValues" time="11.166" classname="compbio.runner.msa.TcoffeeParametersTester"/>
- <testcase name="testConstrainedParametersMinValues" time="5.507" classname="compbio.runner.msa.TcoffeeParametersTester"/>
- <testcase name="testConstrainedParametersRandomValues" time="21.942" classname="compbio.runner.msa.TcoffeeParametersTester"/>
- <testcase name="testDefaultParameters" time="10.988" classname="compbio.runner.msa.TcoffeeParametersTester"/>
- <testcase name="testOptions" time="0.891" classname="compbio.runner.msa.TcoffeeParametersTester"/>
- <testcase name="testParameters" time="12.717" classname="compbio.runner.msa.TcoffeeParametersTester"/>
- <testcase name="testPresets" time="1.094" classname="compbio.runner.msa.TcoffeeParametersTester"/>
- <testcase name="readStatistics" time="0.876" classname="compbio.runner.msa.TcoffeeTester"/>
- <testcase name="testClusterExecute" time="5.526" classname="compbio.runner.msa.TcoffeeTester"/>
- <testcase name="testConfigurationLoading" time="0.099" classname="compbio.runner.msa.TcoffeeTester"/>
- <testcase name="testExecute" time="0.868" classname="compbio.runner.msa.TcoffeeTester"/>
- <testcase name="testNcore" time="0.0010" classname="compbio.runner.msa.TcoffeeTester"/>
- <testcase name="testPersistance" time="1.771" classname="compbio.runner.msa.TcoffeeTester"/>
-</testsuite>
+++ /dev/null
-<table border='1'>
-<tr>
-<th>Class name</th>
-<th>Method name</th>
-<th>Groups</th>
-</tr><tr>
-<td>compbio.engine.client.CommandBuilderTester</td>
-<td> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testOptionsToCommand</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testSpaceDelimiterExecutable</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testCommandBuilding</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testValidateUpperBoundaryConstrainCheck</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testOptionSetInvalidValue</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testValidateBoundaryConstrainCheck</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testValidateValueConstrain</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testCreateParameterWithValidValueConstrain</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testValidateLowerBoundaryConstrainCheck</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testOptionNoDefaultValidate</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testCreateParameter</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testOptionToCommand</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testParameterToCommand</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testCreateNumParameterWithoutValidValue</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testValidate</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td> </td>
-<td>setup</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetTestCommand</td>
-<td> </td></tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersMaxValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testArguments</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testOptions</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testDefaultParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testPresets</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConfiguration</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetAsyncEngine</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testGetSyncEngine</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetTestCommand</td>
-<td> </td></tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testExecute</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testPersistance</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testClusterExecute</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testSetInputTester</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </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> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testClusterEngineConf</td>
-<td>cluster </td>
-</tr>
-<tr>
-<td> </td>
-<td>validateClustalConfiguration</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>validateTcoffeeConfiguration</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>validateMuscleConfiguration</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>validateMafftConfiguration</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td> </td>
-<td>testLoadResources</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testGet</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testCache</td>
-<td>engine </td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetDelay</td>
-<td>engine </td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testgetAllParameters</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testgetAllOptions</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td> </td>
-<td>setup</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testRunOnCluster</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testRunOnClusterAsync</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testPersistance</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>readStatistics</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </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> </td>
-<td>init</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testExecute</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testPersistance</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testNcore</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testClusterExecute</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </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> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testLoadLimits</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetTestCommand</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testBuildCommand</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetTestArgsCommand</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testCancelLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td> </td>
-<td>testMultipleCancelLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td> </td>
-<td>testAsyncCancelOperation</td>
-<td>engine </td>
-</tr>
-<tr>
-<td> </td>
-<td>testAsyncRetrievOperation</td>
-<td>engine </td>
-</tr>
-<tr>
-<td> </td>
-<td>testSubmitLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td> </td>
-<td>testCancelCompletedTaskLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testCancelLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td> </td>
-<td>testMultipleCancelLocally</td>
-<td>engine </td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetTestCommand</td>
-<td> </td></tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testExecute</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testRunOnClusterAsyncCheckStatusShortPoolingTime</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testPersistance</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testClusterExecute</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testSetInputTester</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>readStatistics</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </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> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testReadClustalFile</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testReadClustalFileLongNames</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testReadClustalFileShortNames</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersMaxValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testArguments</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testOptions</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testDefaultParameters</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testParameters</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testPresets</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConfiguration</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testProteinSequenceGeneration</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetFormattedFasta</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testIsAbsolutePath</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testGetClassPath</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testDeepCleanSequence</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testReadWriteFasta</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testisNonAmbNucleotideSequence</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testisProteinSequence</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testCleanSequence</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersMaxValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testArguments</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testOptions</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testDefaultParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testPresets</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConfiguration</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testRunOnCluster</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testPersistance</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testAddParameters</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testOptionsLocally</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>readStatisticsClusterExecution</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testRunWithMatrix</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>readStatistics</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testParser</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetDirectory</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testNanoTime</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testSubmit</td>
-<td>engine cluster </td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testSubmit</td>
-<td>engine cluster </td>
-</tr>
-<tr>
-<td> </td>
-<td>testCancel</td>
-<td>engine cluster </td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>marshallPreset</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>validatePresets</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testUnMarshalling</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testMarshalling</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td> </td>
-<td>setup</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersMaxValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testArguments</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testOptions</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testDefaultParameters</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testParameters</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testPresets</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConfiguration</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetTestCommand</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testBuildCommand</td>
-<td>cluster runner </td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetTestArgsCommand</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>test</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testGetTestCommand</td>
-<td> </td></tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testQueue</td>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersMaxValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersRandomValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConstrainedParametersMinValues</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testArguments</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testOptions</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testDefaultParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testParameters</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConfiguration</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td> </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> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testValidationOnMarshalling</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testUnMarshalling</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testValidation</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testSchemaFromCodeGeneration</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>testMarshalling</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@BeforeMethod</td>
-</tr>
-<tr>
-<td> </td>
-<td>setup</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@AfterMethod</td>
-</tr>
-<tr>
-<td align='center' colspan='3'>@AfterClass</td>
-</tr>
-</table>
+++ /dev/null
-<h2>Groups used for this test run</h2><table border="1">
-<tr> <td align="center"><b>Group name</b></td><td align="center"><b>Methods</b></td></tr><tr><td>cluster</td><td>compbio.runner.msa.TcoffeeTester.testPersistance()<br/>compbio.runner.msa.ProbconsTester.testClusterExecute()<br/>compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()<br/>compbio.runner.msa.ClustalWTester.testRunOnCluster()<br/>compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()<br/>compbio.runner.msa.MuscleTester.testRunOnCluster()<br/>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()<br/>compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()<br/>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()<br/>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()<br/>compbio.runner.msa.MafftTester.testClusterExecute()<br/>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()<br/>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()<br/>compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()<br/>compbio.runner.msa.TcoffeeTester.testClusterExecute()<br/></td></tr>
-<tr><td>engine</td><td>compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()<br/>compbio.engine.local.LocalRunnerTester.testCancelLocally()<br/>compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally()<br/>compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally()<br/>compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally()<br/>compbio.engine.FilePullerTester.testCache()<br/>compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation()<br/>compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation()<br/>compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()<br/>compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()<br/>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()<br/>compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally()<br/>compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally()<br/>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()<br/>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()<br/>compbio.engine.FilePullerTester.testGetDelay()<br/>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()<br/>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()<br/>compbio.engine.FilePullerTester.testPull()<br/></td></tr>
-<tr><td>non_windows</td><td>compbio.runner.msa.MafftTester.readStatistics()<br/>compbio.runner.msa.MafftParametersTester.testParameters()<br/>compbio.runner.msa.MafftParametersTester.testDefaultParameters()<br/>compbio.runner.msa.TcoffeeTester.testExecute()<br/>compbio.runner.msa.MafftParametersTester.testPresets()<br/>compbio.runner.msa.MafftTester.testSetInputTester()<br/>compbio.runner.msa.ProbconsParametersTester.testArguments()<br/>compbio.runner.msa.TcoffeeTester.readStatistics()<br/>compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()<br/>compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()<br/>compbio.runner.msa.MafftTester.testExecute()<br/>compbio.runner.msa.ProbconsTester.readStatistics()<br/>compbio.runner.msa.TcoffeeParametersTester.testArguments()<br/>compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()<br/>compbio.runner.msa.TcoffeeTester.testNcore()<br/>compbio.runner.msa.MafftParametersTester.testOptions()<br/>compbio.runner.msa.ProbconsTester.testSetInputTester()<br/>compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()<br/>compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()<br/>compbio.runner.msa.ProbconsTester.testExecute()<br/>compbio.runner.msa.TcoffeeParametersTester.testParameters()<br/>compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()<br/>compbio.runner.msa.TcoffeeTester.testPersistance()<br/>compbio.runner.msa.ProbconsParametersTester.testOptions()<br/>compbio.runner.msa.ProbconsTester.testClusterExecute()<br/>compbio.runner.msa.TcoffeeParametersTester.testPresets()<br/>compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()<br/>compbio.runner.msa.MafftTester.testPersistance()<br/>compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()<br/>compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()<br/>compbio.runner.msa.MafftParametersTester.testArguments()<br/>compbio.runner.msa.TcoffeeParametersTester.testOptions()<br/>compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()<br/>compbio.runner.msa.ProbconsParametersTester.testParameters()<br/>compbio.runner.msa.MafftTester.testClusterExecute()<br/>compbio.runner.msa.ProbconsTester.testPersistance()<br/>compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()<br/>compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()<br/>compbio.runner.msa.TcoffeeTester.testClusterExecute()<br/></td></tr>
-<tr><td>runner</td><td>compbio.runner.msa.ClustalWTester.testConfigurationLoading()<br/>compbio.runner.msa.MafftTester.readStatistics()<br/>compbio.runner.msa.MafftParametersTester.testParameters()<br/>compbio.runner.msa.MafftParametersTester.testDefaultParameters()<br/>compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues()<br/>compbio.runner.msa.MafftTester.testSetInputTester()<br/>compbio.runner.msa.ProbconsParametersTester.testArguments()<br/>compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()<br/>compbio.runner.msa.ClustalWTester.testRunOnCluster()<br/>compbio.runner.msa.MafftTester.testExecute()<br/>compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues()<br/>compbio.runner.msa.TcoffeeTester.testNcore()<br/>compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()<br/>compbio.runner.msa.MuscleTester.testRunLocally()<br/>compbio.runner.msa.TcoffeeParametersTester.testParameters()<br/>compbio.runner.msa.ProbconsTester.testConfigurationLoading()<br/>compbio.runner.msa.ClustalWTester.testRunWithMatrix()<br/>compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()<br/>compbio.runner.msa.ClustalWTester.testRunLocally()<br/>compbio.runner.msa.ProbconsParametersTester.testOptions()<br/>compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues()<br/>compbio.runner.msa.MafftTester.testPersistance()<br/>compbio.runner.msa.MuscleParametersTester.testParameters()<br/>compbio.runner.msa.MuscleParametersTester.testDefaultParameters()<br/>compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()<br/>compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues()<br/>compbio.runner.msa.MuscleTester.testRunOnCluster()<br/>compbio.runner.msa.ClustalWTester.testOptionsLocally()<br/>compbio.runner.msa.MafftTester.testClusterExecute()<br/>compbio.runner.msa.TcoffeeTester.testConfigurationLoading()<br/>compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()<br/>compbio.runner.msa.ClustalWParametersTester.testParameters()<br/>compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()<br/>compbio.runner.msa.ClustalWParametersTester.testDefaultParameters()<br/>compbio.runner.msa.MuscleTester.testConfigurationLoading()<br/>compbio.runner.msa.TcoffeeTester.testExecute()<br/>compbio.runner.msa.MafftParametersTester.testPresets()<br/>compbio.runner.msa.TcoffeeTester.readStatistics()<br/>compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()<br/>compbio.runner.msa.MuscleTester.readStatistics()<br/>compbio.runner.msa.ClustalWParametersTester.testArguments()<br/>compbio.runner.msa.ProbconsTester.readStatistics()<br/>compbio.runner.msa.TcoffeeParametersTester.testArguments()<br/>compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()<br/>compbio.runner.msa.MafftParametersTester.testOptions()<br/>compbio.runner.msa.ProbconsTester.testSetInputTester()<br/>compbio.runner.msa.MuscleParametersTester.testArguments()<br/>compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()<br/>compbio.runner.msa.ClustalWTester.testPersistance()<br/>compbio.runner.msa.ProbconsTester.testExecute()<br/>compbio.runner.msa.TcoffeeTester.testPersistance()<br/>compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues()<br/>compbio.runner.msa.ProbconsTester.testClusterExecute()<br/>compbio.runner.msa.TcoffeeParametersTester.testPresets()<br/>compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()<br/>compbio.runner.msa.MuscleTester.testPersistance()<br/>compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()<br/>compbio.runner.msa.ClustalWParametersTester.testOptions()<br/>compbio.runner.msa.MuscleParametersTester.testPresets()<br/>compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()<br/>compbio.runner.msa.MafftParametersTester.testArguments()<br/>compbio.runner.msa.MafftTester.testConfigurationLoading()<br/>compbio.runner.msa.TcoffeeParametersTester.testOptions()<br/>compbio.runner.msa.ClustalWTester.readStatistics()<br/>compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()<br/>compbio.runner.msa.ProbconsParametersTester.testParameters()<br/>compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues()<br/>compbio.runner.msa.ProbconsTester.testPersistance()<br/>compbio.runner.msa.ClustalWParametersTester.testPresets()<br/>compbio.runner.msa.MuscleParametersTester.testOptions()<br/>compbio.runner.msa.TcoffeeTester.testClusterExecute()<br/></td></tr>
-</table>
+++ /dev/null
-<html><head><title>Results for Ant suite</title></head>
-<frameset cols="26%,74%">
-<frame src="toc.html" name="navFrame">
-<frame src="main.html" name="mainFrame">
-</frameset>
-</html>
+++ /dev/null
-<html><head><title>Results for Ant suite</title></head>
-<body>Select a result on the left-hand pane.</body></html>
+++ /dev/null
-<h2>Methods run, sorted chronologically</h2><h3>>> means before, << means after</h3><p/><br/><em>Ant suite</em><p/><small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table border="1">
-<tr><th>Time</th><th>Delta (ms)</th><th>Suite<br>configuration</th><th>Test<br>configuration</th><th>Class<br>configuration</th><th>Groups<br>configuration</th><th>Method<br>configuration</th><th>Test<br>method</th><th>Thread</th><th>Instances</th></tr>
-<tr bgcolor="b663a2"> <td>10/02/17 15:34:08</td> <td>0</td> <td> </td><td title=">>compbio.engine.FilePullerTester.init()">>>init</td>
-<td> </td><td> </td><td> </td><td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="60a5eb"> <td>10/02/17 15:34:10</td> <td>1737</td> <td> </td><td title=">>compbio.metadata.PresetTester.loadPresets()">>>loadPresets</td>
-<td> </td><td> </td><td> </td><td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="60a5eb"> <td>10/02/17 15:36:38</td> <td>149837</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.PresetTester.marshallPreset()">marshallPreset</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:39</td> <td>151131</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.readStatistics()">readStatistics</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:37:57</td> <td>228724</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.readStatistics()">readStatistics</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:38:59</td> <td>290965</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleTester.readStatistics()">readStatistics</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:09</td> <td>421361</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.readStatistics()">readStatistics</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:43</td> <td>515257</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.readStatistics()">readStatistics</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:40</td> <td>152310</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()">readStatisticsClusterExecution</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
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-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
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-<tr bgcolor="ee82f7"> <td>10/02/17 15:37:09</td> <td>180414</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.LimitTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
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-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
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-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
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-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
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-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
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-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
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-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
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-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
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-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
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-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
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-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
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-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
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-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
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-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
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-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
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-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
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-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
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-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
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-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
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-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
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-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
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-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
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-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
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-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
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-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
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-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
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-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
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-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
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-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
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-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f0c0d3"> <td>10/02/17 15:34:33</td> <td>24806</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.PulledFileCacheTester.test()">test</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:17</td> <td>8754</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testArguments()">testArguments</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:09</td> <td>180523</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testArguments()">testArguments</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:32</td> <td>264102</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testArguments()">testArguments</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:39:09</td> <td>300748</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testArguments()">testArguments</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:41:30</td> <td>442182</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testArguments()">testArguments</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:50</td> <td>102119</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation()">testAsyncCancelOperation</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:50</td> <td>102168</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation()">testAsyncRetrievOperation</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b663a2"> <td>10/02/17 15:34:11</td> <td>2379</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.FilePullerTester.testCache()">testCache</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="dcb7db"> <td>10/02/17 15:34:48</td> <td>39760</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()">testCancel</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6c84c0"> <td>10/02/17 15:35:29</td> <td>80525</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()">testCancel</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:51</td> <td>102728</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally()">testCancelCompletedTaskLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6160b8"> <td>10/02/17 15:36:37</td> <td>148461</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally()">testCancelCompletedTaskLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:54</td> <td>105781</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally()">testCancelLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6160b8"> <td>10/02/17 15:36:37</td> <td>148798</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.LocalRunnerTester.testCancelLocally()">testCancelLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="838bd2"> <td>10/02/17 15:34:33</td> <td>24445</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.SequenceUtilTester.testCleanSequence()">testCleanSequence</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100065</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()">testClusterEngineConf</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:37:57</td> <td>229363</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testClusterExecute()">testClusterExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:10</td> <td>421803</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.testClusterExecute()">testClusterExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:44</td> <td>516133</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.testClusterExecute()">testClusterExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="94e4fb"> <td>10/02/17 15:34:38</td> <td>29993</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.client.CommandBuilderTester.testCommandBuilding()">testCommandBuilding</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:20</td> <td>12305</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testConfiguration()">testConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:15</td> <td>186680</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testConfiguration()">testConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:40</td> <td>271944</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testConfiguration()">testConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:39:12</td> <td>303651</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testConfiguration()">testConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:41:39</td> <td>450947</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testConfiguration()">testConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:49</td> <td>160431</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testConfigurationLoading()">testConfigurationLoading</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:09</td> <td>240703</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testConfigurationLoading()">testConfigurationLoading</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:00</td> <td>291898</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleTester.testConfigurationLoading()">testConfigurationLoading</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:29</td> <td>441129</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.testConfigurationLoading()">testConfigurationLoading</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:50</td> <td>521659</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.testConfigurationLoading()">testConfigurationLoading</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:20</td> <td>12333</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues()">testConstrainedParametersMaxValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:15</td> <td>186725</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()">testConstrainedParametersMaxValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:40</td> <td>271986</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues()">testConstrainedParametersMaxValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:39:12</td> <td>303681</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()">testConstrainedParametersMaxValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:41:39</td> <td>450948</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()">testConstrainedParametersMaxValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:22</td> <td>14199</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues()">testConstrainedParametersMinValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:18</td> <td>190008</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()">testConstrainedParametersMinValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:42</td> <td>273564</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues()">testConstrainedParametersMinValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:39:50</td> <td>342135</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()">testConstrainedParametersMinValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:41:50</td> <td>462115</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()">testConstrainedParametersMinValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:24</td> <td>15492</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues()">testConstrainedParametersRandomValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:20</td> <td>191380</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()">testConstrainedParametersRandomValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:43</td> <td>274453</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues()">testConstrainedParametersRandomValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:39:51</td> <td>342932</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()">testConstrainedParametersRandomValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:41:56</td> <td>467622</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()">testConstrainedParametersRandomValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150771</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue()">testCreateNumParameterWithoutValidValue</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150787</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testCreateParameter()">testCreateParameter</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150802</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testCreateParameterWithValidValueConstrain()">testCreateParameterWithValidValueConstrain</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="838bd2"> <td>10/02/17 15:34:33</td> <td>24446</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.SequenceUtilTester.testDeepCleanSequence()">testDeepCleanSequence</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:27</td> <td>18651</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testDefaultParameters()">testDefaultParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:27</td> <td>199100</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testDefaultParameters()">testDefaultParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:50</td> <td>282098</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testDefaultParameters()">testDefaultParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:40:53</td> <td>404843</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()">testDefaultParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:18</td> <td>489565</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()">testDefaultParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:09</td> <td>241138</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testExecute()">testExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:29</td> <td>441236</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.testExecute()">testExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:50</td> <td>521758</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.testExecute()">testExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b663a2"> <td>10/02/17 15:34:33</td> <td>24760</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.FilePullerTester.testGet()">testGet</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="7785c4"> <td>10/02/17 15:34:33</td> <td>24462</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.EngineConfiguratorTester.testGetAsyncEngine()">testGetAsyncEngine</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="7bb290"> <td>10/02/17 15:34:39</td> <td>30561</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.client.PathValidatorTester.testGetClassPath()">testGetClassPath</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b663a2"> <td>10/02/17 15:34:33</td> <td>24760</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.FilePullerTester.testGetDelay()">testGetDelay</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="73a7ab"> <td>10/02/17 15:35:48</td> <td>99951</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.DirectoryManagerTester.testGetDirectory()">testGetDirectory</td>
- <td>pool-4-thread-1@98491205</td> <td></td> </tr>
-<tr bgcolor="73a7ab"> <td>10/02/17 15:35:48</td> <td>99957</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.DirectoryManagerTester.testGetDirectory()">testGetDirectory</td>
- <td>pool-4-thread-2@1476184699</td> <td></td> </tr>
-<tr bgcolor="73a7ab"> <td>10/02/17 15:35:48</td> <td>99959</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.DirectoryManagerTester.testGetDirectory()">testGetDirectory</td>
- <td>pool-4-thread-3@819697057</td> <td></td> </tr>
-<tr bgcolor="73a7ab"> <td>10/02/17 15:35:48</td> <td>99959</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.DirectoryManagerTester.testGetDirectory()">testGetDirectory</td>
- <td>pool-4-thread-4@709342045</td> <td></td> </tr>
-<tr bgcolor="989f84"> <td>10/02/17 15:34:33</td> <td>24445</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.FastaSequenceTester.testGetFormattedFasta()">testGetFormattedFasta</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="dcb7db"> <td>10/02/17 15:34:49</td> <td>41033</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()">testGetJobStatus</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:54</td> <td>105819</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()">testGetStatus</td>
- <td>pool-5-thread-1@764103883</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:54</td> <td>105819</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()">testGetStatus</td>
- <td>pool-5-thread-2@341752521</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:54</td> <td>105823</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()">testGetStatus</td>
- <td>pool-5-thread-4@409692872</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:54</td> <td>105823</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()">testGetStatus</td>
- <td>pool-5-thread-3@1513312339</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:15</td> <td>126691</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()">testGetStatus</td>
- <td>pool-5-thread-2@341752521</td> <td></td> </tr>
-<tr bgcolor="7785c4"> <td>10/02/17 15:34:33</td> <td>24759</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.EngineConfiguratorTester.testGetSyncEngine()">testGetSyncEngine</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b19cf0"> <td>10/02/17 15:36:39</td> <td>151130</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.OBTester.testGetTestArgsCommand()">testGetTestArgsCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be776f"> <td>10/02/17 15:36:39</td> <td>151130</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.RPSBlastTester.testGetTestArgsCommand()">testGetTestArgsCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8e92e7"> <td>10/02/17 15:36:39</td> <td>151129</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.MclTester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6b76fa"> <td>10/02/17 15:36:39</td> <td>151130</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.NetNglycTester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b19cf0"> <td>10/02/17 15:36:39</td> <td>151130</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.OBTester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be776f"> <td>10/02/17 15:36:39</td> <td>151131</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.RPSBlastTester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b8c8e6"> <td>10/02/17 15:36:39</td> <td>151131</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.RonnTester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="76e5b2"> <td>10/02/17 15:36:39</td> <td>151131</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.Tmhmm2Tester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="7bb290"> <td>10/02/17 15:34:39</td> <td>30795</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.client.PathValidatorTester.testIsAbsolutePath()">testIsAbsolutePath</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="ee82f7"> <td>10/02/17 15:37:09</td> <td>180475</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.LimitTester.testLoadLimits()">testLoadLimits</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100064</td> <td> </td><td> </td><td title=">>compbio.engine.conf.PropertyHelperManagerTester.testLoadResources()">>>testLoadResources</td>
-<td> </td><td> </td><td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:48</td> <td>100251</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.RunnerConfigMarshallerTester.testMarshalling()">testMarshalling</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="72e4a9"> <td>10/02/17 15:36:38</td> <td>149393</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.OptionMarshallerTester.testMarshalling()">testMarshalling</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147556</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally()">testMultipleCancelLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6160b8"> <td>10/02/17 15:36:37</td> <td>148818</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally()">testMultipleCancelLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522626</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.testNcore()">testNcore</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150817</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate()">testOptionNoDefaultValidate</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150832</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue()">testOptionSetInvalidValue</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150848</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testOptionToCommand()">testOptionToCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:27</td> <td>19210</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testOptions()">testOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:48</td> <td>219617</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testOptions()">testOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:51</td> <td>282763</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testOptions()">testOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>419575</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testOptions()">testOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:29</td> <td>500553</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testOptions()">testOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:49</td> <td>161119</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testOptionsLocally()">testOptionsLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="94e4fb"> <td>10/02/17 15:34:38</td> <td>29994</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.client.CommandBuilderTester.testOptionsToCommand()">testOptionsToCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150863</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testParameterToCommand()">testParameterToCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:30</td> <td>21374</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testParameters()">testParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:52</td> <td>224118</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testParameters()">testParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:53</td> <td>285288</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testParameters()">testParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420039</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testParameters()">testParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:30</td> <td>501445</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testParameters()">testParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="df886b"> <td>10/02/17 15:35:48</td> <td>99948</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.UtilTester.testParser()">testParser</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:51</td> <td>163051</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testPersistance()">testPersistance</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:10</td> <td>241567</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testPersistance()">testPersistance</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:00</td> <td>292212</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleTester.testPersistance()">testPersistance</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>441672</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.testPersistance()">testPersistance</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.testPersistance()">testPersistance</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24131</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testPresets()">testPresets</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226587</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testPresets()">testPresets</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290109</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testPresets()">testPresets</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testPresets()">testPresets</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bb77b9"> <td>10/02/17 15:34:33</td> <td>24437</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.FastaSequenceGeneratorTester.testProteinSequenceGeneration()">testProteinSequenceGeneration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b663a2"> <td>10/02/17 15:34:10</td> <td>1923</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.FilePullerTester.testPull()">testPull</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6fb0a8"> <td>10/02/17 15:35:48</td> <td>99948</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.dundee._QueueTester.testQueue()">testQueue</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="aa97a6"> <td>10/02/17 15:34:32</td> <td>24308</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFile()">testReadClustalFile</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="aa97a6"> <td>10/02/17 15:34:32</td> <td>24330</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileLongNames()">testReadClustalFileLongNames</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="aa97a6"> <td>10/02/17 15:34:33</td> <td>24382</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileShortNames()">testReadClustalFileShortNames</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="838bd2"> <td>10/02/17 15:34:33</td> <td>24446</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.SequenceUtilTester.testReadWriteFasta()">testReadWriteFasta</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:52</td> <td>163482</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testRunLocally()">testRunLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292454</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleTester.testRunLocally()">testRunLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:52</td> <td>163653</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testRunOnCluster()">testRunOnCluster</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleTester.testRunOnCluster()">testRunOnCluster</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:11</td> <td>242600</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()">testRunOnClusterAsyncCheckStatusLongPoolingTime</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:37:08</td> <td>179590</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testRunWithMatrix()">testRunWithMatrix</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:48</td> <td>100287</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.RunnerConfigMarshallerTester.testSchemaFromCodeGeneration()">testSchemaFromCodeGeneration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testSetInputTester()">testSetInputTester</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.testSetInputTester()">testSetInputTester</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="94e4fb"> <td>10/02/17 15:34:39</td> <td>30561</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.client.CommandBuilderTester.testSpaceDelimiterExecutable()">testSpaceDelimiterExecutable</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="dcb7db"> <td>10/02/17 15:35:10</td> <td>61811</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()">testSubmit</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6c84c0"> <td>10/02/17 15:35:30</td> <td>82112</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()">testSubmit</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147825</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()">testSubmitLocally</td>
- <td>pool-6-thread-1@97575625</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147826</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()">testSubmitLocally</td>
- <td>pool-6-thread-2@598639019</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147826</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()">testSubmitLocally</td>
- <td>pool-6-thread-3@772581038</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147828</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()">testSubmitLocally</td>
- <td>pool-6-thread-4@1330799835</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147951</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()">testSubmitLocally</td>
- <td>pool-6-thread-3@772581038</td> <td></td> </tr>
-<tr bgcolor="9ced8e"> <td>10/02/17 15:34:39</td> <td>30795</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()">testTaskList</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:49</td> <td>100858</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.RunnerConfigMarshallerTester.testUnMarshalling()">testUnMarshalling</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="72e4a9"> <td>10/02/17 15:36:38</td> <td>149451</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.OptionMarshallerTester.testUnMarshalling()">testUnMarshalling</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150878</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testValidate()">testValidate</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151082</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testValidateBoundaryConstrainCheck()">testValidateBoundaryConstrainCheck</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151098</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck()">testValidateLowerBoundaryConstrainCheck</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck()">testValidateUpperBoundaryConstrainCheck</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151129</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testValidateValueConstrain()">testValidateValueConstrain</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:50</td> <td>101456</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.RunnerConfigMarshallerTester.testValidation()">testValidation</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:50</td> <td>102108</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling()">testValidationOnMarshalling</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="e6ff6d"> <td>10/02/17 15:36:37</td> <td>149278</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.OptionCombinatorTester.testgetAllOptions()">testgetAllOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="e6ff6d"> <td>10/02/17 15:36:38</td> <td>149390</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.OptionCombinatorTester.testgetAllParameters()">testgetAllParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="838bd2"> <td>10/02/17 15:34:33</td> <td>24462</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.SequenceUtilTester.testisNonAmbNucleotideSequence()">testisNonAmbNucleotideSequence</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="838bd2"> <td>10/02/17 15:34:33</td> <td>24462</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.SequenceUtilTester.testisProteinSequence()">testisProteinSequence</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100169</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration()">validateClustalConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100212</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration()">validateMafftConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100214</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration()">validateMuscleConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="60a5eb"> <td>10/02/17 15:36:39</td> <td>150736</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.PresetTester.validatePresets()">validatePresets</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100218</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration()">validateTcoffeeConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-</table>
+++ /dev/null
-<h2>Methods that were not run</h2><table>
-<tr><td>compbio.runner._impl.RPSBlastTester.testBuildCommand</td></tr>
-<tr><td>compbio.runner._impl.OBTester.testBuildCommand</td></tr>
-<tr><td>compbio.runner.msa.MuscleTester.testRunOnClusterAsync</td></tr>
-<tr><td>compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce</td></tr>
-<tr><td>compbio.runner.msa.ClustalWTester.testAddParameters</td></tr>
-<tr><td>compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes</td></tr>
-<tr><td>compbio.runner._impl.MclTester.testBuildCommand</td></tr>
-<tr><td>compbio.runner._impl.DisEMBLTester.testBuildCommand</td></tr>
-<tr><td>compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusShortPoolingTime</td></tr>
-<tr><td>compbio.runner._impl.Tmhmm2Tester.testBuildCommand</td></tr>
-<tr><td>compbio.engine.conf.DirectoryManagerTester.testNanoTime</td></tr>
-<tr><td>compbio.runner._impl.NetNglycTester.testBuildCommand</td></tr>
-<tr><td>compbio.runner._impl.RonnTester.testBuildCommand</td></tr>
-</table>
\ No newline at end of file
+++ /dev/null
-<h2>Methods run, sorted chronologically</h2><h3>>> means before, << means after</h3><p/><br/><em>Ant suite</em><p/><small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table border="1">
-<tr><th>Time</th><th>Delta (ms)</th><th>Suite<br>configuration</th><th>Test<br>configuration</th><th>Class<br>configuration</th><th>Groups<br>configuration</th><th>Method<br>configuration</th><th>Test<br>method</th><th>Thread</th><th>Instances</th></tr>
-<tr bgcolor="b663a2"> <td>10/02/17 15:34:08</td> <td>0</td> <td> </td><td title=">>compbio.engine.FilePullerTester.init()">>>init</td>
-<td> </td><td> </td><td> </td><td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="60a5eb"> <td>10/02/17 15:34:10</td> <td>1737</td> <td> </td><td title=">>compbio.metadata.PresetTester.loadPresets()">>>loadPresets</td>
-<td> </td><td> </td><td> </td><td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b663a2"> <td>10/02/17 15:34:10</td> <td>1923</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.FilePullerTester.testPull()">testPull</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b663a2"> <td>10/02/17 15:34:11</td> <td>2379</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.FilePullerTester.testCache()">testCache</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:17</td> <td>8754</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testArguments()">testArguments</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:20</td> <td>12305</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testConfiguration()">testConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:20</td> <td>12333</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues()">testConstrainedParametersMaxValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:22</td> <td>14199</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues()">testConstrainedParametersMinValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:24</td> <td>15492</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues()">testConstrainedParametersRandomValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:27</td> <td>18651</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testDefaultParameters()">testDefaultParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:27</td> <td>19210</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testOptions()">testOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:30</td> <td>21374</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testParameters()">testParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24054</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ClustalWParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="807ca8"> <td>10/02/17 15:34:32</td> <td>24131</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWParametersTester.testPresets()">testPresets</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="aa97a6"> <td>10/02/17 15:34:32</td> <td>24308</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFile()">testReadClustalFile</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="aa97a6"> <td>10/02/17 15:34:32</td> <td>24330</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileLongNames()">testReadClustalFileLongNames</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="aa97a6"> <td>10/02/17 15:34:33</td> <td>24382</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileShortNames()">testReadClustalFileShortNames</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bb77b9"> <td>10/02/17 15:34:33</td> <td>24437</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.FastaSequenceGeneratorTester.testProteinSequenceGeneration()">testProteinSequenceGeneration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="989f84"> <td>10/02/17 15:34:33</td> <td>24445</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.FastaSequenceTester.testGetFormattedFasta()">testGetFormattedFasta</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="838bd2"> <td>10/02/17 15:34:33</td> <td>24445</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.SequenceUtilTester.testCleanSequence()">testCleanSequence</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="838bd2"> <td>10/02/17 15:34:33</td> <td>24446</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.SequenceUtilTester.testDeepCleanSequence()">testDeepCleanSequence</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="838bd2"> <td>10/02/17 15:34:33</td> <td>24446</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.SequenceUtilTester.testReadWriteFasta()">testReadWriteFasta</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="838bd2"> <td>10/02/17 15:34:33</td> <td>24462</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.SequenceUtilTester.testisNonAmbNucleotideSequence()">testisNonAmbNucleotideSequence</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="838bd2"> <td>10/02/17 15:34:33</td> <td>24462</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.data.sequence.SequenceUtilTester.testisProteinSequence()">testisProteinSequence</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="7785c4"> <td>10/02/17 15:34:33</td> <td>24462</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.EngineConfiguratorTester.testGetAsyncEngine()">testGetAsyncEngine</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="7785c4"> <td>10/02/17 15:34:33</td> <td>24759</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.EngineConfiguratorTester.testGetSyncEngine()">testGetSyncEngine</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b663a2"> <td>10/02/17 15:34:33</td> <td>24760</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.FilePullerTester.testGetDelay()">testGetDelay</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b663a2"> <td>10/02/17 15:34:33</td> <td>24760</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.FilePullerTester.testGet()">testGet</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f0c0d3"> <td>10/02/17 15:34:33</td> <td>24806</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.PulledFileCacheTester.test()">test</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="94e4fb"> <td>10/02/17 15:34:38</td> <td>29993</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.client.CommandBuilderTester.testCommandBuilding()">testCommandBuilding</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="94e4fb"> <td>10/02/17 15:34:38</td> <td>29994</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.client.CommandBuilderTester.testOptionsToCommand()">testOptionsToCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="94e4fb"> <td>10/02/17 15:34:39</td> <td>30561</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.client.CommandBuilderTester.testSpaceDelimiterExecutable()">testSpaceDelimiterExecutable</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="7bb290"> <td>10/02/17 15:34:39</td> <td>30561</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.client.PathValidatorTester.testGetClassPath()">testGetClassPath</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="7bb290"> <td>10/02/17 15:34:39</td> <td>30795</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.client.PathValidatorTester.testIsAbsolutePath()">testIsAbsolutePath</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9ced8e"> <td>10/02/17 15:34:39</td> <td>30795</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()">testTaskList</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="dcb7db"> <td>10/02/17 15:34:48</td> <td>39760</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()">testCancel</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="dcb7db"> <td>10/02/17 15:34:49</td> <td>41033</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()">testGetJobStatus</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="dcb7db"> <td>10/02/17 15:35:10</td> <td>61811</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()">testSubmit</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6c84c0"> <td>10/02/17 15:35:29</td> <td>80525</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()">testCancel</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6c84c0"> <td>10/02/17 15:35:30</td> <td>82112</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()">testSubmit</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="df886b"> <td>10/02/17 15:35:48</td> <td>99948</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.drmaa.UtilTester.testParser()">testParser</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6fb0a8"> <td>10/02/17 15:35:48</td> <td>99948</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.cluster.dundee._QueueTester.testQueue()">testQueue</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="73a7ab"> <td>10/02/17 15:35:48</td> <td>99951</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.DirectoryManagerTester.testGetDirectory()">testGetDirectory</td>
- <td>pool-4-thread-1@98491205</td> <td></td> </tr>
-<tr bgcolor="73a7ab"> <td>10/02/17 15:35:48</td> <td>99957</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.DirectoryManagerTester.testGetDirectory()">testGetDirectory</td>
- <td>pool-4-thread-2@1476184699</td> <td></td> </tr>
-<tr bgcolor="73a7ab"> <td>10/02/17 15:35:48</td> <td>99959</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.DirectoryManagerTester.testGetDirectory()">testGetDirectory</td>
- <td>pool-4-thread-3@819697057</td> <td></td> </tr>
-<tr bgcolor="73a7ab"> <td>10/02/17 15:35:48</td> <td>99959</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.DirectoryManagerTester.testGetDirectory()">testGetDirectory</td>
- <td>pool-4-thread-4@709342045</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100064</td> <td> </td><td> </td><td title=">>compbio.engine.conf.PropertyHelperManagerTester.testLoadResources()">>>testLoadResources</td>
-<td> </td><td> </td><td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100065</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()">testClusterEngineConf</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100169</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration()">validateClustalConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100212</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration()">validateMafftConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100214</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration()">validateMuscleConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f8c6df"> <td>10/02/17 15:35:48</td> <td>100218</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration()">validateTcoffeeConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:50</td> <td>102092</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.engine.conf.RunnerConfigMarshallerTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:48</td> <td>100251</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.RunnerConfigMarshallerTester.testMarshalling()">testMarshalling</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:50</td> <td>102092</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.engine.conf.RunnerConfigMarshallerTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:48</td> <td>100287</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.RunnerConfigMarshallerTester.testSchemaFromCodeGeneration()">testSchemaFromCodeGeneration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:50</td> <td>102092</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.engine.conf.RunnerConfigMarshallerTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:49</td> <td>100858</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.RunnerConfigMarshallerTester.testUnMarshalling()">testUnMarshalling</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:50</td> <td>102092</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.engine.conf.RunnerConfigMarshallerTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:50</td> <td>101456</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.RunnerConfigMarshallerTester.testValidation()">testValidation</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:50</td> <td>102092</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.engine.conf.RunnerConfigMarshallerTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="92bbba"> <td>10/02/17 15:35:50</td> <td>102108</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling()">testValidationOnMarshalling</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:50</td> <td>102119</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation()">testAsyncCancelOperation</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:50</td> <td>102168</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation()">testAsyncRetrievOperation</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:51</td> <td>102728</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally()">testCancelCompletedTaskLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:54</td> <td>105781</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally()">testCancelLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:54</td> <td>105819</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()">testGetStatus</td>
- <td>pool-5-thread-1@764103883</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:54</td> <td>105819</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()">testGetStatus</td>
- <td>pool-5-thread-2@341752521</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:54</td> <td>105823</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()">testGetStatus</td>
- <td>pool-5-thread-4@409692872</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:35:54</td> <td>105823</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()">testGetStatus</td>
- <td>pool-5-thread-3@1513312339</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:15</td> <td>126691</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()">testGetStatus</td>
- <td>pool-5-thread-2@341752521</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147556</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally()">testMultipleCancelLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147825</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()">testSubmitLocally</td>
- <td>pool-6-thread-1@97575625</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147826</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()">testSubmitLocally</td>
- <td>pool-6-thread-2@598639019</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147826</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()">testSubmitLocally</td>
- <td>pool-6-thread-3@772581038</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147828</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()">testSubmitLocally</td>
- <td>pool-6-thread-4@1330799835</td> <td></td> </tr>
-<tr bgcolor="bf8172"> <td>10/02/17 15:36:36</td> <td>147951</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()">testSubmitLocally</td>
- <td>pool-6-thread-3@772581038</td> <td></td> </tr>
-<tr bgcolor="6160b8"> <td>10/02/17 15:36:37</td> <td>148461</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally()">testCancelCompletedTaskLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6160b8"> <td>10/02/17 15:36:37</td> <td>148798</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.LocalRunnerTester.testCancelLocally()">testCancelLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6160b8"> <td>10/02/17 15:36:37</td> <td>148818</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally()">testMultipleCancelLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="e6ff6d"> <td>10/02/17 15:36:37</td> <td>149279</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.OptionCombinatorTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="e6ff6d"> <td>10/02/17 15:36:37</td> <td>149278</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.OptionCombinatorTester.testgetAllOptions()">testgetAllOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="e6ff6d"> <td>10/02/17 15:36:37</td> <td>149279</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.OptionCombinatorTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="e6ff6d"> <td>10/02/17 15:36:38</td> <td>149390</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.OptionCombinatorTester.testgetAllParameters()">testgetAllParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="72e4a9"> <td>10/02/17 15:36:38</td> <td>149451</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.OptionMarshallerTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="72e4a9"> <td>10/02/17 15:36:38</td> <td>149393</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.OptionMarshallerTester.testMarshalling()">testMarshalling</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="72e4a9"> <td>10/02/17 15:36:38</td> <td>149451</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.OptionMarshallerTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="72e4a9"> <td>10/02/17 15:36:38</td> <td>149451</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.OptionMarshallerTester.testUnMarshalling()">testUnMarshalling</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="60a5eb"> <td>10/02/17 15:36:38</td> <td>149837</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.PresetTester.marshallPreset()">marshallPreset</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="60a5eb"> <td>10/02/17 15:36:39</td> <td>150736</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.PresetTester.validatePresets()">validatePresets</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150771</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue()">testCreateNumParameterWithoutValidValue</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150787</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testCreateParameter()">testCreateParameter</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150802</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testCreateParameterWithValidValueConstrain()">testCreateParameterWithValidValueConstrain</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150817</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate()">testOptionNoDefaultValidate</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150832</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue()">testOptionSetInvalidValue</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150848</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testOptionToCommand()">testOptionToCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150863</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testParameterToCommand()">testParameterToCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>150878</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testValidate()">testValidate</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151082</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testValidateBoundaryConstrainCheck()">testValidateBoundaryConstrainCheck</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151098</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck()">testValidateLowerBoundaryConstrainCheck</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck()">testValidateUpperBoundaryConstrainCheck</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151114</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.metadata.RunnerConfigTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="a2a86d"> <td>10/02/17 15:36:39</td> <td>151129</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.metadata.RunnerConfigTester.testValidateValueConstrain()">testValidateValueConstrain</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8e92e7"> <td>10/02/17 15:36:39</td> <td>151129</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.MclTester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6b76fa"> <td>10/02/17 15:36:39</td> <td>151130</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.NetNglycTester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b19cf0"> <td>10/02/17 15:36:39</td> <td>151130</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.OBTester.testGetTestArgsCommand()">testGetTestArgsCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b19cf0"> <td>10/02/17 15:36:39</td> <td>151130</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.OBTester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be776f"> <td>10/02/17 15:36:39</td> <td>151130</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.RPSBlastTester.testGetTestArgsCommand()">testGetTestArgsCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be776f"> <td>10/02/17 15:36:39</td> <td>151131</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.RPSBlastTester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b8c8e6"> <td>10/02/17 15:36:39</td> <td>151131</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.RonnTester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="76e5b2"> <td>10/02/17 15:36:39</td> <td>151131</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner._impl.Tmhmm2Tester.testGetTestCommand()">testGetTestCommand</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:39</td> <td>151131</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.readStatistics()">readStatistics</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:40</td> <td>152310</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()">readStatisticsClusterExecution</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:49</td> <td>160431</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testConfigurationLoading()">testConfigurationLoading</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:49</td> <td>161119</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testOptionsLocally()">testOptionsLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:51</td> <td>163051</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testPersistance()">testPersistance</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:52</td> <td>163482</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testRunLocally()">testRunLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:36:52</td> <td>163653</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testRunOnCluster()">testRunOnCluster</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="9b7d64"> <td>10/02/17 15:37:08</td> <td>179590</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ClustalWTester.testRunWithMatrix()">testRunWithMatrix</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="ee82f7"> <td>10/02/17 15:37:09</td> <td>180414</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.LimitTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="ee82f7"> <td>10/02/17 15:37:09</td> <td>180475</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.LimitTester.testLoadLimits()">testLoadLimits</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:09</td> <td>180523</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testArguments()">testArguments</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:15</td> <td>186680</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testConfiguration()">testConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:15</td> <td>186725</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()">testConstrainedParametersMaxValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:18</td> <td>190008</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()">testConstrainedParametersMinValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:20</td> <td>191380</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()">testConstrainedParametersRandomValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:27</td> <td>199100</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testDefaultParameters()">testDefaultParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:48</td> <td>219617</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testOptions()">testOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:52</td> <td>224118</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testParameters()">testParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226540</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="8cb49d"> <td>10/02/17 15:37:55</td> <td>226587</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftParametersTester.testPresets()">testPresets</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:37:57</td> <td>228724</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.readStatistics()">readStatistics</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:37:57</td> <td>229363</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testClusterExecute()">testClusterExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:09</td> <td>240703</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testConfigurationLoading()">testConfigurationLoading</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:09</td> <td>241138</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testExecute()">testExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:10</td> <td>241567</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testPersistance()">testPersistance</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:11</td> <td>242600</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()">testRunOnClusterAsyncCheckStatusLongPoolingTime</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MafftTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="65d88a"> <td>10/02/17 15:38:32</td> <td>264017</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MafftTester.testSetInputTester()">testSetInputTester</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:32</td> <td>264102</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testArguments()">testArguments</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:40</td> <td>271944</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testConfiguration()">testConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:40</td> <td>271986</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues()">testConstrainedParametersMaxValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:42</td> <td>273564</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues()">testConstrainedParametersMinValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:43</td> <td>274453</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues()">testConstrainedParametersRandomValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:50</td> <td>282098</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testDefaultParameters()">testDefaultParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:51</td> <td>282763</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testOptions()">testOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:53</td> <td>285288</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testParameters()">testParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290061</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="6e88b9"> <td>10/02/17 15:38:58</td> <td>290109</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleParametersTester.testPresets()">testPresets</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:38:59</td> <td>290965</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleTester.readStatistics()">readStatistics</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:00</td> <td>291898</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleTester.testConfigurationLoading()">testConfigurationLoading</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:00</td> <td>292212</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleTester.testPersistance()">testPersistance</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292454</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleTester.testRunLocally()">testRunLocally</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.MuscleTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="93a66f"> <td>10/02/17 15:39:01</td> <td>292556</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.MuscleTester.testRunOnCluster()">testRunOnCluster</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:39:09</td> <td>300748</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testArguments()">testArguments</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:39:12</td> <td>303651</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testConfiguration()">testConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:39:12</td> <td>303681</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()">testConstrainedParametersMaxValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:39:50</td> <td>342135</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()">testConstrainedParametersMinValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:39:51</td> <td>342932</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()">testConstrainedParametersRandomValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:40:53</td> <td>404843</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()">testDefaultParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>419575</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testOptions()">testOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420008</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="f6dfac"> <td>10/02/17 15:41:08</td> <td>420039</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsParametersTester.testParameters()">testParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:09</td> <td>421361</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.readStatistics()">readStatistics</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:10</td> <td>421803</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.testClusterExecute()">testClusterExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:29</td> <td>441129</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.testConfigurationLoading()">testConfigurationLoading</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:29</td> <td>441236</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.testExecute()">testExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>441672</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.testPersistance()">testPersistance</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="be6e87"> <td>10/02/17 15:41:30</td> <td>442181</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.testSetInputTester()">testSetInputTester</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:41:30</td> <td>442182</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testArguments()">testArguments</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:41:39</td> <td>450947</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testConfiguration()">testConfiguration</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:41:39</td> <td>450948</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()">testConstrainedParametersMaxValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:41:50</td> <td>462115</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()">testConstrainedParametersMinValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:41:56</td> <td>467622</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()">testConstrainedParametersRandomValues</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:18</td> <td>489565</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()">testDefaultParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:29</td> <td>500553</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testOptions()">testOptions</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:30</td> <td>501445</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testParameters()">testParameters</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeParametersTester.setup()">>>setup</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="b973ea"> <td>10/02/17 15:42:42</td> <td>514162</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeParametersTester.testPresets()">testPresets</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:43</td> <td>515257</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.readStatistics()">readStatistics</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:44</td> <td>516133</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.testClusterExecute()">testClusterExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:50</td> <td>521659</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.testConfigurationLoading()">testConfigurationLoading</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:50</td> <td>521758</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.testExecute()">testExecute</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522626</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.testNcore()">testNcore</td>
- <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.TcoffeeTester.init()">>>init</td>
-<td> </td> <td>main@277466206</td> <td></td> </tr>
-<tr bgcolor="c9737c"> <td>10/02/17 15:42:51</td> <td>522627</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.TcoffeeTester.testPersistance()">testPersistance</td>
- <td>main@277466206</td> <td></td> </tr>
-</table>
+++ /dev/null
-<h2>Reporter output</h2><table></table>
\ No newline at end of file
+++ /dev/null
-<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
-<suite thread-count="5" skipfailedinvocationCounts="false" verbose="3" name="Failed suite [Ant suite]" junit="false" annotations="JDK" data-provider-thread-count="10">
- <test name="Ant test(failed)" junit="false" annotations="JDK">
- <groups>
- <run>
- <exclude name="performance"/>
- </run>
- </groups>
- <classes>
- <class name="compbio.engine.FilePullerTester">
- <methods>
- <include name="init"/>
- </methods>
- </class>
- <class name="compbio.runner.msa.TcoffeeParametersTester">
- <methods>
- <include name="setup"/>
- </methods>
- </class>
- <class name="compbio.metadata.OptionCombinatorTester">
- <methods>
- <include name="setup"/>
- </methods>
- </class>
- <class name="compbio.runner.msa.TcoffeeTester">
- <methods>
- <include name="init"/>
- </methods>
- </class>
- <class name="compbio.runner.msa.MafftTester">
- <methods>
- <include name="init"/>
- <include name="testRunOnClusterAsyncCheckStatusShortPoolingTime"/>
- </methods>
- </class>
- <class name="compbio.engine.conf.PropertyHelperManagerTester">
- <methods>
- <include name="testLocalEngineConf"/>
- <include name="testLoadResources"/>
- </methods>
- </class>
- <class name="compbio.runner.msa.MafftParametersTester">
- <methods>
- <include name="setup"/>
- </methods>
- </class>
- <class name="compbio.metadata.RunnerConfigTester">
- <methods>
- <include name="setup"/>
- </methods>
- </class>
- <class name="compbio.runner.msa.LimitTester">
- <methods>
- <include name="setup"/>
- </methods>
- </class>
- <class name="compbio.runner.msa.ProbconsParametersTester">
- <methods>
- <include name="setup"/>
- </methods>
- </class>
- <class name="compbio.runner.msa.MuscleTester">
- <methods>
- <include name="init"/>
- </methods>
- </class>
- <class name="compbio.metadata.PresetTester">
- <methods>
- <include name="loadPresets"/>
- </methods>
- </class>
- <class name="compbio.runner.msa.ProbconsTester">
- <methods>
- <include name="init"/>
- </methods>
- </class>
- <class name="compbio.runner.msa.ClustalWParametersTester">
- <methods>
- <include name="setup"/>
- </methods>
- </class>
- <class name="compbio.metadata.OptionMarshallerTester">
- <methods>
- <include name="setup"/>
- </methods>
- </class>
- <class name="compbio.engine.conf.RunnerConfigMarshallerTester">
- <methods>
- <include name="setup"/>
- </methods>
- </class>
- <class name="compbio.runner.msa.MuscleParametersTester">
- <methods>
- <include name="setup"/>
- </methods>
- </class>
- </classes>
- </test>
-</suite>
+++ /dev/null
-<html><head><title>testng.xml for Ant suite</title></head><body><tt><!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd"><br/><suite thread-count="5" skipfailedinvocationCounts="false" verbose="3" name="Ant suite" junit="false" annotations="JDK" data-provider-thread-count="10"><br/> <test name="Ant test" junit="false"><br/> <groups><br/> <run><br/> <exclude name="performance"/><br/> </run><br/> </groups><br/> <classes><br/> <class name="compbio.data._structure.JnetAnnotation$AType"/><br/> <class name="compbio.data._structure.JnetAnnotation"/><br/> <class name="compbio.data._structure.JpredAnnotation"/><br/> <class name="compbio.data._structure.JpredResult"/><br/> <class name="compbio.data.msa.MsaWS"/><br/> <class name="compbio.data.msa.jaxws.Align"/><br/> <class name="compbio.data.msa.jaxws.AlignResponse"/><br/> <class name="compbio.data.msa.jaxws.CancelJob"/><br/> <class name="compbio.data.msa.jaxws.CancelJobResponse"/><br/> <class name="compbio.data.msa.jaxws.CustomAlign"/><br/> <class name="compbio.data.msa.jaxws.CustomAlignResponse"/><br/> <class name="compbio.data.msa.jaxws.GetJobStatus"/><br/> <class name="compbio.data.msa.jaxws.GetJobStatusResponse"/><br/> <class name="compbio.data.msa.jaxws.GetLimit"/><br/> <class name="compbio.data.msa.jaxws.GetLimitResponse"/><br/> <class name="compbio.data.msa.jaxws.GetLimits"/><br/> <class name="compbio.data.msa.jaxws.GetLimitsResponse"/><br/> <class name="compbio.data.msa.jaxws.GetPresets"/><br/> <class name="compbio.data.msa.jaxws.GetPresetsResponse"/><br/> <class name="compbio.data.msa.jaxws.GetProgress"/><br/> <class name="compbio.data.msa.jaxws.GetProgressResponse"/><br/> <class name="compbio.data.msa.jaxws.GetResult"/><br/> <class name="compbio.data.msa.jaxws.GetResultResponse"/><br/> <class name="compbio.data.msa.jaxws.GetRunnerOptions"/><br/> <class name="compbio.data.msa.jaxws.GetRunnerOptionsResponse"/><br/> <class name="compbio.data.msa.jaxws.JobExecutionExceptionBean"/><br/> <class name="compbio.data.msa.jaxws.JobSubmissionExceptionBean"/><br/> <class name="compbio.data.msa.jaxws.LimitExceededExceptionBean"/><br/> <class name="compbio.data.msa.jaxws.PresetAlign"/><br/> <class name="compbio.data.msa.jaxws.PresetAlignResponse"/><br/> <class name="compbio.data.msa.jaxws.PullExecStatistics"/><br/> <class name="compbio.data.msa.jaxws.PullExecStatisticsResponse"/><br/> <class name="compbio.data.msa.jaxws.PullFile"/><br/> <class name="compbio.data.msa.jaxws.PullFileResponse"/><br/> <class name="compbio.data.msa.jaxws.ResultNotAvailableExceptionBean"/><br/> <class name="compbio.data.msa.jaxws.UnsupportedRuntimeExceptionBean"/><br/> <class name="compbio.data.msa.jaxws.WrongParameterExceptionBean"/><br/> <class name="compbio.data.sequence.Alignment"/><br/> <class name="compbio.data.sequence.AlignmentMetadata"/><br/> <class name="compbio.data.sequence.ClustalAlignmentUtil"/><br/> <class name="compbio.data.sequence.ClustalAlignmentUtilTester"/><br/> <class name="compbio.data.sequence.FastaGeneratorManager"/><br/> <class name="compbio.data.sequence.FastaSequence"/><br/> <class name="compbio.data.sequence.FastaSequenceGenerator$1"/><br/> <class name="compbio.data.sequence.FastaSequenceGenerator$DNAAlphabet"/><br/> <class name="compbio.data.sequence.FastaSequenceGenerator$Letters"/><br/> <class name="compbio.data.sequence.FastaSequenceGenerator$ProteinAlphabet"/><br/> <class name="compbio.data.sequence.FastaSequenceGenerator$SeqType"/><br/> <class name="compbio.data.sequence.FastaSequenceGenerator"/><br/> <class name="compbio.data.sequence.FastaSequenceGeneratorTester"/><br/> <class name="compbio.data.sequence.FastaSequenceTester"/><br/> <class name="compbio.data.sequence.Program"/><br/> <class name="compbio.data.sequence.SequenceUtil"/><br/> <class name="compbio.data.sequence.SequenceUtilTester"/><br/> <class name="compbio.data.sequence.UnknownFileFormatException"/><br/> <class name="compbio.engine.AsyncExecutor"/><br/> <class name="compbio.engine.Cleaner"/><br/> <class name="compbio.engine.ClusterJobId"/><br/> <class name="compbio.engine.Configurator"/><br/> <class name="compbio.engine.EngineConfiguratorTester"/><br/> <class name="compbio.engine.FilePuller"/><br/> <class name="compbio.engine.FilePullerTester"/><br/> <class name="compbio.engine.Job"/><br/> <class name="compbio.engine.LoadBalancer"/><br/> <class name="compbio.engine.ProgressGetter"/><br/> <class name="compbio.engine.PulledFileCache"/><br/> <class name="compbio.engine.PulledFileCacheTester"/><br/> <class name="compbio.engine.SubmissionManager"/><br/> <class name="compbio.engine.SyncExecutor"/><br/> <class name="compbio.engine.client.ClusterNativeSpecExecutable"/><br/> <class name="compbio.engine.client.CommandBuilder$Parameter"/><br/> <class name="compbio.engine.client.CommandBuilder"/><br/> <class name="compbio.engine.client.CommandBuilderTester"/><br/> <class name="compbio.engine.client.ConfExecutable"/><br/> <class name="compbio.engine.client.ConfiguredExecutable"/><br/> <class name="compbio.engine.client.EnvVariableProcessor"/><br/> <class name="compbio.engine.client.Executable$ExecProvider"/><br/> <class name="compbio.engine.client.Executable"/><br/> <class name="compbio.engine.client.PathValidator"/><br/> <class name="compbio.engine.client.PathValidatorTester"/><br/> <class name="compbio.engine.client.PipedExecutable"/><br/> <class name="compbio.engine.client.RunConfiguration"/><br/> <class name="compbio.engine.client.SkeletalExecutable"/><br/> <class name="compbio.engine.client.Util"/><br/> <class name="compbio.engine.cluster.drmaa.AsyncJobRunner"/><br/> <class name="compbio.engine.cluster.drmaa.ClusterSession$1"/><br/> <class name="compbio.engine.cluster.drmaa.ClusterSession"/><br/> <class name="compbio.engine.cluster.drmaa.ClusterSessionTester"/><br/> <class name="compbio.engine.cluster.drmaa.ClusterUtil"/><br/> <class name="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/><br/> <class name="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/><br/> <class name="compbio.engine.cluster.drmaa.JobRunner"/><br/> <class name="compbio.engine.cluster.drmaa.StatisticManager"/><br/> <class name="compbio.engine.cluster.drmaa.UtilTester"/><br/> <class name="compbio.engine.cluster.drmaa._DrmaaExample"/><br/> <class name="compbio.engine.cluster.drmaa._JobStatus"/><br/> <class name="compbio.engine.cluster.dundee._Queue$1"/><br/> <class name="compbio.engine.cluster.dundee._Queue"/><br/> <class name="compbio.engine.cluster.dundee._QueueConstraints"/><br/> <class name="compbio.engine.cluster.dundee._QueueTester"/><br/> <class name="compbio.engine.conf.DirectoryManager"/><br/> <class name="compbio.engine.conf.DirectoryManagerTester"/><br/> <class name="compbio.engine.conf.PropertyHelperManager"/><br/> <class name="compbio.engine.conf.PropertyHelperManagerTester"/><br/> <class name="compbio.engine.conf.RunnerConfigMarshaller$MySchemaOutputResolver"/><br/> <class name="compbio.engine.conf.RunnerConfigMarshaller"/><br/> <class name="compbio.engine.conf.RunnerConfigMarshallerTester"/><br/> <class name="compbio.engine.conf._Key"/><br/> <class name="compbio.engine.local.AsyncLocalRunner"/><br/> <class name="compbio.engine.local.AsyncLocalRunnerTester"/><br/> <class name="compbio.engine.local.EngineResourcesLeakTester"/><br/> <class name="compbio.engine.local.ExecutableWrapper$1"/><br/> <class name="compbio.engine.local.ExecutableWrapper"/><br/> <class name="compbio.engine.local.LocalEngineUtil"/><br/> <class name="compbio.engine.local.LocalExecutorService$1"/><br/> <class name="compbio.engine.local.LocalExecutorService"/><br/> <class name="compbio.engine.local.LocalRunner"/><br/> <class name="compbio.engine.local.LocalRunnerTester"/><br/> <class name="compbio.engine.local.StreamGobbler$OutputType"/><br/> <class name="compbio.engine.local.StreamGobbler"/><br/> <class name="compbio.engine.local._TrackingExecutor$1"/><br/> <class name="compbio.engine.local._TrackingExecutor$2"/><br/> <class name="compbio.engine.local._TrackingExecutor"/><br/> <class name="compbio.metadata.AllTestSuit"/><br/> <class name="compbio.metadata.Argument"/><br/> <class name="compbio.metadata.ChunkHolder"/><br/> <class name="compbio.metadata.JobExecutionException"/><br/> <class name="compbio.metadata.JobStatus"/><br/> <class name="compbio.metadata.JobSubmissionException"/><br/> <class name="compbio.metadata.Limit"/><br/> <class name="compbio.metadata.LimitExceededException"/><br/> <class name="compbio.metadata.LimitsManager"/><br/> <class name="compbio.metadata.Option"/><br/> <class name="compbio.metadata.OptionCombinatorTester"/><br/> <class name="compbio.metadata.OptionMarshallerTester"/><br/> <class name="compbio.metadata.Parameter"/><br/> <class name="compbio.metadata.Preset"/><br/> <class name="compbio.metadata.PresetManager"/><br/> <class name="compbio.metadata.PresetTester"/><br/> <class name="compbio.metadata.ResultNotAvailableException"/><br/> <class name="compbio.metadata.RunnerConfig"/><br/> <class name="compbio.metadata.RunnerConfigTester"/><br/> <class name="compbio.metadata.UnsupportedRuntimeException"/><br/> <class name="compbio.metadata.ValueConstrain$1"/><br/> <class name="compbio.metadata.ValueConstrain$Type"/><br/> <class name="compbio.metadata.ValueConstrain"/><br/> <class name="compbio.metadata.WrongParameterException"/><br/> <class name="compbio.pipeline._jpred.BlastParser$Psiseq"/><br/> <class name="compbio.pipeline._jpred.BlastParser"/><br/> <class name="compbio.pipeline._jpred.Jpred4"/><br/> <class name="compbio.pipeline._jpred.PScore"/><br/> <class name="compbio.pipeline._jpred.Pairwise"/><br/> <class name="compbio.runner.OptionCombinator"/><br/> <class name="compbio.runner.Util"/><br/> <class name="compbio.runner._NativeSpecHelper"/><br/> <class name="compbio.runner._SkeletalCommandBuilder"/><br/> <class name="compbio.runner._impl.BlastAll$blastType"/><br/> <class name="compbio.runner._impl.BlastAll$dataBase"/><br/> <class name="compbio.runner._impl.BlastAll"/><br/> <class name="compbio.runner._impl.BlastParameters"/><br/> <class name="compbio.runner._impl.DisEMBLTester"/><br/> <class name="compbio.runner._impl.Disembl"/><br/> <class name="compbio.runner._impl.Environment"/><br/> <class name="compbio.runner._impl.Mcl"/><br/> <class name="compbio.runner._impl.MclTester"/><br/> <class name="compbio.runner._impl.NetNglyc"/><br/> <class name="compbio.runner._impl.NetNglycTester"/><br/> <class name="compbio.runner._impl.OB"/><br/> <class name="compbio.runner._impl.OBTester"/><br/> <class name="compbio.runner._impl.PSIBlast$blastType"/><br/> <class name="compbio.runner._impl.PSIBlast$dataBase"/><br/> <class name="compbio.runner._impl.PSIBlast"/><br/> <class name="compbio.runner._impl.RPSBlast$DB"/><br/> <class name="compbio.runner._impl.RPSBlast"/><br/> <class name="compbio.runner._impl.RPSBlastTester"/><br/> <class name="compbio.runner._impl.Ronn"/><br/> <class name="compbio.runner._impl.RonnTester"/><br/> <class name="compbio.runner._impl.Runners"/><br/> <class name="compbio.runner._impl.Tmhmm2"/><br/> <class name="compbio.runner._impl.Tmhmm2Tester"/><br/> <class name="compbio.runner._jpred._Jpred"/><br/> <class name="compbio.runner.msa.ClustalW"/><br/> <class name="compbio.runner.msa.ClustalWParametersTester"/><br/> <class name="compbio.runner.msa.ClustalWTester"/><br/> <class name="compbio.runner.msa.LimitTester"/><br/> <class name="compbio.runner.msa.Mafft"/><br/> <class name="compbio.runner.msa.MafftParametersTester"/><br/> <class name="compbio.runner.msa.MafftTester"/><br/> <class name="compbio.runner.msa.Muscle"/><br/> <class name="compbio.runner.msa.MuscleParametersTester"/><br/> <class name="compbio.runner.msa.MuscleTester"/><br/> <class name="compbio.runner.msa.Probcons"/><br/> <class name="compbio.runner.msa.ProbconsParametersTester"/><br/> <class name="compbio.runner.msa.ProbconsTester"/><br/> <class name="compbio.runner.msa.Tcoffee"/><br/> <class name="compbio.runner.msa.TcoffeeParametersTester"/><br/> <class name="compbio.runner.msa.TcoffeeTester"/><br/> <class name="compbio.runner.psiblast.PsiBlast"/><br/> <class name="compbio.ws.client.Jws2Client$Services"/><br/> <class name="compbio.ws.client.Jws2Client"/><br/> <class name="compbio.ws.client.WSTester"/><br/> <class name="compbio.ws.server.ClustalWS"/><br/> <class name="compbio.ws.server.MafftWS"/><br/> <class name="compbio.ws.server.MuscleWS"/><br/> <class name="compbio.ws.server.ProbconsWS"/><br/> <class name="compbio.ws.server.SimpleWSPublisher"/><br/> <class name="compbio.ws.server.TcoffeeWS"/><br/> <class name="compbio.ws.server.WSUtil"/><br/> </classes><br/> </test><br/></suite><br/></tt></body></html>
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-<html>
-<head>
-<title>Results for Ant suite</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-</head>
-<body>
-<h3><p align="center">Results for<br/><em>Ant suite</em></p></h3>
-<table border='1' width='100%'>
-<tr valign='top'>
-<td>1 test</td>
-<td><a target='mainFrame' href='classes.html'>40 classes</a></td>
-<td>154 methods:<br/>
- <a target='mainFrame' href='methods.html'>chronological</a><br/>
- <a target='mainFrame' href='methods-alphabetical.html'>alphabetical</a><br/>
- <a target='mainFrame' href='methods-not-run.html'>not run (13)</a></td>
-</tr>
-<tr>
-<td><a target='mainFrame' href='groups.html'>4 groups</a></td>
-<td><a target='mainFrame' href='reporter-output.html'>reporter output</a></td>
-<td><a target='mainFrame' href='testng.xml.html'>testng.xml</a></td>
-</tr></table>
-<table width='100%' class='test-passed'>
-<tr><td>
-<table style='width: 100%'><tr><td valign='top'>Ant test (165/0/0)</td><td valign='top' align='right'>
- <a href='Ant test.html' target='mainFrame'>Results</a>
-</td></tr></table>
-</td></tr><p/>
-</table>
-</body></html>
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-<html>
-<head>
-<title>TestNG: Ant test(failed)</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-
-<style type="text/css">
-.log { display: none;}
-.stack-trace { display: none;}
-</style>
-<script type="text/javascript">
-<!--
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-</head>
-<body>
-<h2 align='center'>Ant test(failed)</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>1/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Mon Feb 08 18:30:13 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>1 seconds (1098 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td>performance </td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-passed'>
-<tr><td colspan='4' align='center'><b>PASSED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.runner.msa.ProbconsTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test(failed)</td>
-<td>compbio.runner.msa.ProbconsTester@60cbf9bd</td><td>0</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
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-[SuiteResult Ant test(failed)]
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-<?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="Ant test(failed)" failures="0" tests="1" time="1.098" errors="0">
- <properties/>
- <testcase name="readStatistics" time="0.565" classname="compbio.runner.msa.ProbconsTester"/>
-</testsuite>
+++ /dev/null
-<table border='1'>
-<tr>
-<th>Class name</th>
-<th>Method name</th>
-<th>Groups</th>
-</tr><tr>
-<td>compbio.runner.msa.ProbconsTester</td>
-<td> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testExecute</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testPersistance</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testClusterExecute</td>
-<td>cluster runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testSetInputTester</td>
-<td>runner non_windows </td>
-</tr>
-<tr>
-<td> </td>
-<td>testConfigurationLoading</td>
-<td>runner </td>
-</tr>
-<tr>
-<td> </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> </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>
-</table>
+++ /dev/null
-<h2>Groups used for this test run</h2><table border="1">
-<tr> <td align="center"><b>Group name</b></td><td align="center"><b>Methods</b></td></tr><tr><td>non_windows</td><td>compbio.runner.msa.ProbconsTester.readStatistics()<br/></td></tr>
-<tr><td>runner</td><td>compbio.runner.msa.ProbconsTester.readStatistics()<br/></td></tr>
-</table>
+++ /dev/null
-<html><head><title>Results for Failed suite [Ant suite]</title></head>
-<frameset cols="26%,74%">
-<frame src="toc.html" name="navFrame">
-<frame src="main.html" name="mainFrame">
-</frameset>
-</html>
+++ /dev/null
-<html><head><title>Results for Failed suite [Ant suite]</title></head>
-<body>Select a result on the left-hand pane.</body></html>
+++ /dev/null
-<h2>Methods run, sorted chronologically</h2><h3>>> means before, << means after</h3><p/><br/><em>Failed suite [Ant suite]</em><p/><small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table border="1">
-<tr><th>Time</th><th>Delta (ms)</th><th>Suite<br>configuration</th><th>Test<br>configuration</th><th>Class<br>configuration</th><th>Groups<br>configuration</th><th>Method<br>configuration</th><th>Test<br>method</th><th>Thread</th><th>Instances</th></tr>
-<tr bgcolor="aa8cd1"> <td>10/02/08 18:30:13</td> <td>0</td> <td> </td><td title=">>compbio.engine.FilePullerTester.init()">>>init</td>
-<td> </td><td> </td><td> </td><td> </td> <td>main@1369543768</td> <td></td> </tr>
-<tr bgcolor="80ccb6"> <td>10/02/08 18:30:14</td> <td>525</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@1369543768</td> <td></td> </tr>
-<tr bgcolor="a46761"> <td>10/02/08 18:30:14</td> <td>452</td> <td> </td><td title=">>compbio.metadata.PresetTester.loadPresets()">>>loadPresets</td>
-<td> </td><td> </td><td> </td><td> </td> <td>main@1369543768</td> <td></td> </tr>
-<tr bgcolor="80ccb6"> <td>10/02/08 18:30:14</td> <td>526</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.readStatistics()">readStatistics</td>
- <td>main@1369543768</td> <td></td> </tr>
-</table>
+++ /dev/null
-<h2>Methods that were not run</h2><table>
-<tr><td>compbio.metadata.OptionCombinatorTester.testgetAllParameters</td></tr>
-<tr><td>compbio.runner.msa.MafftParametersTester.testParameters</td></tr>
-<tr><td>compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues</td></tr>
-<tr><td>compbio.runner.msa.ProbconsParametersTester.testArguments</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues</td></tr>
-<tr><td>compbio.runner.msa.MafftTester.testExecute</td></tr>
-<tr><td>compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration</td></tr>
-<tr><td>compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusShortPoolingTime</td></tr>
-<tr><td>compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue</td></tr>
-<tr><td>compbio.metadata.OptionMarshallerTester.testMarshalling</td></tr>
-<tr><td>compbio.engine.FilePullerTester.testGetDelay</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeParametersTester.testParameters</td></tr>
-<tr><td>compbio.runner.msa.ProbconsTester.testConfigurationLoading</td></tr>
-<tr><td>compbio.engine.conf.RunnerConfigMarshallerTester.testValidation</td></tr>
-<tr><td>compbio.runner.msa.MuscleParametersTester.testParameters</td></tr>
-<tr><td>compbio.runner.msa.MafftTester.testPersistance</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testParameterToCommand</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate</td></tr>
-<tr><td>compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues</td></tr>
-<tr><td>compbio.runner.msa.MafftTester.testClusterExecute</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeTester.testConfigurationLoading</td></tr>
-<tr><td>compbio.runner.msa.ClustalWParametersTester.testParameters</td></tr>
-<tr><td>compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration</td></tr>
-<tr><td>compbio.runner.msa.LimitTester.testLoadLimits</td></tr>
-<tr><td>compbio.metadata.PresetTester.marshallPreset</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeTester.readStatistics</td></tr>
-<tr><td>compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration</td></tr>
-<tr><td>compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testValidateValueConstrain</td></tr>
-<tr><td>compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime</td></tr>
-<tr><td>compbio.runner.msa.MafftParametersTester.testOptions</td></tr>
-<tr><td>compbio.runner.msa.ProbconsTester.testSetInputTester</td></tr>
-<tr><td>compbio.engine.conf.RunnerConfigMarshallerTester.testUnMarshalling</td></tr>
-<tr><td>compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues</td></tr>
-<tr><td>compbio.runner.msa.MuscleTester.testPersistance</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues</td></tr>
-<tr><td>compbio.runner.msa.ClustalWParametersTester.testOptions</td></tr>
-<tr><td>compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeParametersTester.testOptions</td></tr>
-<tr><td>compbio.runner.msa.ProbconsParametersTester.testConfiguration</td></tr>
-<tr><td>compbio.runner.msa.ProbconsParametersTester.testDefaultParameters</td></tr>
-<tr><td>compbio.engine.conf.RunnerConfigMarshallerTester.testSchemaFromCodeGeneration</td></tr>
-<tr><td>compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues</td></tr>
-<tr><td>compbio.runner.msa.MuscleParametersTester.testOptions</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testOptionToCommand</td></tr>
-<tr><td>compbio.runner.msa.MafftTester.readStatistics</td></tr>
-<tr><td>compbio.runner.msa.MafftParametersTester.testDefaultParameters</td></tr>
-<tr><td>compbio.runner.msa.MafftParametersTester.testConfiguration</td></tr>
-<tr><td>compbio.runner.msa.MafftTester.testSetInputTester</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testCreateParameter</td></tr>
-<tr><td>compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling</td></tr>
-<tr><td>compbio.engine.conf.RunnerConfigMarshallerTester.testMarshalling</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeTester.testNcore</td></tr>
-<tr><td>compbio.metadata.OptionCombinatorTester.testgetAllOptions</td></tr>
-<tr><td>compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues</td></tr>
-<tr><td>compbio.engine.FilePullerTester.testPull</td></tr>
-<tr><td>compbio.runner.msa.MuscleTester.testRunLocally</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeParametersTester.testConfiguration</td></tr>
-<tr><td>compbio.runner.msa.ProbconsParametersTester.testOptions</td></tr>
-<tr><td>compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues</td></tr>
-<tr><td>compbio.runner.msa.MuscleParametersTester.testDefaultParameters</td></tr>
-<tr><td>compbio.runner.msa.MuscleParametersTester.testConfiguration</td></tr>
-<tr><td>compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues</td></tr>
-<tr><td>compbio.runner.msa.MuscleTester.testRunOnCluster</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testValidateBoundaryConstrainCheck</td></tr>
-<tr><td>compbio.runner.msa.ClustalWParametersTester.testConfiguration</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues</td></tr>
-<tr><td>compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues</td></tr>
-<tr><td>compbio.runner.msa.ClustalWParametersTester.testDefaultParameters</td></tr>
-<tr><td>compbio.runner.msa.MuscleTester.testConfigurationLoading</td></tr>
-<tr><td>compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf</td></tr>
-<tr><td>compbio.runner.msa.MafftParametersTester.testPresets</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeTester.testExecute</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testValidate</td></tr>
-<tr><td>compbio.metadata.PresetTester.validatePresets</td></tr>
-<tr><td>compbio.engine.FilePullerTester.testCache</td></tr>
-<tr><td>compbio.runner.msa.MuscleTester.readStatistics</td></tr>
-<tr><td>compbio.runner.msa.ClustalWParametersTester.testArguments</td></tr>
-<tr><td>compbio.metadata.OptionMarshallerTester.testUnMarshalling</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testCreateParameterWithValidValueConstrain</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeParametersTester.testArguments</td></tr>
-<tr><td>compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration</td></tr>
-<tr><td>compbio.runner.msa.MuscleParametersTester.testArguments</td></tr>
-<tr><td>compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues</td></tr>
-<tr><td>compbio.runner.msa.ProbconsTester.testExecute</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeTester.testPersistance</td></tr>
-<tr><td>compbio.engine.conf.PropertyHelperManagerTester.testLocalEngineConf</td></tr>
-<tr><td>compbio.runner.msa.ProbconsTester.testClusterExecute</td></tr>
-<tr><td>compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeParametersTester.testPresets</td></tr>
-<tr><td>compbio.runner.msa.MuscleTester.testRunOnClusterAsync</td></tr>
-<tr><td>compbio.runner.msa.MuscleParametersTester.testPresets</td></tr>
-<tr><td>compbio.runner.msa.MafftParametersTester.testArguments</td></tr>
-<tr><td>compbio.runner.msa.MafftTester.testConfigurationLoading</td></tr>
-<tr><td>compbio.runner.msa.ProbconsParametersTester.testParameters</td></tr>
-<tr><td>compbio.engine.FilePullerTester.testGet</td></tr>
-<tr><td>compbio.runner.msa.ProbconsTester.testPersistance</td></tr>
-<tr><td>compbio.runner.msa.ClustalWParametersTester.testPresets</td></tr>
-<tr><td>compbio.runner.msa.TcoffeeTester.testClusterExecute</td></tr>
-</table>
\ No newline at end of file
+++ /dev/null
-<h2>Methods run, sorted chronologically</h2><h3>>> means before, << means after</h3><p/><br/><em>Failed suite [Ant suite]</em><p/><small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table border="1">
-<tr><th>Time</th><th>Delta (ms)</th><th>Suite<br>configuration</th><th>Test<br>configuration</th><th>Class<br>configuration</th><th>Groups<br>configuration</th><th>Method<br>configuration</th><th>Test<br>method</th><th>Thread</th><th>Instances</th></tr>
-<tr bgcolor="aa8cd1"> <td>10/02/08 18:30:13</td> <td>0</td> <td> </td><td title=">>compbio.engine.FilePullerTester.init()">>>init</td>
-<td> </td><td> </td><td> </td><td> </td> <td>main@1369543768</td> <td></td> </tr>
-<tr bgcolor="a46761"> <td>10/02/08 18:30:14</td> <td>452</td> <td> </td><td title=">>compbio.metadata.PresetTester.loadPresets()">>>loadPresets</td>
-<td> </td><td> </td><td> </td><td> </td> <td>main@1369543768</td> <td></td> </tr>
-<tr bgcolor="80ccb6"> <td>10/02/08 18:30:14</td> <td>525</td> <td> </td><td> </td><td> </td><td> </td><td title=">>compbio.runner.msa.ProbconsTester.init()">>>init</td>
-<td> </td> <td>main@1369543768</td> <td></td> </tr>
-<tr bgcolor="80ccb6"> <td>10/02/08 18:30:14</td> <td>526</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.runner.msa.ProbconsTester.readStatistics()">readStatistics</td>
- <td>main@1369543768</td> <td></td> </tr>
-</table>
+++ /dev/null
-<h2>Reporter output</h2><table></table>
\ No newline at end of file
+++ /dev/null
-<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
-<suite thread-count="5" skipfailedinvocationCounts="false" verbose="3" name="Failed suite [Failed suite [Ant suite]]" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10">
- <test name="Ant test(failed)(failed)" junit="false" parallel="false" annotations="JDK">
- <classes>
- <class name="compbio.engine.FilePullerTester">
- <methods>
- <include name="init"/>
- </methods>
- </class>
- <class name="compbio.runner.tcoffee.TcoffeeParametersTester">
- <methods>
- <include name="testPresets"/>
- <include name="setup"/>
- </methods>
- </class>
- <class name="compbio.data.msa.meta.PresetTester">
- <methods>
- <include name="loadPresets"/>
- </methods>
- </class>
- </classes>
- </test>
-</suite>
+++ /dev/null
-<html><head><title>testng.xml for Failed suite [Ant suite]</title></head><body><tt><!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd"><br/><suite thread-count="5" skipfailedinvocationCounts="false" verbose="3" name="Failed suite [Ant suite]" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10"><br/> <test name="Ant test(failed)" junit="false" annotations="JDK"><br/> <groups><br/> <run><br/> <exclude name="performance"/><br/> </run><br/> </groups><br/> <classes><br/> <class name="compbio.runner.msa.MuscleTester"><br/> <methods><br/> <include name="init"/><br/> </methods><br/> </class><br/> <class name="compbio.runner.msa.LimitTester"><br/> <methods><br/> <include name="setup"/><br/> </methods><br/> </class><br/> <class name="compbio.runner.msa.ClustalWParametersTester"><br/> <methods><br/> <include name="setup"/><br/> </methods><br/> </class><br/> <class name="compbio.runner.msa.TcoffeeParametersTester"><br/> <methods><br/> <include name="setup"/><br/> </methods><br/> </class><br/> <class name="compbio.metadata.OptionMarshallerTester"><br/> <methods><br/> <include name="setup"/><br/> </methods><br/> </class><br/> <class name="compbio.metadata.PresetTester"><br/> <methods><br/> <include name="loadPresets"/><br/> </methods><br/> </class><br/> <class name="compbio.runner.msa.MafftTester"><br/> <methods><br/> <include name="init"/><br/> </methods><br/> </class><br/> <class name="compbio.runner.msa.ProbconsTester"><br/> <methods><br/> <include name="readStatistics"/><br/> <include name="init"/><br/> </methods><br/> </class><br/> <class name="compbio.runner.msa.MuscleParametersTester"><br/> <methods><br/> <include name="setup"/><br/> </methods><br/> </class><br/> <class name="compbio.engine.conf.PropertyHelperManagerTester"><br/> <methods><br/> <include name="testLoadResources"/><br/> </methods><br/> </class><br/> <class name="compbio.metadata.RunnerConfigTester"><br/> <methods><br/> <include name="setup"/><br/> </methods><br/> </class><br/> <class name="compbio.runner.msa.MafftParametersTester"><br/> <methods><br/> <include name="setup"/><br/> </methods><br/> </class><br/> <class name="compbio.metadata.OptionCombinatorTester"><br/> <methods><br/> <include name="setup"/><br/> </methods><br/> </class><br/> <class name="compbio.runner.msa.ProbconsParametersTester"><br/> <methods><br/> <include name="setup"/><br/> </methods><br/> </class><br/> <class name="compbio.runner.msa.TcoffeeTester"><br/> <methods><br/> <include name="init"/><br/> </methods><br/> </class><br/> <class name="compbio.engine.FilePullerTester"><br/> <methods><br/> <include name="init"/><br/> </methods><br/> </class><br/> <class name="compbio.engine.conf.RunnerConfigMarshallerTester"><br/> <methods><br/> <include name="setup"/><br/> </methods><br/> </class><br/> </classes><br/> </test><br/></suite><br/></tt></body></html>
\ No newline at end of file
+++ /dev/null
-<html>
-<head>
-<title>Results for Failed suite [Ant suite]</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-</head>
-<body>
-<h3><p align="center">Results for<br/><em>Failed suite [Ant suite]</em></p></h3>
-<table border='1' width='100%'>
-<tr valign='top'>
-<td>1 test</td>
-<td><a target='mainFrame' href='classes.html'>1 class</a></td>
-<td>1 method:<br/>
- <a target='mainFrame' href='methods.html'>chronological</a><br/>
- <a target='mainFrame' href='methods-alphabetical.html'>alphabetical</a><br/>
- <a target='mainFrame' href='methods-not-run.html'>not run (103)</a></td>
-</tr>
-<tr>
-<td><a target='mainFrame' href='groups.html'>2 groups</a></td>
-<td><a target='mainFrame' href='reporter-output.html'>reporter output</a></td>
-<td><a target='mainFrame' href='testng.xml.html'>testng.xml</a></td>
-</tr></table>
-<table width='100%' class='test-passed'>
-<tr><td>
-<table style='width: 100%'><tr><td valign='top'>Ant test(failed) (1/0/0)</td><td valign='top' align='right'>
- <a href='Ant test(failed).html' target='mainFrame'>Results</a>
-</td></tr></table>
-</td></tr><p/>
-</table>
-</body></html>
\ No newline at end of file
+++ /dev/null
-<table border='1'>
-<tr>
-<th>Class name</th>
-<th>Method name</th>
-<th>Groups</th>
-</tr><tr>
-<td>compbio.engine.local.EngineResourcesLeakTester</td>
-<td> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>loadEngineRetrieveResultsManyTimes</td>
-<td>engine </td>
-</tr>
-<tr>
-<td> </td>
-<td>loadEngineRetrieveResultsOnce</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>
-</table>
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.engine.local.EngineResourcesLeakTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-
-<style type="text/css">
-.log { display: none;}
-.stack-trace { display: none;}
-</style>
-<script type="text/javascript">
-<!--
-function flip(e) {
- current = e.style.display;
- if (current == 'block') {
- e.style.display = 'none';
- return 0;
- }
- else {
- e.style.display = 'block';
- return 1;
- }
-}
-
-function toggleBox(szDivId, elem, msg1, msg2)
-{
- var res = -1; if (document.getElementById) {
- res = flip(document.getElementById(szDivId));
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- else if (document.all) {
- // this is the way old msie versions work
- res = flip(document.all[szDivId]);
- }
- if(elem) {
- if(res == 0) elem.innerHTML = msg1; else elem.innerHTML = msg2;
- }
-
-}
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-function toggleAllBoxes() {
- if (document.getElementsByTagName) {
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- }
- }
-}
-
-// -->
-</script>
-
-</head>
-<body>
-<h2 align='center'>compbio.engine.local.EngineResourcesLeakTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>0/2/0</td>
-</tr><tr>
-<td>Started on:</td><td>Wed Jan 27 15:33:57 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>1 seconds (1330 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-failed'>
-<tr><td colspan='4' align='center'><b>FAILED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes()'><b>loadEngineRetrieveResultsManyTimes</b><br>Test class:compbio.engine.local.EngineResourcesLeakTester</td>
-<td>compbio.engine.local.EngineResourcesLeakTester@444cee32</td><td>1</td>
-<td><div><pre>java.lang.AssertionError: expected:<true> but was:<false>
- at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes(EngineResourcesLeakTester.java:45)
-... Removed 27 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1046333844", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1046333844'><pre>java.lang.AssertionError: expected:<true> but was:<false>
- at org.testng.Assert.fail(Assert.java:86)
- at org.testng.Assert.failNotEquals(Assert.java:440)
- at org.testng.Assert.assertTrue(Assert.java:34)
- at org.testng.Assert.assertNotNull(Assert.java:354)
- at org.testng.Assert.assertNotNull(Assert.java:344)
- at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes(EngineResourcesLeakTester.java:45)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce()'><b>loadEngineRetrieveResultsOnce</b><br>Test class:compbio.engine.local.EngineResourcesLeakTester</td>
-<td>compbio.engine.local.EngineResourcesLeakTester@444cee32</td><td>0</td>
-<td><div><pre>java.lang.AssertionError: expected:<true> but was:<false>
- at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce(EngineResourcesLeakTester.java:113)
-... Removed 27 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace453897055", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace453897055'><pre>java.lang.AssertionError: expected:<true> but was:<false>
- at org.testng.Assert.fail(Assert.java:86)
- at org.testng.Assert.failNotEquals(Assert.java:440)
- at org.testng.Assert.assertTrue(Assert.java:34)
- at org.testng.Assert.assertNotNull(Assert.java:354)
- at org.testng.Assert.assertNotNull(Assert.java:344)
- at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce(EngineResourcesLeakTester.java:113)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.engine.local.EngineResourcesLeakTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="compbio.engine.local.EngineResourcesLeakTester" failures="2" tests="2" time="1.33" errors="0">
- <properties/>
- <testcase name="loadEngineRetrieveResultsManyTimes" time="1.248" classname="compbio.engine.local.EngineResourcesLeakTester">
- <failure type="java.lang.AssertionError" message="expected:&lt;true&gt; but was:&lt;false&gt;">
- <![CDATA[java.lang.AssertionError: expected:<true> but was:<false>
- at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes(EngineResourcesLeakTester.java:45)
-... Removed 27 stack frames]]>
- </failure>
- </testcase>
- <testcase name="loadEngineRetrieveResultsOnce" time="0.074" classname="compbio.engine.local.EngineResourcesLeakTester">
- <failure type="java.lang.AssertionError" message="expected:&lt;true&gt; but was:&lt;false&gt;">
- <![CDATA[java.lang.AssertionError: expected:<true> but was:<false>
- at compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce(EngineResourcesLeakTester.java:113)
-... Removed 27 stack frames]]>
- </failure>
- </testcase>
-</testsuite>
+++ /dev/null
-<h2>Groups used for this test run</h2><table border="1">
-<tr> <td align="center"><b>Group name</b></td><td align="center"><b>Methods</b></td></tr><tr><td>engine</td><td>compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce()<br/>compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes()<br/></td></tr>
-</table>
+++ /dev/null
-<html><head><title>Results for JWS2</title></head>
-<frameset cols="26%,74%">
-<frame src="toc.html" name="navFrame">
-<frame src="main.html" name="mainFrame">
-</frameset>
-</html>
+++ /dev/null
-<html><head><title>Results for JWS2</title></head>
-<body>Select a result on the left-hand pane.</body></html>
+++ /dev/null
-<h2>Methods run, sorted chronologically</h2><h3>>> means before, << means after</h3><p/><br/><em>JWS2</em><p/><small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table border="1">
-<tr><th>Time</th><th>Delta (ms)</th><th>Suite<br>configuration</th><th>Test<br>configuration</th><th>Class<br>configuration</th><th>Groups<br>configuration</th><th>Method<br>configuration</th><th>Test<br>method</th><th>Thread</th><th>Instances</th></tr>
-<tr bgcolor="95c083"> <td>10/01/27 15:33:57</td> <td>0</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes()">loadEngineRetrieveResultsManyTimes</td>
- <td>main@1663273938</td> <td></td> </tr>
-<tr bgcolor="95c083"> <td>10/01/27 15:33:58</td> <td>1249</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce()">loadEngineRetrieveResultsOnce</td>
- <td>main@1663273938</td> <td></td> </tr>
-</table>
+++ /dev/null
-<h2>Methods that were not run</h2><table>
-</table>
\ No newline at end of file
+++ /dev/null
-<h2>Methods run, sorted chronologically</h2><h3>>> means before, << means after</h3><p/><br/><em>JWS2</em><p/><small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table border="1">
-<tr><th>Time</th><th>Delta (ms)</th><th>Suite<br>configuration</th><th>Test<br>configuration</th><th>Class<br>configuration</th><th>Groups<br>configuration</th><th>Method<br>configuration</th><th>Test<br>method</th><th>Thread</th><th>Instances</th></tr>
-<tr bgcolor="95c083"> <td>10/01/27 15:33:57</td> <td>0</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsManyTimes()">loadEngineRetrieveResultsManyTimes</td>
- <td>main@1663273938</td> <td></td> </tr>
-<tr bgcolor="95c083"> <td>10/01/27 15:33:58</td> <td>1249</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.local.EngineResourcesLeakTester.loadEngineRetrieveResultsOnce()">loadEngineRetrieveResultsOnce</td>
- <td>main@1663273938</td> <td></td> </tr>
-</table>
+++ /dev/null
-<h2>Reporter output</h2><table></table>
\ No newline at end of file
+++ /dev/null
-<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
-<suite thread-count="5" skipfailedinvocationCounts="false" verbose="1" name="Failed suite [JWS2]" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10">
- <test name="compbio.engine.local.EngineResourcesLeakTester(failed)" junit="false" parallel="false" annotations="JDK">
- <classes>
- <class name="compbio.engine.local.EngineResourcesLeakTester">
- <methods>
- <include name="loadEngineRetrieveResultsOnce"/>
- <include name="loadEngineRetrieveResultsManyTimes"/>
- </methods>
- </class>
- </classes>
- </test>
-</suite>
+++ /dev/null
-<html><head><title>testng.xml for JWS2</title></head><body><tt><!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd"><br/><suite thread-count="5" skipfailedinvocationCounts="false" verbose="1" name="JWS2" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10"><br/> <test verbose="2" name="compbio.engine.local.EngineResourcesLeakTester" junit="false" annotations="JDK"><br/> <classes><br/> <class name="compbio.engine.local.EngineResourcesLeakTester"/><br/> </classes><br/> </test><br/></suite><br/></tt></body></html>
\ No newline at end of file
+++ /dev/null
-<html>
-<head>
-<title>Results for JWS2</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-</head>
-<body>
-<h3><p align="center">Results for<br/><em>JWS2</em></p></h3>
-<table border='1' width='100%'>
-<tr valign='top'>
-<td>1 test</td>
-<td><a target='mainFrame' href='classes.html'>1 class</a></td>
-<td>2 methods:<br/>
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- <a target='mainFrame' href='methods-alphabetical.html'>alphabetical</a><br/>
- <a target='mainFrame' href='methods-not-run.html'>not run (0)</a></td>
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-</tr></table>
-<table width='100%' class='test-failed'>
-<tr><td>
-<table style='width: 100%'><tr><td valign='top'>compbio.engine.local.EngineResourcesLeakTester (0/2/0)</td><td valign='top' align='right'>
- <a href='compbio.engine.local.EngineResourcesLeakTester.html' target='mainFrame'>Results</a>
-</td></tr></table>
-</td></tr><p/>
-</table>
-</body></html>
\ No newline at end of file
+++ /dev/null
-<table border='1'>
-<tr>
-<th>Class name</th>
-<th>Method name</th>
-<th>Groups</th>
-</tr><tr>
-<td>compbio.engine.conf.PropertyHelperManagerTester</td>
-<td> </td><td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@Test</td>
-</tr>
-<tr>
-<td> </td>
-<td>testClusterEngineConf</td>
-<td>cluster </td>
-</tr>
-<tr>
-<td> </td>
-<td>validateClustalConfiguration</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>validateTcoffeeConfiguration</td>
-<td> </td></tr>
-<tr>
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-<td>validateMuscleConfiguration</td>
-<td> </td></tr>
-<tr>
-<td> </td>
-<td>validateMafftConfiguration</td>
-<td> </td></tr>
-<tr>
-<td align='center' colspan='3'>@BeforeClass</td>
-</tr>
-<tr>
-<td> </td>
-<td>testLoadResources</td>
-<td> </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>
-</table>
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.engine.cluster.drmaa.ClusterSessionTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
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-<h2 align='center'>compbio.engine.cluster.drmaa.ClusterSessionTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>1/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Mon Dec 21 16:10:22 GMT 2009</td>
-</tr>
-<tr><td>Total time:</td><td>13 seconds (13917 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-passed'>
-<tr><td colspan='4' align='center'><b>PASSED TESTS</b></td></tr>
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-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()'><b>testTaskList</b><br>Test class:compbio.engine.cluster.drmaa.ClusterSessionTester</td>
-<td>compbio.engine.cluster.drmaa.ClusterSessionTester@2321ab80</td><td>13</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.engine.cluster.drmaa.ClusterSessionTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="compbio.engine.cluster.drmaa.ClusterSessionTester" failures="0" tests="1" time="13.917" errors="0">
- <properties/>
- <testcase name="testTaskList" time="13.91" classname="compbio.engine.cluster.drmaa.ClusterSessionTester"/>
-</testsuite>
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester</title>
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-<h2 align='center'>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>3/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Mon Dec 21 16:16:04 GMT 2009</td>
-</tr>
-<tr><td>Total time:</td><td>31 seconds (31283 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
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-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()'><b>testCancel</b><br>Test class:compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester</td>
-<td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@2c76e369</td><td>0</td>
-<td><div><pre>compbio.engine.ResultNotAvailableException: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/ClustalW#556313082813930709 with file name TO1381.clustal.cluster.out is not found!
- at compbio.data.sequence.ClustalAlignmentUtil.readClustalFile(ClustalAlignmentUtil.java:258)
- at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:54)
- at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:15)
- at compbio.runner.ConfExecutable.getResults(ConfExecutable.java:158)
- at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:94)
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace270071071", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace270071071'><pre>compbio.engine.ResultNotAvailableException: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/ClustalW#556313082813930709 with file name TO1381.clustal.cluster.out is not found!
- at compbio.data.sequence.ClustalAlignmentUtil.readClustalFile(ClustalAlignmentUtil.java:258)
- at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:54)
- at compbio.runner.clustal.ClustalW.getResults(ClustalW.java:15)
- at compbio.runner.ConfExecutable.getResults(ConfExecutable.java:158)
- at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:94)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()'><b>testGetJobStatus</b><br>Test class:compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester</td>
-<td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@2c76e369</td><td>11</td>
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-<td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@2c76e369</td><td>18</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
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- <testcase name="testSubmit" time="18.976" classname="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
-</testsuite>
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.engine.cluster.drmaa.DrmaaClusterEngineTester</title>
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-<td></td>
-</tr>
-</table><p>
-</body>
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\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.engine.cluster.drmaa.DrmaaClusterEngineTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
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+++ /dev/null
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-// -->
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-</head>
-<body>
-<h2 align='center'>compbio.engine.conf.DirectoryManagerTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>6/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Thu Jan 07 16:48:50 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>0 seconds (209 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
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-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-passed'>
-<tr><td colspan='4' align='center'><b>PASSED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
-<td>compbio.engine.conf.DirectoryManagerTester@2ca6d51e</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
-<td>compbio.engine.conf.DirectoryManagerTester@2ca6d51e</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
-<td>compbio.engine.conf.DirectoryManagerTester@2ca6d51e</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
-<td>compbio.engine.conf.DirectoryManagerTester@2ca6d51e</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.DirectoryManagerTester.testLongDirName()'><b>testLongDirName</b><br>Test class:compbio.engine.conf.DirectoryManagerTester</td>
-<td>compbio.engine.conf.DirectoryManagerTester@2ca6d51e</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.DirectoryManagerTester.testNanoTime()'><b>testNanoTime</b><br>Test class:compbio.engine.conf.DirectoryManagerTester</td>
-<td>compbio.engine.conf.DirectoryManagerTester@2ca6d51e</td><td>0</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.engine.conf.DirectoryManagerTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="compbio.engine.conf.DirectoryManagerTester" failures="0" tests="6" time="0.209" errors="0">
- <properties/>
- <testcase name="testGetDirectory" time="0.196" classname="compbio.engine.conf.DirectoryManagerTester"/>
- <testcase name="testGetDirectory" time="0.196" classname="compbio.engine.conf.DirectoryManagerTester"/>
- <testcase name="testGetDirectory" time="0.195" classname="compbio.engine.conf.DirectoryManagerTester"/>
- <testcase name="testGetDirectory" time="0.195" classname="compbio.engine.conf.DirectoryManagerTester"/>
- <testcase name="testLongDirName" time="0.0" classname="compbio.engine.conf.DirectoryManagerTester"/>
- <testcase name="testNanoTime" time="0.0010" classname="compbio.engine.conf.DirectoryManagerTester"/>
-</testsuite>
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.engine.conf.PropertyHelperManagerTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-
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-
-// -->
-</script>
-
-</head>
-<body>
-<h2 align='center'>compbio.engine.conf.PropertyHelperManagerTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>5/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Wed Feb 17 15:33:15 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>0 seconds (723 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-passed'>
-<tr><td colspan='4' align='center'><b>PASSED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()'><b>testClusterEngineConf</b><br>Test class:compbio.engine.conf.PropertyHelperManagerTester</td>
-<td>compbio.engine.conf.PropertyHelperManagerTester@4e99353f</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration()'><b>validateClustalConfiguration</b><br>Test class:compbio.engine.conf.PropertyHelperManagerTester</td>
-<td>compbio.engine.conf.PropertyHelperManagerTester@4e99353f</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration()'><b>validateMafftConfiguration</b><br>Test class:compbio.engine.conf.PropertyHelperManagerTester</td>
-<td>compbio.engine.conf.PropertyHelperManagerTester@4e99353f</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration()'><b>validateMuscleConfiguration</b><br>Test class:compbio.engine.conf.PropertyHelperManagerTester</td>
-<td>compbio.engine.conf.PropertyHelperManagerTester@4e99353f</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration()'><b>validateTcoffeeConfiguration</b><br>Test class:compbio.engine.conf.PropertyHelperManagerTester</td>
-<td>compbio.engine.conf.PropertyHelperManagerTester@4e99353f</td><td>0</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.engine.conf.PropertyHelperManagerTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="compbio.engine.conf.PropertyHelperManagerTester" failures="0" tests="5" time="0.723" errors="0">
- <properties/>
- <testcase name="testClusterEngineConf" time="0.012" classname="compbio.engine.conf.PropertyHelperManagerTester"/>
- <testcase name="validateClustalConfiguration" time="0.054" classname="compbio.engine.conf.PropertyHelperManagerTester"/>
- <testcase name="validateMafftConfiguration" time="0.011" classname="compbio.engine.conf.PropertyHelperManagerTester"/>
- <testcase name="validateMuscleConfiguration" time="0.011" classname="compbio.engine.conf.PropertyHelperManagerTester"/>
- <testcase name="validateTcoffeeConfiguration" time="0.017" classname="compbio.engine.conf.PropertyHelperManagerTester"/>
-</testsuite>
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.engine.local.EngineResourcesLeakTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-
-<style type="text/css">
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- }
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-
-// -->
-</script>
-
-</head>
-<body>
-<h2 align='center'>compbio.engine.local.EngineResourcesLeakTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>0/1/0</td>
-</tr><tr>
-<td>Started on:</td><td>Tue Jan 26 17:00:52 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>0 seconds (782 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-failed'>
-<tr><td colspan='4' align='center'><b>FAILED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.engine.local.EngineResourcesLeakTester.loadEngine()'><b>loadEngine</b><br>Test class:compbio.engine.local.EngineResourcesLeakTester</td>
-<td>compbio.engine.local.EngineResourcesLeakTester@116471f</td><td>0</td>
-<td><div><pre>java.lang.IllegalArgumentException: Working directory: H:\workspace\clustengine\/homes/pvtroshin/workspace/clustengine/jobsout/local\ClustalW#86210242684128 is inaccessible or does not exist!\r
- at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89)\r
- at compbio.engine.local.AsyncLocalRunner.submitJob(AsyncLocalRunner.java:75)\r
- at compbio.engine.local.EngineResourcesLeakTester.loadEngine(EngineResourcesLeakTester.java:28)\r
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1913643", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1913643'><pre>java.lang.IllegalArgumentException: Working directory: H:\workspace\clustengine\/homes/pvtroshin/workspace/clustengine/jobsout/local\ClustalW#86210242684128 is inaccessible or does not exist!\r
- at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89)\r
- at compbio.engine.local.AsyncLocalRunner.submitJob(AsyncLocalRunner.java:75)\r
- at compbio.engine.local.EngineResourcesLeakTester.loadEngine(EngineResourcesLeakTester.java:28)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r
- at java.lang.reflect.Method.invoke(Method.java:597)\r
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:644)\r
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:546)\r
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:700)\r
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1002)\r
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:137)\r
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:121)\r
- at org.testng.TestRunner.runWorkers(TestRunner.java:908)\r
- at org.testng.TestRunner.privateRun(TestRunner.java:617)\r
- at org.testng.TestRunner.run(TestRunner.java:498)\r
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:329)\r
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:324)\r
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:296)\r
- at org.testng.SuiteRunner.run(SuiteRunner.java:201)\r
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:915)\r
- at org.testng.TestNG.runSuitesLocally(TestNG.java:879)\r
- at org.testng.TestNG.run(TestNG.java:787)\r
- at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:75)\r
- at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:127)\r
-</pre></div></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.engine.local.EngineResourcesLeakTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>\r
-<testsuite name="compbio.engine.local.EngineResourcesLeakTester" failures="1" tests="1" time="0.782" errors="0">\r
- <properties/>\r
- <testcase name="loadEngine" time="0.766" classname="compbio.engine.local.EngineResourcesLeakTester">\r
- <failure type="java.lang.IllegalArgumentException" message="Working directory: H:\workspace\clustengine\/homes/pvtroshin/workspace/clustengine/jobsout/local\ClustalW#86210242684128 is inaccessible or does not exist!">\r
- <![CDATA[java.lang.IllegalArgumentException: Working directory: H:\workspace\clustengine\/homes/pvtroshin/workspace/clustengine/jobsout/local\ClustalW#86210242684128 is inaccessible or does not exist!\r
- at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89)\r
- at compbio.engine.local.AsyncLocalRunner.submitJob(AsyncLocalRunner.java:75)\r
- at compbio.engine.local.EngineResourcesLeakTester.loadEngine(EngineResourcesLeakTester.java:28)\r
-... Removed 22 stack frames]]>\r
- </failure>\r
- </testcase>\r
-</testsuite>\r
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.metadata.PresetTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-
-<style type="text/css">
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-.stack-trace { display: none;}
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-</script>
-
-</head>
-<body>
-<h2 align='center'>compbio.metadata.PresetTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>0/0/2</td>
-</tr><tr>
-<td>Started on:</td><td>Mon Jan 25 15:45:52 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>0 seconds (110 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-failed'>
-<tr><td colspan='4' align='center'><b>FAILED CONFIGURATIONS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.metadata.PresetTester.loadPresets()'><b>loadPresets</b><br>Test class:compbio.metadata.PresetTester</td>
-<td>null</td><td>0</td>
-<td><div><pre>java.lang.AssertionError: null\r
- at compbio.metadata.PresetTester.loadPresets(PresetTester.java:85)\r
-... Removed 20 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace10059989", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace10059989'><pre>java.lang.AssertionError: null\r
- at org.testng.Assert.fail(Assert.java:87)\r
- at compbio.metadata.PresetTester.loadPresets(PresetTester.java:85)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r
- at java.lang.reflect.Method.invoke(Method.java:597)\r
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:644)\r
- at org.testng.internal.Invoker.invokeConfigurationMethod(Invoker.java:443)\r
- at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:160)\r
- at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:90)\r
- at org.testng.TestRunner.beforeRun(TestRunner.java:522)\r
- at org.testng.TestRunner.run(TestRunner.java:490)\r
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:329)\r
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:324)\r
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:296)\r
- at org.testng.SuiteRunner.run(SuiteRunner.java:201)\r
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:915)\r
- at org.testng.TestNG.runSuitesLocally(TestNG.java:879)\r
- at org.testng.TestNG.run(TestNG.java:787)\r
- at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:75)\r
- at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:127)\r
-</pre></div></td>
-</tr>
-</table><p>
-<table width='100%' border='1' class='invocation-skipped'>
-<tr><td colspan='4' align='center'><b>SKIPPED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.metadata.PresetTester.marshallPreset()'><b>marshallPreset</b><br>Test class:compbio.metadata.PresetTester</td>
-<td>compbio.metadata.PresetTester@1171b26</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.metadata.PresetTester.validatePresets()'><b>validatePresets</b><br>Test class:compbio.metadata.PresetTester</td>
-<td>compbio.metadata.PresetTester@1171b26</td><td>0</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.metadata.PresetTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>\r
-<testsuite name="compbio.metadata.PresetTester" failures="0" tests="2" time="0.11" errors="0">\r
- <properties/>\r
- <testcase name="@BeforeTest loadPresets" time="0.0" classname="compbio.metadata.PresetTester">\r
- <failure type="java.lang.AssertionError" message="null">\r
- <![CDATA[java.lang.AssertionError: null\r
- at compbio.metadata.PresetTester.loadPresets(PresetTester.java:85)\r
-... Removed 20 stack frames]]>\r
- </failure>\r
- </testcase>\r
- <testcase name="marshallPreset" time="0.0" classname="compbio.metadata.PresetTester">\r
- <skipped/>\r
- </testcase>\r
- <testcase name="validatePresets" time="0.0" classname="compbio.metadata.PresetTester">\r
- <skipped/>\r
- </testcase>\r
-</testsuite>\r
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.runner.CommandBuilderTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-
-<style type="text/css">
-.log { display: none;}
-.stack-trace { display: none;}
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-function toggleBox(szDivId, elem, msg1, msg2)
-{
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-
-// -->
-</script>
-
-</head>
-<body>
-<h2 align='center'>compbio.runner.CommandBuilderTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>1/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Thu Jan 14 14:12:38 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>0 seconds (32 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-passed'>
-<tr><td colspan='4' align='center'><b>PASSED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.runner.CommandBuilderTester.testCommandBuilding()'><b>testCommandBuilding</b><br>Test class:compbio.runner.CommandBuilderTester</td>
-<td>compbio.runner.CommandBuilderTester@34a1fc</td><td>0</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.runner.CommandBuilderTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>\r
-<testsuite name="compbio.runner.CommandBuilderTester" failures="0" tests="1" time="0.032" errors="0">\r
- <properties/>\r
- <testcase name="testCommandBuilding" time="0.016" classname="compbio.runner.CommandBuilderTester"/>\r
-</testsuite>\r
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.runner.clustal.ClustalWParametersTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-
-<style type="text/css">
-.log { display: none;}
-.stack-trace { display: none;}
-</style>
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- if(elem) {
- if(res == 0) elem.innerHTML = msg1; else elem.innerHTML = msg2;
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-
-// -->
-</script>
-
-</head>
-<body>
-<h2 align='center'>compbio.runner.clustal.ClustalWParametersTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>0/8/0</td>
-</tr><tr>
-<td>Started on:</td><td>Mon Dec 21 18:09:47 GMT 2009</td>
-</tr>
-<tr><td>Total time:</td><td>2 seconds (2219 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-failed'>
-<tr><td colspan='3' align='center'><b>FAILED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.runner.clustal.ClustalWParametersTester.testArguments()'>testArguments</td>
-<td>0</td>
-<td><div><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979987799825706 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)\r
- at compbio.runner.clustal.ClustalWParametersTester.testArguments(ClustalWParametersTester.java:137)\r
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace24166053", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace24166053'><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979987799825706 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)\r
- at compbio.runner.clustal.ClustalWParametersTester.testArguments(ClustalWParametersTester.java:137)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r
- at java.lang.reflect.Method.invoke(Method.java:597)\r
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)\r
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)\r
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)\r
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)\r
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)\r
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)\r
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)\r
- at org.testng.TestRunner.privateRun(TestRunner.java:592)\r
- at org.testng.TestRunner.run(TestRunner.java:486)\r
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)\r
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)\r
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)\r
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)\r
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)\r
- at org.testng.TestNG.runSuitesLocally(TestNG.java:842)\r
- at org.testng.TestNG.run(TestNG.java:751)\r
- at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)\r
- at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)\r
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMaxValues()'>testConstrainedParametersMaxValues</td>
-<td>0</td>
-<td><div><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979988961908025 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174)\r
- at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMaxValues(ClustalWParametersTester.java:151)\r
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace30308427", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace30308427'><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979988961908025 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174)\r
- at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMaxValues(ClustalWParametersTester.java:151)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r
- at java.lang.reflect.Method.invoke(Method.java:597)\r
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)\r
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)\r
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)\r
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)\r
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)\r
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)\r
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)\r
- at org.testng.TestRunner.privateRun(TestRunner.java:592)\r
- at org.testng.TestRunner.run(TestRunner.java:486)\r
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)\r
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)\r
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)\r
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)\r
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)\r
- at org.testng.TestNG.runSuitesLocally(TestNG.java:842)\r
- at org.testng.TestNG.run(TestNG.java:751)\r
- at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)\r
- at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)\r
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMinValues()'>testConstrainedParametersMinValues</td>
-<td>0</td>
-<td><div><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#70979988327544395 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174)\r
- at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMinValues(ClustalWParametersTester.java:144)\r
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace9949215", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace9949215'><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#70979988327544395 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174)\r
- at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMinValues(ClustalWParametersTester.java:144)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r
- at java.lang.reflect.Method.invoke(Method.java:597)\r
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)\r
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)\r
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)\r
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)\r
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)\r
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)\r
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)\r
- at org.testng.TestRunner.privateRun(TestRunner.java:592)\r
- at org.testng.TestRunner.run(TestRunner.java:486)\r
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)\r
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)\r
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)\r
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)\r
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)\r
- at org.testng.TestNG.runSuitesLocally(TestNG.java:842)\r
- at org.testng.TestNG.run(TestNG.java:751)\r
- at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)\r
- at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)\r
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersRandomValues()'>testConstrainedParametersRandomValues</td>
-<td>0</td>
-<td><div><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#46979989070571443 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersRandomValues(ClustalWParametersTester.java:164)\r
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace25934938", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace25934938'><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#46979989070571443 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersRandomValues(ClustalWParametersTester.java:164)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r
- at java.lang.reflect.Method.invoke(Method.java:597)\r
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)\r
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)\r
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)\r
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)\r
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)\r
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)\r
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)\r
- at org.testng.TestRunner.privateRun(TestRunner.java:592)\r
- at org.testng.TestRunner.run(TestRunner.java:486)\r
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)\r
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)\r
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)\r
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)\r
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)\r
- at org.testng.TestNG.runSuitesLocally(TestNG.java:842)\r
- at org.testng.TestNG.run(TestNG.java:751)\r
- at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)\r
- at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)\r
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.runner.clustal.ClustalWParametersTester.testDefaultParameters()'>testDefaultParameters</td>
-<td>0</td>
-<td><div><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#38979988048124217 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.testDefaultParameters(ClustalWParametersTester.java:105)\r
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace11854491", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace11854491'><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#38979988048124217 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.testDefaultParameters(ClustalWParametersTester.java:105)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r
- at java.lang.reflect.Method.invoke(Method.java:597)\r
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)\r
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)\r
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)\r
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)\r
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)\r
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)\r
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)\r
- at org.testng.TestRunner.privateRun(TestRunner.java:592)\r
- at org.testng.TestRunner.run(TestRunner.java:486)\r
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)\r
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)\r
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)\r
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)\r
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)\r
- at org.testng.TestNG.runSuitesLocally(TestNG.java:842)\r
- at org.testng.TestNG.run(TestNG.java:751)\r
- at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)\r
- at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)\r
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.runner.clustal.ClustalWParametersTester.testOptions()'>testOptions</td>
-<td>0</td>
-<td><div><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979988189879815 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)\r
- at compbio.runner.clustal.ClustalWParametersTester.testOptions(ClustalWParametersTester.java:122)\r
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace26460367", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace26460367'><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979988189879815 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)\r
- at compbio.runner.clustal.ClustalWParametersTester.testOptions(ClustalWParametersTester.java:122)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r
- at java.lang.reflect.Method.invoke(Method.java:597)\r
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)\r
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)\r
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)\r
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)\r
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)\r
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)\r
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)\r
- at org.testng.TestRunner.privateRun(TestRunner.java:592)\r
- at org.testng.TestRunner.run(TestRunner.java:486)\r
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)\r
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)\r
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)\r
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)\r
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)\r
- at org.testng.TestNG.runSuitesLocally(TestNG.java:842)\r
- at org.testng.TestNG.run(TestNG.java:751)\r
- at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)\r
- at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)\r
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.runner.clustal.ClustalWParametersTester.testParameters()'>testParameters</td>
-<td>0</td>
-<td><div><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979987926880363 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)\r
- at compbio.runner.clustal.ClustalWParametersTester.testParameters(ClustalWParametersTester.java:129)\r
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace3932167", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace3932167'><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979987926880363 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)\r
- at compbio.runner.clustal.ClustalWParametersTester.testParameters(ClustalWParametersTester.java:129)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r
- at java.lang.reflect.Method.invoke(Method.java:597)\r
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)\r
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)\r
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)\r
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)\r
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)\r
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)\r
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)\r
- at org.testng.TestRunner.privateRun(TestRunner.java:592)\r
- at org.testng.TestRunner.run(TestRunner.java:486)\r
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)\r
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)\r
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)\r
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)\r
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)\r
- at org.testng.TestNG.runSuitesLocally(TestNG.java:842)\r
- at org.testng.TestNG.run(TestNG.java:751)\r
- at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)\r
- at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)\r
-</pre></div></td>
-</tr>
-<tr>
-<td title='compbio.runner.clustal.ClustalWParametersTester.testPresets()'>testPresets</td>
-<td>0</td>
-<td><div><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#85979987545393788 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.testPresets(ClustalWParametersTester.java:231)\r
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace26156414", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace26156414'><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#85979987545393788 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.testPresets(ClustalWParametersTester.java:231)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r
- at java.lang.reflect.Method.invoke(Method.java:597)\r
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:607)\r
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:517)\r
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:669)\r
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:956)\r
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:126)\r
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:110)\r
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)\r
- at org.testng.TestRunner.privateRun(TestRunner.java:592)\r
- at org.testng.TestRunner.run(TestRunner.java:486)\r
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)\r
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)\r
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)\r
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)\r
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:877)\r
- at org.testng.TestNG.runSuitesLocally(TestNG.java:842)\r
- at org.testng.TestNG.run(TestNG.java:751)\r
- at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:73)\r
- at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:124)\r
-</pre></div></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.runner.clustal.ClustalWParametersTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>\r
-<testsuite name="compbio.runner.clustal.ClustalWParametersTester" failures="8" tests="8" time="2.219" errors="0">\r
- <properties/>\r
- <testcase name="testPresets" time="0.344" classname="compbio.runner.clustal.ClustalWParametersTester">\r
- <failure type="java.lang.IllegalArgumentException" message="Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#85979987545393788 is inaccessible or does not exist!">\r
- <![CDATA[java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#85979987545393788 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.testPresets(ClustalWParametersTester.java:231)\r
-... Removed 22 stack frames]]>\r
- </failure>\r
- </testcase>\r
- <testcase name="testArguments" time="0.062" classname="compbio.runner.clustal.ClustalWParametersTester">\r
- <failure type="java.lang.IllegalArgumentException" message="Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979987799825706 is inaccessible or does not exist!">\r
- <![CDATA[java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979987799825706 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)\r
- at compbio.runner.clustal.ClustalWParametersTester.testArguments(ClustalWParametersTester.java:137)\r
-... Removed 22 stack frames]]>\r
- </failure>\r
- </testcase>\r
- <testcase name="testParameters" time="0.063" classname="compbio.runner.clustal.ClustalWParametersTester">\r
- <failure type="java.lang.IllegalArgumentException" message="Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979987926880363 is inaccessible or does not exist!">\r
- <![CDATA[java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979987926880363 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)\r
- at compbio.runner.clustal.ClustalWParametersTester.testParameters(ClustalWParametersTester.java:129)\r
-... Removed 22 stack frames]]>\r
- </failure>\r
- </testcase>\r
- <testcase name="testDefaultParameters" time="0.031" classname="compbio.runner.clustal.ClustalWParametersTester">\r
- <failure type="java.lang.IllegalArgumentException" message="Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#38979988048124217 is inaccessible or does not exist!">\r
- <![CDATA[java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#38979988048124217 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.testDefaultParameters(ClustalWParametersTester.java:105)\r
-... Removed 22 stack frames]]>\r
- </failure>\r
- </testcase>\r
- <testcase name="testOptions" time="0.047" classname="compbio.runner.clustal.ClustalWParametersTester">\r
- <failure type="java.lang.IllegalArgumentException" message="Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979988189879815 is inaccessible or does not exist!">\r
- <![CDATA[java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#74979988189879815 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:183)\r
- at compbio.runner.clustal.ClustalWParametersTester.testOptions(ClustalWParametersTester.java:122)\r
-... Removed 22 stack frames]]>\r
- </failure>\r
- </testcase>\r
- <testcase name="testConstrainedParametersMinValues" time="0.546" classname="compbio.runner.clustal.ClustalWParametersTester">\r
- <failure type="java.lang.IllegalArgumentException" message="Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#70979988327544395 is inaccessible or does not exist!">\r
- <![CDATA[java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#70979988327544395 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174)\r
- at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMinValues(ClustalWParametersTester.java:144)\r
-... Removed 22 stack frames]]>\r
- </failure>\r
- </testcase>\r
- <testcase name="testConstrainedParametersMaxValues" time="0.031" classname="compbio.runner.clustal.ClustalWParametersTester">\r
- <failure type="java.lang.IllegalArgumentException" message="Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979988961908025 is inaccessible or does not exist!">\r
- <![CDATA[java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#42979988961908025 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.test(ClustalWParametersTester.java:174)\r
- at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersMaxValues(ClustalWParametersTester.java:151)\r
-... Removed 22 stack frames]]>\r
- </failure>\r
- </testcase>\r
- <testcase name="testConstrainedParametersRandomValues" time="0.031" classname="compbio.runner.clustal.ClustalWParametersTester">\r
- <failure type="java.lang.IllegalArgumentException" message="Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#46979989070571443 is inaccessible or does not exist!">\r
- <![CDATA[java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/testoutput/local\ClustalW#46979989070571443 is inaccessible or does not exist!\r
- at compbio.engine.PathValidator.validateDirectory(PathValidator.java:73)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:57)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:69)\r
- at compbio.runner.clustal.ClustalWParametersTester.singleTest(ClustalWParametersTester.java:202)\r
- at compbio.runner.clustal.ClustalWParametersTester.testConstrainedParametersRandomValues(ClustalWParametersTester.java:164)\r
-... Removed 22 stack frames]]>\r
- </failure>\r
- </testcase>\r
-</testsuite>\r
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.runner.clustal.ClustalWTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
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-<h2 align='center'>compbio.runner.clustal.ClustalWTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>1/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Fri Jan 15 16:55:36 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>0 seconds (285 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-passed'>
-<tr><td colspan='4' align='center'><b>PASSED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.runner.clustal.ClustalWTester.testRunWithMatrix()'><b>testRunWithMatrix</b><br>Test class:compbio.runner.clustal.ClustalWTester</td>
-<td>compbio.runner.clustal.ClustalWTester@3d860038</td><td>0</td>
-<td></td>
-</tr>
-</table><p>
-</body>
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\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.runner.clustal.ClustalWTester]
\ No newline at end of file
+++ /dev/null
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+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.runner.clustal.LimitTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
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-<h2 align='center'>compbio.runner.clustal.LimitTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>1/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Mon Dec 21 17:22:34 GMT 2009</td>
-</tr>
-<tr><td>Total time:</td><td>0 seconds (719 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-passed'>
-<tr><td colspan='3' align='center'><b>PASSED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.runner.clustal.LimitTester.testLoadLimits()'>testLoadLimits</td>
-<td>0</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.runner.clustal.LimitTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>\r
-<testsuite name="compbio.runner.clustal.LimitTester" failures="0" tests="1" time="0.719" errors="0">\r
- <properties/>\r
- <testcase name="testLoadLimits" time="0.0" classname="compbio.runner.clustal.LimitTester"/>\r
-</testsuite>\r
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.runner.mafft.MafftTester</title>
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- e.style.display = 'block';
- return 1;
- }
-}
-
-function toggleBox(szDivId, elem, msg1, msg2)
-{
- var res = -1; if (document.getElementById) {
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- }
- if(elem) {
- if(res == 0) elem.innerHTML = msg1; else elem.innerHTML = msg2;
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- }
- }
- }
-}
-
-// -->
-</script>
-
-</head>
-<body>
-<h2 align='center'>compbio.runner.mafft.MafftTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>1/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Mon Jan 25 17:07:55 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>0 seconds (682 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-passed'>
-<tr><td colspan='4' align='center'><b>PASSED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.runner.mafft.MafftTester.testExecute()'><b>testExecute</b><br>Test class:compbio.runner.mafft.MafftTester</td>
-<td>compbio.runner.mafft.MafftTester@13b8f864</td><td>0</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.runner.mafft.MafftTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="compbio.runner.mafft.MafftTester" failures="0" tests="1" time="0.682" errors="0">
- <properties/>
- <testcase name="testExecute" time="0.205" classname="compbio.runner.mafft.MafftTester"/>
-</testsuite>
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.runner.muscle.MuscleTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
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-
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-</script>
-
-</head>
-<body>
-<h2 align='center'>compbio.runner.muscle.MuscleTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>0/1/0</td>
-</tr><tr>
-<td>Started on:</td><td>Mon Jan 25 17:08:34 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>6 seconds (6782 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-failed'>
-<tr><td colspan='4' align='center'><b>FAILED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.runner.muscle.MuscleTester.testRunLocally()'><b>testRunLocally</b><br>Test class:compbio.runner.muscle.MuscleTester</td>
-<td>compbio.runner.muscle.MuscleTester@18020cc</td><td>1</td>
-<td><div><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/jobsout/local\Muscle#939914322508148 is inaccessible or does not exist!\r
- at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89)\r
- at compbio.runner.muscle.MuscleTester.testRunLocally(MuscleTester.java:173)\r
-... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace24417480", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace24417480'><pre>java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/jobsout/local\Muscle#939914322508148 is inaccessible or does not exist!\r
- at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89)\r
- at compbio.runner.muscle.MuscleTester.testRunLocally(MuscleTester.java:173)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)\r
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)\r
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)\r
- at java.lang.reflect.Method.invoke(Method.java:597)\r
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:644)\r
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:546)\r
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:700)\r
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1002)\r
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:137)\r
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:121)\r
- at org.testng.TestRunner.runWorkers(TestRunner.java:908)\r
- at org.testng.TestRunner.privateRun(TestRunner.java:617)\r
- at org.testng.TestRunner.run(TestRunner.java:498)\r
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:329)\r
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:324)\r
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:296)\r
- at org.testng.SuiteRunner.run(SuiteRunner.java:201)\r
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:915)\r
- at org.testng.TestNG.runSuitesLocally(TestNG.java:879)\r
- at org.testng.TestNG.run(TestNG.java:787)\r
- at org.testng.remote.RemoteTestNG.run(RemoteTestNG.java:75)\r
- at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:127)\r
-</pre></div></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.runner.muscle.MuscleTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>\r
-<testsuite name="compbio.runner.muscle.MuscleTester" failures="1" tests="1" time="6.782" errors="0">\r
- <properties/>\r
- <testcase name="testRunLocally" time="1.344" classname="compbio.runner.muscle.MuscleTester">\r
- <failure type="java.lang.IllegalArgumentException" message="Working directory: /homes/pvtroshin/workspace/clustengine/jobsout/local\Muscle#939914322508148 is inaccessible or does not exist!">\r
- <![CDATA[java.lang.IllegalArgumentException: Working directory: /homes/pvtroshin/workspace/clustengine/jobsout/local\Muscle#939914322508148 is inaccessible or does not exist!\r
- at compbio.engine.client.PathValidator.validateDirectory(PathValidator.java:93)\r
- at compbio.engine.local.ExecutableWrapper.<init>(ExecutableWrapper.java:87)\r
- at compbio.engine.local.LocalRunner.executeJob(LocalRunner.java:89)\r
- at compbio.runner.muscle.MuscleTester.testRunLocally(MuscleTester.java:173)\r
-... Removed 22 stack frames]]>\r
- </failure>\r
- </testcase>\r
-</testsuite>\r
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.runner.probcons.ProbconsParametersTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
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-// -->
-</script>
-
-</head>
-<body>
-<h2 align='center'>compbio.runner.probcons.ProbconsParametersTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>7/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Mon Jan 11 16:11:14 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>140 seconds (140484 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-passed'>
-<tr><td colspan='4' align='center'><b>PASSED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.runner.probcons.ProbconsParametersTester.testArguments()'><b>testArguments</b><br>Test class:compbio.runner.probcons.ProbconsParametersTester</td>
-<td>compbio.runner.probcons.ProbconsParametersTester@6513cf0</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.probcons.ProbconsParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:compbio.runner.probcons.ProbconsParametersTester</td>
-<td>compbio.runner.probcons.ProbconsParametersTester@6513cf0</td><td>37</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.probcons.ProbconsParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:compbio.runner.probcons.ProbconsParametersTester</td>
-<td>compbio.runner.probcons.ProbconsParametersTester@6513cf0</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.probcons.ProbconsParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:compbio.runner.probcons.ProbconsParametersTester</td>
-<td>compbio.runner.probcons.ProbconsParametersTester@6513cf0</td><td>74</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.probcons.ProbconsParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:compbio.runner.probcons.ProbconsParametersTester</td>
-<td>compbio.runner.probcons.ProbconsParametersTester@6513cf0</td><td>24</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.probcons.ProbconsParametersTester.testOptions()'><b>testOptions</b><br>Test class:compbio.runner.probcons.ProbconsParametersTester</td>
-<td>compbio.runner.probcons.ProbconsParametersTester@6513cf0</td><td>0</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.probcons.ProbconsParametersTester.testParameters()'><b>testParameters</b><br>Test class:compbio.runner.probcons.ProbconsParametersTester</td>
-<td>compbio.runner.probcons.ProbconsParametersTester@6513cf0</td><td>1</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.runner.probcons.ProbconsParametersTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="compbio.runner.probcons.ProbconsParametersTester" failures="0" tests="7" time="140.484" errors="0">
- <properties/>
- <testcase name="testArguments" time="1.804" classname="compbio.runner.probcons.ProbconsParametersTester"/>
- <testcase name="testConstrainedParametersMaxValues" time="37.083" classname="compbio.runner.probcons.ProbconsParametersTester"/>
- <testcase name="testConstrainedParametersMinValues" time="0.883" classname="compbio.runner.probcons.ProbconsParametersTester"/>
- <testcase name="testConstrainedParametersRandomValues" time="74.573" classname="compbio.runner.probcons.ProbconsParametersTester"/>
- <testcase name="testDefaultParameters" time="24.066" classname="compbio.runner.probcons.ProbconsParametersTester"/>
- <testcase name="testOptions" time="0.416" classname="compbio.runner.probcons.ProbconsParametersTester"/>
- <testcase name="testParameters" time="1.264" classname="compbio.runner.probcons.ProbconsParametersTester"/>
-</testsuite>
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.runner.probcons.ProbconsTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
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-
-// -->
-</script>
-
-</head>
-<body>
-<h2 align='center'>compbio.runner.probcons.ProbconsTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>0/1/0</td>
-</tr><tr>
-<td>Started on:</td><td>Fri Jan 15 17:16:57 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>0 seconds (549 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-failed'>
-<tr><td colspan='4' align='center'><b>FAILED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.runner.probcons.ProbconsTester.testExecute()'><b>testExecute</b><br>Test class:compbio.runner.probcons.ProbconsTester</td>
-<td>compbio.runner.probcons.ProbconsTester@5cbfe9d</td><td>0</td>
-<td><div><pre>java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Probcons#2856735923136709 with file name output.txt is not found!
- at compbio.runner.probcons.ProbconsTester.testExecute(ProbconsTester.java:99)
-... Removed 23 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace40515936", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace40515936'><pre>java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Probcons#2856735923136709 with file name output.txt is not found!
- at org.testng.Assert.fail(Assert.java:86)
- at compbio.runner.probcons.ProbconsTester.testExecute(ProbconsTester.java:99)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.runner.probcons.ProbconsTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="compbio.runner.probcons.ProbconsTester" failures="1" tests="1" time="0.549" errors="0">
- <properties/>
- <testcase name="testExecute" time="0.084" classname="compbio.runner.probcons.ProbconsTester">
- <failure type="java.lang.AssertionError" message="Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Probcons#2856735923136709 with file name output.txt is not found!">
- <![CDATA[java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Probcons#2856735923136709 with file name output.txt is not found!
- at compbio.runner.probcons.ProbconsTester.testExecute(ProbconsTester.java:99)
-... Removed 23 stack frames]]>
- </failure>
- </testcase>
-</testsuite>
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.runner.tcoffee.TcoffeeParametersTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
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-
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-</script>
-
-</head>
-<body>
-<h2 align='center'>compbio.runner.tcoffee.TcoffeeParametersTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>8/0/0</td>
-</tr><tr>
-<td>Started on:</td><td>Fri Jan 15 12:35:10 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>69 seconds (69406 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-passed'>
-<tr><td colspan='4' align='center'><b>PASSED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.runner.tcoffee.TcoffeeParametersTester.testArguments()'><b>testArguments</b><br>Test class:compbio.runner.tcoffee.TcoffeeParametersTester</td>
-<td>compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7</td><td>5</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.tcoffee.TcoffeeParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:compbio.runner.tcoffee.TcoffeeParametersTester</td>
-<td>compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7</td><td>8</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.tcoffee.TcoffeeParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:compbio.runner.tcoffee.TcoffeeParametersTester</td>
-<td>compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7</td><td>4</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.tcoffee.TcoffeeParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:compbio.runner.tcoffee.TcoffeeParametersTester</td>
-<td>compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7</td><td>17</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.tcoffee.TcoffeeParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:compbio.runner.tcoffee.TcoffeeParametersTester</td>
-<td>compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7</td><td>21</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.tcoffee.TcoffeeParametersTester.testOptions()'><b>testOptions</b><br>Test class:compbio.runner.tcoffee.TcoffeeParametersTester</td>
-<td>compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7</td><td>1</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.tcoffee.TcoffeeParametersTester.testParameters()'><b>testParameters</b><br>Test class:compbio.runner.tcoffee.TcoffeeParametersTester</td>
-<td>compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7</td><td>9</td>
-<td></td>
-</tr>
-<tr>
-<td title='compbio.runner.tcoffee.TcoffeeParametersTester.testPresets()'><b>testPresets</b><br>Test class:compbio.runner.tcoffee.TcoffeeParametersTester</td>
-<td>compbio.runner.tcoffee.TcoffeeParametersTester@2b12e7f7</td><td>0</td>
-<td></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.runner.tcoffee.TcoffeeParametersTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="compbio.runner.tcoffee.TcoffeeParametersTester" failures="0" tests="8" time="69.406" errors="0">
- <properties/>
- <testcase name="testArguments" time="5.571" classname="compbio.runner.tcoffee.TcoffeeParametersTester"/>
- <testcase name="testConstrainedParametersMaxValues" time="8.818" classname="compbio.runner.tcoffee.TcoffeeParametersTester"/>
- <testcase name="testConstrainedParametersMinValues" time="4.639" classname="compbio.runner.tcoffee.TcoffeeParametersTester"/>
- <testcase name="testConstrainedParametersRandomValues" time="17.665" classname="compbio.runner.tcoffee.TcoffeeParametersTester"/>
- <testcase name="testDefaultParameters" time="21.51" classname="compbio.runner.tcoffee.TcoffeeParametersTester"/>
- <testcase name="testOptions" time="1.176" classname="compbio.runner.tcoffee.TcoffeeParametersTester"/>
- <testcase name="testParameters" time="9.572" classname="compbio.runner.tcoffee.TcoffeeParametersTester"/>
- <testcase name="testPresets" time="0.439" classname="compbio.runner.tcoffee.TcoffeeParametersTester"/>
-</testsuite>
+++ /dev/null
-<html>
-<head>
-<title>TestNG: compbio.runner.tcoffee.TcoffeeTester</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-
-<style type="text/css">
-.log { display: none;}
-.stack-trace { display: none;}
-</style>
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-
-</head>
-<body>
-<h2 align='center'>compbio.runner.tcoffee.TcoffeeTester</h2><table border='1' align="center">
-<tr>
-<td>Tests passed/Failed/Skipped:</td><td>0/1/0</td>
-</tr><tr>
-<td>Started on:</td><td>Fri Jan 15 17:10:30 GMT 2010</td>
-</tr>
-<tr><td>Total time:</td><td>1 seconds (1723 ms)</td>
-</tr><tr>
-<td>Included groups:</td><td></td>
-</tr><tr>
-<td>Excluded groups:</td><td></td>
-</tr>
-</table><p/>
-<small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table width='100%' border='1' class='invocation-failed'>
-<tr><td colspan='4' align='center'><b>FAILED TESTS</b></td></tr>
-<tr><td><b>Test method</b></td>
-<td><b>Instance</b></td>
-<td width="10%"><b>Time (seconds)</b></td>
-<td width="30%"><b>Exception</b></td>
-</tr>
-<tr>
-<td title='compbio.runner.tcoffee.TcoffeeTester.testExecute()'><b>testExecute</b><br>Test class:compbio.runner.tcoffee.TcoffeeTester</td>
-<td>compbio.runner.tcoffee.TcoffeeTester@13b8f864</td><td>1</td>
-<td><div><pre>java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Tcoffee#3546348664347709 with file name tcoffee.out is not found!
- at compbio.runner.tcoffee.TcoffeeTester.testExecute(TcoffeeTester.java:92)
-... Removed 23 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1624207630", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
-<div class='stack-trace' id='stack-trace1624207630'><pre>java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Tcoffee#3546348664347709 with file name tcoffee.out is not found!
- at org.testng.Assert.fail(Assert.java:86)
- at compbio.runner.tcoffee.TcoffeeTester.testExecute(TcoffeeTester.java:92)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-</pre></div></td>
-</tr>
-</table><p>
-</body>
-</html>
\ No newline at end of file
+++ /dev/null
-[SuiteResult compbio.runner.tcoffee.TcoffeeTester]
\ No newline at end of file
+++ /dev/null
-<?xml version="1.0" encoding="UTF-8"?>
-<testsuite name="compbio.runner.tcoffee.TcoffeeTester" failures="1" tests="1" time="1.723" errors="0">
- <properties/>
- <testcase name="testExecute" time="1.233" classname="compbio.runner.tcoffee.TcoffeeTester">
- <failure type="java.lang.AssertionError" message="Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Tcoffee#3546348664347709 with file name tcoffee.out is not found!">
- <![CDATA[java.lang.AssertionError: Result for the jobId /homes/pvtroshin/workspace/clustengine/testoutput/local/Tcoffee#3546348664347709 with file name tcoffee.out is not found!
- at compbio.runner.tcoffee.TcoffeeTester.testExecute(TcoffeeTester.java:92)
-... Removed 23 stack frames]]>
- </failure>
- </testcase>
-</testsuite>
+++ /dev/null
-<h2>Groups used for this test run</h2><table border="1">
-<tr> <td align="center"><b>Group name</b></td><td align="center"><b>Methods</b></td></tr><tr><td>cluster</td><td>compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()<br/></td></tr>
-</table>
+++ /dev/null
-<html><head><title>Results for clustengine</title></head>
-<frameset cols="26%,74%">
-<frame src="toc.html" name="navFrame">
-<frame src="main.html" name="mainFrame">
-</frameset>
-</html>
+++ /dev/null
-<html><head><title>Results for clustengine</title></head>
-<body>Select a result on the left-hand pane.</body></html>
+++ /dev/null
-<h2>Methods run, sorted chronologically</h2><h3>>> means before, << means after</h3><p/><br/><em>clustengine</em><p/><small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table border="1">
-<tr><th>Time</th><th>Delta (ms)</th><th>Suite<br>configuration</th><th>Test<br>configuration</th><th>Class<br>configuration</th><th>Groups<br>configuration</th><th>Method<br>configuration</th><th>Test<br>method</th><th>Thread</th><th>Instances</th></tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:16</td> <td>0</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()">testClusterEngineConf</td>
- <td>main@1421571929</td> <td></td> </tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:15</td> <td>-606</td> <td> </td><td> </td><td title=">>compbio.engine.conf.PropertyHelperManagerTester.testLoadResources()">>>testLoadResources</td>
-<td> </td><td> </td><td> </td> <td>main@1421571929</td> <td></td> </tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:16</td> <td>13</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration()">validateClustalConfiguration</td>
- <td>main@1421571929</td> <td></td> </tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:16</td> <td>68</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration()">validateMafftConfiguration</td>
- <td>main@1421571929</td> <td></td> </tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:16</td> <td>80</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration()">validateMuscleConfiguration</td>
- <td>main@1421571929</td> <td></td> </tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:16</td> <td>92</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration()">validateTcoffeeConfiguration</td>
- <td>main@1421571929</td> <td></td> </tr>
-</table>
+++ /dev/null
-<h2>Methods that were not run</h2><table>
-</table>
\ No newline at end of file
+++ /dev/null
-<h2>Methods run, sorted chronologically</h2><h3>>> means before, << means after</h3><p/><br/><em>clustengine</em><p/><small><i>(Hover the method name to see the test class name)</i></small><p/>
-<table border="1">
-<tr><th>Time</th><th>Delta (ms)</th><th>Suite<br>configuration</th><th>Test<br>configuration</th><th>Class<br>configuration</th><th>Groups<br>configuration</th><th>Method<br>configuration</th><th>Test<br>method</th><th>Thread</th><th>Instances</th></tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:15</td> <td>0</td> <td> </td><td> </td><td title=">>compbio.engine.conf.PropertyHelperManagerTester.testLoadResources()">>>testLoadResources</td>
-<td> </td><td> </td><td> </td> <td>main@1421571929</td> <td></td> </tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:16</td> <td>606</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()">testClusterEngineConf</td>
- <td>main@1421571929</td> <td></td> </tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:16</td> <td>619</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration()">validateClustalConfiguration</td>
- <td>main@1421571929</td> <td></td> </tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:16</td> <td>674</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration()">validateMafftConfiguration</td>
- <td>main@1421571929</td> <td></td> </tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:16</td> <td>686</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration()">validateMuscleConfiguration</td>
- <td>main@1421571929</td> <td></td> </tr>
-<tr bgcolor="8d9c66"> <td>10/02/17 15:33:16</td> <td>698</td> <td> </td><td> </td><td> </td><td> </td><td> </td><td title="compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration()">validateTcoffeeConfiguration</td>
- <td>main@1421571929</td> <td></td> </tr>
-</table>
+++ /dev/null
-<h2>Reporter output</h2><table></table>
\ No newline at end of file
+++ /dev/null
-<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
-<suite thread-count="5" skipfailedinvocationCounts="false" verbose="1" name="Failed suite [clustengine]" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10">
- <test name="compbio.engine.conf.PropertyHelperManagerTester(failed)" junit="false" parallel="false" annotations="JDK">
- <classes>
- <class name="compbio.engine.conf.PropertyHelperManagerTester">
- <methods>
- <include name="testLocalEngineConf"/>
- <include name="testLoadResources"/>
- </methods>
- </class>
- </classes>
- </test>
-</suite>
+++ /dev/null
-<html><head><title>testng.xml for clustengine</title></head><body><tt><!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd"><br/><suite thread-count="5" skipfailedinvocationCounts="false" verbose="1" name="clustengine" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10"><br/> <test verbose="2" name="compbio.engine.conf.PropertyHelperManagerTester" junit="false" annotations="JDK"><br/> <classes><br/> <class name="compbio.engine.conf.PropertyHelperManagerTester"/><br/> </classes><br/> </test><br/></suite><br/></tt></body></html>
\ No newline at end of file
+++ /dev/null
-<html>
-<head>
-<title>Results for clustengine</title>
-<link href="../testng.css" rel="stylesheet" type="text/css" />
-<link href="../my-testng.css" rel="stylesheet" type="text/css" />
-</head>
-<body>
-<h3><p align="center">Results for<br/><em>clustengine</em></p></h3>
-<table border='1' width='100%'>
-<tr valign='top'>
-<td>1 test</td>
-<td><a target='mainFrame' href='classes.html'>1 class</a></td>
-<td>5 methods:<br/>
- <a target='mainFrame' href='methods.html'>chronological</a><br/>
- <a target='mainFrame' href='methods-alphabetical.html'>alphabetical</a><br/>
- <a target='mainFrame' href='methods-not-run.html'>not run (0)</a></td>
-</tr>
-<tr>
-<td><a target='mainFrame' href='groups.html'>1 group</a></td>
-<td><a target='mainFrame' href='reporter-output.html'>reporter output</a></td>
-<td><a target='mainFrame' href='testng.xml.html'>testng.xml</a></td>
-</tr></table>
-<table width='100%' class='test-passed'>
-<tr><td>
-<table style='width: 100%'><tr><td valign='top'>compbio.engine.conf.PropertyHelperManagerTester (5/0/0)</td><td valign='top' align='right'>
- <a href='compbio.engine.conf.PropertyHelperManagerTester.html' target='mainFrame'>Results</a>
-</td></tr></table>
-</td></tr><p/>
-</table>
-</body></html>
\ No newline at end of file
+++ /dev/null
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.1//EN http://www.w3.org/TR/xhtml11/DTD/xhtml11.dtd">
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-<table cellspacing=0 cellpadding=0 class="param">
-<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>
-<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>
-</table>
-<a id="summary"></a>
-<table cellspacing=0 cellpadding=0 class="passed">
-<tr><th>Class</th><th>Method</th><th># of<br/>Scenarios</th><th>Time<br/>(Msecs)</th></tr>
-<tr><th colspan="4">Ant test — passed</th></tr>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-<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>
-</table>
-<h1>Ant test</h1>
-<a id="m1"></a><h2>compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFile</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m2"></a><h2>compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileLongNames</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m3"></a><h2>compbio.data.sequence.ClustalAlignmentUtilTester:testReadClustalFileShortNames</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m4"></a><h2>compbio.data.sequence.FastaSequenceGeneratorTester:testProteinSequenceGeneration</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m5"></a><h2>compbio.data.sequence.FastaSequenceTester:testGetFormattedFasta</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m6"></a><h2>compbio.data.sequence.SequenceUtilTester:testCleanSequence</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m7"></a><h2>compbio.data.sequence.SequenceUtilTester:testDeepCleanSequence</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m8"></a><h2>compbio.data.sequence.SequenceUtilTester:testReadWriteFasta</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m9"></a><h2>compbio.data.sequence.SequenceUtilTester:testisNonAmbNucleotideSequence</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m10"></a><h2>compbio.data.sequence.SequenceUtilTester:testisProteinSequence</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m11"></a><h2>compbio.engine.EngineConfiguratorTester:testGetAsyncEngine</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m12"></a><h2>compbio.engine.EngineConfiguratorTester:testGetSyncEngine</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m13"></a><h2>compbio.engine.FilePullerTester:testCache</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m14"></a><h2>compbio.engine.FilePullerTester:testGet</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m15"></a><h2>compbio.engine.FilePullerTester:testGetDelay</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m16"></a><h2>compbio.engine.FilePullerTester:testPull</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m17"></a><h2>compbio.engine.PulledFileCacheTester:test</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m18"></a><h2>compbio.engine.client.CommandBuilderTester:testCommandBuilding</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m19"></a><h2>compbio.engine.client.CommandBuilderTester:testOptionsToCommand</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m20"></a><h2>compbio.engine.client.CommandBuilderTester:testSpaceDelimiterExecutable</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m21"></a><h2>compbio.engine.client.PathValidatorTester:testGetClassPath</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m22"></a><h2>compbio.engine.client.PathValidatorTester:testIsAbsolutePath</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m23"></a><h2>compbio.engine.cluster.drmaa.ClusterSessionTester:testTaskList</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m24"></a><h2>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testCancel</h2>
-<div style="padding-left:3em">
-<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>
-compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
-<br/>at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
-<br/>at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
-<br/>at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
-<br/>23 lines not shown
-<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>
-compbio.runner.Util.readClustalFile(Util.java:126)
-<br/>at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
-<br/>at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
-<br/>at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
-<br/>at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m25"></a><h2>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testGetJobStatus</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m26"></a><h2>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester:testSubmit</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m27"></a><h2>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testCancel</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m28"></a><h2>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester:testSubmit</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m29"></a><h2>compbio.engine.cluster.drmaa.UtilTester:testParser</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m30"></a><h2>compbio.engine.cluster.dundee._QueueTester:testQueue</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m31"></a><h2>compbio.engine.conf.DirectoryManagerTester:testGetDirectory</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m32"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:testClusterEngineConf</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m33"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateClustalConfiguration</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m34"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateMafftConfiguration</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m35"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateMuscleConfiguration</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m36"></a><h2>compbio.engine.conf.PropertyHelperManagerTester:validateTcoffeeConfiguration</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m37"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testMarshalling</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m38"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testSchemaFromCodeGeneration</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m39"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testUnMarshalling</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m40"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testValidation</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m41"></a><h2>compbio.engine.conf.RunnerConfigMarshallerTester:testValidationOnMarshalling</h2>
-<div style="padding-left:3em">
-<p>null</p>
-com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
-<br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
-<br/>at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
-<br/>at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
-<br/>at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
-<br/>23 lines not shown
-<p>Caused by cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.</p>
-com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
-<br/>at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
-<br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
-<br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
-<br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
-<br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
-<br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
-<br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
-<br/>at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
-<br/>at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
-<br/>at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
-<br/>at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
-<br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
-<br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
-<br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
-<br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
-<br/>at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
-<br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
-<br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
-<br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
-<br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
-<br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
-<br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
-<br/>at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
-<br/>at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
-<br/>at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m42"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testAsyncCancelOperation</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m43"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testAsyncRetrievOperation</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m44"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testCancelCompletedTaskLocally</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m45"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testCancelLocally</h2>
-<div style="padding-left:3em">
-<p>null</p>
-java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
-<br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
-<br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
-<br/>at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
-<br/>at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m46"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testGetStatus</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m47"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testMultipleCancelLocally</h2>
-<div style="padding-left:3em">
-<p>null</p>
-java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
-<br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
-<br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
-<br/>at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
-<br/>at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m48"></a><h2>compbio.engine.local.AsyncLocalRunnerTester:testSubmitLocally</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m49"></a><h2>compbio.engine.local.LocalRunnerTester:testCancelCompletedTaskLocally</h2>
-<div style="padding-left:3em">
-<p>null</p>
-java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
-<br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
-<br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
-<br/>at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
-<br/>at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m50"></a><h2>compbio.engine.local.LocalRunnerTester:testCancelLocally</h2>
-<div style="padding-left:3em">
-<p>null</p>
-java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
-<br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
-<br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
-<br/>at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
-<br/>at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m51"></a><h2>compbio.engine.local.LocalRunnerTester:testMultipleCancelLocally</h2>
-<div style="padding-left:3em">
-<p>null</p>
-java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
-<br/>at java.util.concurrent.FutureTask.get(FutureTask.java:83)
-<br/>at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
-<br/>at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
-<br/>at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m52"></a><h2>compbio.metadata.OptionCombinatorTester:testgetAllOptions</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m53"></a><h2>compbio.metadata.OptionCombinatorTester:testgetAllParameters</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m54"></a><h2>compbio.metadata.OptionMarshallerTester:testMarshalling</h2>
-<div style="padding-left:3em">
-<p>null</p>
-com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
-<br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
-<br/>at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
-<br/>at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
-<br/>at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
-<br/>23 lines not shown
-<p>Caused by cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.</p>
-com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
-<br/>at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
-<br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
-<br/>at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
-<br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
-<br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
-<br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
-<br/>at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
-<br/>at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
-<br/>at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
-<br/>at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
-<br/>at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
-<br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
-<br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
-<br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
-<br/>at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
-<br/>at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
-<br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
-<br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
-<br/>at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
-<br/>at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
-<br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
-<br/>at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
-<br/>at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
-<br/>at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
-<br/>at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m55"></a><h2>compbio.metadata.OptionMarshallerTester:testUnMarshalling</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m56"></a><h2>compbio.metadata.PresetTester:marshallPreset</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m57"></a><h2>compbio.metadata.PresetTester:validatePresets</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m58"></a><h2>compbio.metadata.RunnerConfigTester:testCreateNumParameterWithoutValidValue</h2>
-<div style="padding-left:3em">
-<p>Attempting to set default value for parameter: Option name: Matrix
-Description: DNA weight matrix
-URL: null
-Is required: false
-
- Without possible values! Please define possible value first!</p>
-compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
-<br/>at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m59"></a><h2>compbio.metadata.RunnerConfigTester:testCreateParameter</h2>
-<div style="padding-left:3em">
-<p>Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-POSSIBLE VALUES:
-BLOSUM
-GONNET
-ID
-PAM
-
-</p>
-compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
-<br/>at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m60"></a><h2>compbio.metadata.RunnerConfigTester:testCreateParameterWithValidValueConstrain</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m61"></a><h2>compbio.metadata.RunnerConfigTester:testOptionNoDefaultValidate</h2>
-<div style="padding-left:3em">
-<p>Default value is required as multiple optionNames are defined for option: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
---ABMAT
---BBBB
-</p>
-compbio.metadata.Option.validate(Option.java:317)
-<br/>at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m62"></a><h2>compbio.metadata.RunnerConfigTester:testOptionSetInvalidValue</h2>
-<div style="padding-left:3em">
-<p>Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
---ABMAT
---BBBB
-</p>
-compbio.metadata.Option.setDefaultValue(Option.java:130)
-<br/>at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m63"></a><h2>compbio.metadata.RunnerConfigTester:testOptionToCommand</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m64"></a><h2>compbio.metadata.RunnerConfigTester:testParameterToCommand</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m65"></a><h2>compbio.metadata.RunnerConfigTester:testValidate</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m66"></a><h2>compbio.metadata.RunnerConfigTester:testValidateBoundaryConstrainCheck</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m67"></a><h2>compbio.metadata.RunnerConfigTester:testValidateLowerBoundaryConstrainCheck</h2>
-<div style="padding-left:3em">
-<p>Attempting to set default value outside boundaries defined by the constraint: Type: Float
-Min: -10.12
-Max: 0
-
- For parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-Type: Float
-Min: -10.12
-Max: 0
-
-</p>
-compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
-<br/>at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m68"></a><h2>compbio.metadata.RunnerConfigTester:testValidateUpperBoundaryConstrainCheck</h2>
-<div style="padding-left:3em">
-<p>Attempting to set default value outside boundaries defined by the constraint: Type: Float
-Min: -10.12
-Max: 0
-
- For parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-Type: Float
-Min: -10.12
-Max: 0
-
-</p>
-compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
-<br/>at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m69"></a><h2>compbio.metadata.RunnerConfigTester:testValidateValueConstrain</h2>
-<div style="padding-left:3em">
-<p>Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
-</p>
-compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
-<br/>at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
-<br/>23 lines not shown
-</div>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m70"></a><h2>compbio.runner._impl.MclTester:testGetTestCommand</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m71"></a><h2>compbio.runner._impl.NetNglycTester:testGetTestCommand</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m72"></a><h2>compbio.runner._impl.OBTester:testGetTestArgsCommand</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m73"></a><h2>compbio.runner._impl.OBTester:testGetTestCommand</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m74"></a><h2>compbio.runner._impl.RPSBlastTester:testGetTestArgsCommand</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m75"></a><h2>compbio.runner._impl.RPSBlastTester:testGetTestCommand</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m76"></a><h2>compbio.runner._impl.RonnTester:testGetTestCommand</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m77"></a><h2>compbio.runner._impl.Tmhmm2Tester:testGetTestCommand</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m78"></a><h2>compbio.runner.msa.ClustalWParametersTester:testArguments</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m79"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConfiguration</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m80"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersMaxValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m81"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersMinValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m82"></a><h2>compbio.runner.msa.ClustalWParametersTester:testConstrainedParametersRandomValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m83"></a><h2>compbio.runner.msa.ClustalWParametersTester:testDefaultParameters</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m84"></a><h2>compbio.runner.msa.ClustalWParametersTester:testOptions</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m85"></a><h2>compbio.runner.msa.ClustalWParametersTester:testParameters</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m86"></a><h2>compbio.runner.msa.ClustalWParametersTester:testPresets</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m87"></a><h2>compbio.runner.msa.ClustalWTester:readStatistics</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m88"></a><h2>compbio.runner.msa.ClustalWTester:readStatisticsClusterExecution</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m89"></a><h2>compbio.runner.msa.ClustalWTester:testConfigurationLoading</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m90"></a><h2>compbio.runner.msa.ClustalWTester:testOptionsLocally</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m91"></a><h2>compbio.runner.msa.ClustalWTester:testPersistance</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m92"></a><h2>compbio.runner.msa.ClustalWTester:testRunLocally</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m93"></a><h2>compbio.runner.msa.ClustalWTester:testRunOnCluster</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m94"></a><h2>compbio.runner.msa.ClustalWTester:testRunWithMatrix</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m95"></a><h2>compbio.runner.msa.LimitTester:testLoadLimits</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m96"></a><h2>compbio.runner.msa.MafftParametersTester:testArguments</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m97"></a><h2>compbio.runner.msa.MafftParametersTester:testConfiguration</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m98"></a><h2>compbio.runner.msa.MafftParametersTester:testConstrainedParametersMaxValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m99"></a><h2>compbio.runner.msa.MafftParametersTester:testConstrainedParametersMinValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m100"></a><h2>compbio.runner.msa.MafftParametersTester:testConstrainedParametersRandomValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m101"></a><h2>compbio.runner.msa.MafftParametersTester:testDefaultParameters</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m102"></a><h2>compbio.runner.msa.MafftParametersTester:testOptions</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m103"></a><h2>compbio.runner.msa.MafftParametersTester:testParameters</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m104"></a><h2>compbio.runner.msa.MafftParametersTester:testPresets</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m105"></a><h2>compbio.runner.msa.MafftTester:readStatistics</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m106"></a><h2>compbio.runner.msa.MafftTester:testClusterExecute</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m107"></a><h2>compbio.runner.msa.MafftTester:testConfigurationLoading</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m108"></a><h2>compbio.runner.msa.MafftTester:testExecute</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m109"></a><h2>compbio.runner.msa.MafftTester:testPersistance</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m110"></a><h2>compbio.runner.msa.MafftTester:testRunOnClusterAsyncCheckStatusLongPoolingTime</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m111"></a><h2>compbio.runner.msa.MafftTester:testSetInputTester</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m112"></a><h2>compbio.runner.msa.MuscleParametersTester:testArguments</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m113"></a><h2>compbio.runner.msa.MuscleParametersTester:testConfiguration</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m114"></a><h2>compbio.runner.msa.MuscleParametersTester:testConstrainedParametersMaxValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m115"></a><h2>compbio.runner.msa.MuscleParametersTester:testConstrainedParametersMinValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m116"></a><h2>compbio.runner.msa.MuscleParametersTester:testConstrainedParametersRandomValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m117"></a><h2>compbio.runner.msa.MuscleParametersTester:testDefaultParameters</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m118"></a><h2>compbio.runner.msa.MuscleParametersTester:testOptions</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m119"></a><h2>compbio.runner.msa.MuscleParametersTester:testParameters</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m120"></a><h2>compbio.runner.msa.MuscleParametersTester:testPresets</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m121"></a><h2>compbio.runner.msa.MuscleTester:readStatistics</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m122"></a><h2>compbio.runner.msa.MuscleTester:testConfigurationLoading</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m123"></a><h2>compbio.runner.msa.MuscleTester:testPersistance</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m124"></a><h2>compbio.runner.msa.MuscleTester:testRunLocally</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m125"></a><h2>compbio.runner.msa.MuscleTester:testRunOnCluster</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m126"></a><h2>compbio.runner.msa.ProbconsParametersTester:testArguments</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m127"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConfiguration</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m128"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersMaxValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m129"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersMinValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m130"></a><h2>compbio.runner.msa.ProbconsParametersTester:testConstrainedParametersRandomValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m131"></a><h2>compbio.runner.msa.ProbconsParametersTester:testDefaultParameters</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m132"></a><h2>compbio.runner.msa.ProbconsParametersTester:testOptions</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m133"></a><h2>compbio.runner.msa.ProbconsParametersTester:testParameters</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m134"></a><h2>compbio.runner.msa.ProbconsTester:readStatistics</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m135"></a><h2>compbio.runner.msa.ProbconsTester:testClusterExecute</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m136"></a><h2>compbio.runner.msa.ProbconsTester:testConfigurationLoading</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m137"></a><h2>compbio.runner.msa.ProbconsTester:testExecute</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m138"></a><h2>compbio.runner.msa.ProbconsTester:testPersistance</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m139"></a><h2>compbio.runner.msa.ProbconsTester:testSetInputTester</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m140"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testArguments</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m141"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConfiguration</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m142"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersMaxValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m143"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersMinValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m144"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testConstrainedParametersRandomValues</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m145"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testDefaultParameters</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m146"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testOptions</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m147"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testParameters</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m148"></a><h2>compbio.runner.msa.TcoffeeParametersTester:testPresets</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m149"></a><h2>compbio.runner.msa.TcoffeeTester:readStatistics</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m150"></a><h2>compbio.runner.msa.TcoffeeTester:testClusterExecute</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m151"></a><h2>compbio.runner.msa.TcoffeeTester:testConfigurationLoading</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m152"></a><h2>compbio.runner.msa.TcoffeeTester:testExecute</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m153"></a><h2>compbio.runner.msa.TcoffeeTester:testNcore</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-<a id="m154"></a><h2>compbio.runner.msa.TcoffeeTester:testPersistance</h2>
-<p class="totop"><a href="#summary">back to summary</a></p>
-</body></html>
+++ /dev/null
-<html>
-<head><title>Test results</title><link href="./testng.css" rel="stylesheet" type="text/css" />
-<link href="./my-testng.css" rel="stylesheet" type="text/css" />
-</head><body>
-<h2><p align='center'>Test results</p></h2>
-<table border='1' width='100%' class='main-page'><tr><th>Suite</th><th>Passed</th><th>Failed</th><th>Skipped</th><th>testng.xml</th></tr>
-<tr align='center' class='invocation-passed'><td><em>Total</em></td><td><em>165</em></td><td><em>0</em></td><td><em>0</em></td><td> </td></tr>
-<tr align='center' class='invocation-passed'><td><a href='Ant suite/index.html'>Ant suite</a></td>
-<td>165</td><td>0</td><td>0</td><td><a href='Ant suite/testng.xml.html'>Link</a></td></tr></table></body></html>
+++ /dev/null
-<!DOCTYPE suite SYSTEM "http://testng.org/testng-1.0.dtd">
-<suite thread-count="5" skipfailedinvocationCounts="false" verbose="1" name="Failed suite [clustengine]" junit="false" parallel="false" annotations="JDK" data-provider-thread-count="10">
- <test name="compbio.engine.conf.PropertyHelperManagerTester(failed)" junit="false" parallel="false" annotations="JDK">
- <classes>
- <class name="compbio.engine.conf.PropertyHelperManagerTester">
- <methods>
- <include name="testLocalEngineConf"/>
- <include name="testLoadResources"/>
- </methods>
- </class>
- </classes>
- </test>
-</suite>
+++ /dev/null
-<testng-results>
- <reporter-output>
- </reporter-output>
- <suite name="Ant suite">
- <groups>
- <group name="engine">
- <method signature="compbio.engine.FilePullerTester.testGetDelay()" name="testGetDelay" class="compbio.engine.FilePullerTester"/>
- <method signature="compbio.engine.FilePullerTester.testPull()" name="testPull" class="compbio.engine.FilePullerTester"/>
- <method signature="compbio.engine.FilePullerTester.testCache()" name="testCache" class="compbio.engine.FilePullerTester"/>
- <method signature="compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()" name="testTaskList" class="compbio.engine.cluster.drmaa.ClusterSessionTester"/>
- <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
- <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()" name="testGetJobStatus" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
- <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
- <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
- <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
- <method signature="compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation()" name="testAsyncCancelOperation" class="compbio.engine.local.AsyncLocalRunnerTester"/>
- <method signature="compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation()" name="testAsyncRetrievOperation" class="compbio.engine.local.AsyncLocalRunnerTester"/>
- <method signature="compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
- <method signature="compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally()" name="testCancelLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
- <method signature="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()" name="testGetStatus" class="compbio.engine.local.AsyncLocalRunnerTester"/>
- <method signature="compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally()" name="testMultipleCancelLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
- <method signature="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()" name="testSubmitLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
- <method signature="compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" class="compbio.engine.local.LocalRunnerTester"/>
- <method signature="compbio.engine.local.LocalRunnerTester.testCancelLocally()" name="testCancelLocally" class="compbio.engine.local.LocalRunnerTester"/>
- <method signature="compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally()" name="testMultipleCancelLocally" class="compbio.engine.local.LocalRunnerTester"/>
- </group>
- <group name="cluster">
- <method signature="compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()" name="testTaskList" class="compbio.engine.cluster.drmaa.ClusterSessionTester"/>
- <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
- <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()" name="testGetJobStatus" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
- <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
- <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
- <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
- <method signature="compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()" name="testClusterEngineConf" class="compbio.engine.conf.PropertyHelperManagerTester"/>
- <method signature="compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()" name="readStatisticsClusterExecution" class="compbio.runner.msa.ClustalWTester"/>
- <method signature="compbio.runner.msa.ClustalWTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.ClustalWTester"/>
- <method signature="compbio.runner.msa.MafftTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MuscleTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.MuscleTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.TcoffeeTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.TcoffeeTester"/>
- </group>
- <group name="runner">
- <method signature="compbio.runner.msa.ClustalWParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.ClustalWParametersTester"/>
- <method signature="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.ClustalWParametersTester"/>
- <method signature="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.ClustalWParametersTester"/>
- <method signature="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.ClustalWParametersTester"/>
- <method signature="compbio.runner.msa.ClustalWParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.ClustalWParametersTester"/>
- <method signature="compbio.runner.msa.ClustalWParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.ClustalWParametersTester"/>
- <method signature="compbio.runner.msa.ClustalWParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.ClustalWParametersTester"/>
- <method signature="compbio.runner.msa.ClustalWParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.ClustalWParametersTester"/>
- <method signature="compbio.runner.msa.ClustalWTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.ClustalWTester"/>
- <method signature="compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()" name="readStatisticsClusterExecution" class="compbio.runner.msa.ClustalWTester"/>
- <method signature="compbio.runner.msa.ClustalWTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.ClustalWTester"/>
- <method signature="compbio.runner.msa.ClustalWTester.testOptionsLocally()" name="testOptionsLocally" class="compbio.runner.msa.ClustalWTester"/>
- <method signature="compbio.runner.msa.ClustalWTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.ClustalWTester"/>
- <method signature="compbio.runner.msa.ClustalWTester.testRunLocally()" name="testRunLocally" class="compbio.runner.msa.ClustalWTester"/>
- <method signature="compbio.runner.msa.ClustalWTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.ClustalWTester"/>
- <method signature="compbio.runner.msa.ClustalWTester.testRunWithMatrix()" name="testRunWithMatrix" class="compbio.runner.msa.ClustalWTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testExecute()" name="testExecute" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MuscleParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.MuscleParametersTester"/>
- <method signature="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.MuscleParametersTester"/>
- <method signature="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.MuscleParametersTester"/>
- <method signature="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.MuscleParametersTester"/>
- <method signature="compbio.runner.msa.MuscleParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.MuscleParametersTester"/>
- <method signature="compbio.runner.msa.MuscleParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.MuscleParametersTester"/>
- <method signature="compbio.runner.msa.MuscleParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.MuscleParametersTester"/>
- <method signature="compbio.runner.msa.MuscleParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.MuscleParametersTester"/>
- <method signature="compbio.runner.msa.MuscleTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.MuscleTester"/>
- <method signature="compbio.runner.msa.MuscleTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.MuscleTester"/>
- <method signature="compbio.runner.msa.MuscleTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.MuscleTester"/>
- <method signature="compbio.runner.msa.MuscleTester.testRunLocally()" name="testRunLocally" class="compbio.runner.msa.MuscleTester"/>
- <method signature="compbio.runner.msa.MuscleTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.MuscleTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.testExecute()" name="testExecute" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.TcoffeeTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.TcoffeeTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.TcoffeeTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.testExecute()" name="testExecute" class="compbio.runner.msa.TcoffeeTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.testNcore()" name="testNcore" class="compbio.runner.msa.TcoffeeTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.TcoffeeTester"/>
- </group>
- <group name="non_windows">
- <method signature="compbio.runner.msa.MafftParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.MafftParametersTester"/>
- <method signature="compbio.runner.msa.MafftTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testExecute()" name="testExecute" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.MafftTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.MafftTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.testExecute()" name="testExecute" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.ProbconsTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.ProbconsTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.TcoffeeParametersTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.TcoffeeTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.TcoffeeTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.testExecute()" name="testExecute" class="compbio.runner.msa.TcoffeeTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.testNcore()" name="testNcore" class="compbio.runner.msa.TcoffeeTester"/>
- <method signature="compbio.runner.msa.TcoffeeTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.TcoffeeTester"/>
- </group>
- </groups>
- <test name="Ant test">
- <class name="compbio.engine.client.CommandBuilderTester">
- <test-method status="PASS" signature="testCommandBuilding()" name="testCommandBuilding" duration-ms="1" started-at="2010-02-17T15:34:38Z" finished-at="2010-02-17T15:34:38Z">
- </test-method>
- <test-method status="PASS" signature="testOptionsToCommand()" name="testOptionsToCommand" duration-ms="567" started-at="2010-02-17T15:34:38Z" finished-at="2010-02-17T15:34:39Z">
- </test-method>
- <test-method status="PASS" signature="testSpaceDelimiterExecutable()" name="testSpaceDelimiterExecutable" duration-ms="0" started-at="2010-02-17T15:34:39Z" finished-at="2010-02-17T15:34:39Z">
- </test-method>
- </class>
- <class name="compbio.metadata.RunnerConfigTester">
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="34" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testCreateNumParameterWithoutValidValue()" name="testCreateNumParameterWithoutValidValue" duration-ms="1" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- <exception class="java.lang.IllegalStateException">
- <message>
- <![CDATA[Attempting to set default value for parameter: Option name: Matrix
-Description: DNA weight matrix
-URL: null
-Is required: false
-
- Without possible values! Please define possible value first!]]>
- </message>
- <full-stacktrace>
- <![CDATA[java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
-Description: DNA weight matrix
-URL: null
-Is required: false
-
- Without possible values! Please define possible value first!
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
- at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testCreateParameter()" name="testCreateParameter" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- <exception class="compbio.metadata.WrongParameterException">
- <message>
- <![CDATA[Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-POSSIBLE VALUES:
-BLOSUM
-GONNET
-ID
-PAM
-
-]]>
- </message>
- <full-stacktrace>
- <![CDATA[compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-POSSIBLE VALUES:
-BLOSUM
-GONNET
-ID
-PAM
-
-
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
- at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testCreateParameterWithValidValueConstrain()" name="testCreateParameterWithValidValueConstrain" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testOptionNoDefaultValidate()" name="testOptionNoDefaultValidate" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- <exception class="javax.xml.bind.ValidationException">
- <message>
- <![CDATA[Default value is required as multiple optionNames are defined for option: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
---ABMAT
---BBBB
-]]>
- </message>
- <full-stacktrace>
- <![CDATA[javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
---ABMAT
---BBBB
-
- at compbio.metadata.Option.validate(Option.java:317)
- at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testOptionSetInvalidValue()" name="testOptionSetInvalidValue" duration-ms="1" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- <exception class="compbio.metadata.WrongParameterException">
- <message>
- <![CDATA[Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
---ABMAT
---BBBB
-]]>
- </message>
- <full-stacktrace>
- <![CDATA[compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
---ABMAT
---BBBB
-
- at compbio.metadata.Option.setDefaultValue(Option.java:130)
- at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testOptionToCommand()" name="testOptionToCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testParameterToCommand()" name="testParameterToCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testValidate()" name="testValidate" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="203" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testValidateBoundaryConstrainCheck()" name="testValidateBoundaryConstrainCheck" duration-ms="1" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testValidateLowerBoundaryConstrainCheck()" name="testValidateLowerBoundaryConstrainCheck" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- <exception class="compbio.metadata.WrongParameterException">
- <message>
- <![CDATA[Attempting to set default value outside boundaries defined by the constraint: Type: Float
-Min: -10.12
-Max: 0
-
- For parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-Type: Float
-Min: -10.12
-Max: 0
-
-]]>
- </message>
- <full-stacktrace>
- <![CDATA[compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
-Min: -10.12
-Max: 0
-
- For parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-Type: Float
-Min: -10.12
-Max: 0
-
-
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
- at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testValidateUpperBoundaryConstrainCheck()" name="testValidateUpperBoundaryConstrainCheck" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- <exception class="compbio.metadata.WrongParameterException">
- <message>
- <![CDATA[Attempting to set default value outside boundaries defined by the constraint: Type: Float
-Min: -10.12
-Max: 0
-
- For parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-Type: Float
-Min: -10.12
-Max: 0
-
-]]>
- </message>
- <full-stacktrace>
- <![CDATA[compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
-Min: -10.12
-Max: 0
-
- For parameter: Option name: Matrix1
-Description: Protein weight matrix
-URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
-Is required: true
-Option Names:
---AAMATRIX
-Type: Float
-Min: -10.12
-Max: 0
-
-
- at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
- at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testValidateValueConstrain()" name="testValidateValueConstrain" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- <exception class="javax.xml.bind.ValidationException">
- <message>
- <![CDATA[Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
-]]>
- </message>
- <full-stacktrace>
- <![CDATA[javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
-
- at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
- at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- </class>
- <class name="compbio.runner._impl.NetNglycTester">
- <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- </class>
- <class name="compbio.engine.EngineConfiguratorTester">
- <test-method status="PASS" signature="testGetAsyncEngine()" name="testGetAsyncEngine" duration-ms="296" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- <test-method status="PASS" signature="testGetSyncEngine()" name="testGetSyncEngine" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- </class>
- <class name="compbio.runner.msa.MafftParametersTester">
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="47" started-at="2010-02-17T15:37:09Z" finished-at="2010-02-17T15:37:09Z">
- </test-method>
- <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="6103" started-at="2010-02-17T15:37:09Z" finished-at="2010-02-17T15:37:15Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="54" started-at="2010-02-17T15:37:15Z" finished-at="2010-02-17T15:37:15Z">
- </test-method>
- <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="1" started-at="2010-02-17T15:37:15Z" finished-at="2010-02-17T15:37:15Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="44" started-at="2010-02-17T15:37:15Z" finished-at="2010-02-17T15:37:15Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="3235" started-at="2010-02-17T15:37:15Z" finished-at="2010-02-17T15:37:18Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="47" started-at="2010-02-17T15:37:18Z" finished-at="2010-02-17T15:37:18Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="1326" started-at="2010-02-17T15:37:18Z" finished-at="2010-02-17T15:37:19Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="45" started-at="2010-02-17T15:37:19Z" finished-at="2010-02-17T15:37:20Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="7672" started-at="2010-02-17T15:37:20Z" finished-at="2010-02-17T15:37:27Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="47" started-at="2010-02-17T15:37:27Z" finished-at="2010-02-17T15:37:27Z">
- </test-method>
- <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="20463" started-at="2010-02-17T15:37:27Z" finished-at="2010-02-17T15:37:48Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="55" started-at="2010-02-17T15:37:48Z" finished-at="2010-02-17T15:37:48Z">
- </test-method>
- <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="4449" started-at="2010-02-17T15:37:48Z" finished-at="2010-02-17T15:37:52Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="52" started-at="2010-02-17T15:37:52Z" finished-at="2010-02-17T15:37:52Z">
- </test-method>
- <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="2422" started-at="2010-02-17T15:37:52Z" finished-at="2010-02-17T15:37:55Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="47" started-at="2010-02-17T15:37:55Z" finished-at="2010-02-17T15:37:55Z">
- </test-method>
- <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="2136" started-at="2010-02-17T15:37:55Z" finished-at="2010-02-17T15:37:57Z">
- </test-method>
- </class>
- <class name="compbio.runner._impl.RonnTester">
- <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- </class>
- <class name="compbio.runner.msa.ProbconsTester">
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:09Z" finished-at="2010-02-17T15:41:09Z">
- </test-method>
- <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="441" started-at="2010-02-17T15:41:09Z" finished-at="2010-02-17T15:41:10Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:41:10Z" finished-at="2010-02-17T15:41:10Z">
- </test-method>
- <test-method status="PASS" signature="testClusterExecute()" name="testClusterExecute" duration-ms="19326" started-at="2010-02-17T15:41:10Z" finished-at="2010-02-17T15:41:29Z">
- </test-method>
- <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="107" started-at="2010-02-17T15:41:29Z" finished-at="2010-02-17T15:41:29Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:29Z" finished-at="2010-02-17T15:41:29Z">
- </test-method>
- <test-method status="PASS" signature="testExecute()" name="testExecute" duration-ms="436" started-at="2010-02-17T15:41:29Z" finished-at="2010-02-17T15:41:30Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:29Z" finished-at="2010-02-17T15:41:29Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:30Z">
- </test-method>
- <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="509" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:30Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:30Z">
- </test-method>
- <test-method status="PASS" signature="testSetInputTester()" name="testSetInputTester" duration-ms="0" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:30Z">
- </test-method>
- </class>
- <class name="compbio.engine.conf.PropertyHelperManagerTester">
- <test-method status="PASS" signature="testLoadResources()" name="testLoadResources" is-config="true" duration-ms="2" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- <test-method status="PASS" signature="testClusterEngineConf()" name="testClusterEngineConf" duration-ms="104" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- <test-method status="PASS" signature="validateClustalConfiguration()" name="validateClustalConfiguration" duration-ms="43" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- <test-method status="PASS" signature="validateMafftConfiguration()" name="validateMafftConfiguration" duration-ms="1" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- <test-method status="PASS" signature="validateMuscleConfiguration()" name="validateMuscleConfiguration" duration-ms="4" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- <test-method status="PASS" signature="validateTcoffeeConfiguration()" name="validateTcoffeeConfiguration" duration-ms="4" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- </class>
- <class name="compbio.metadata.OptionCombinatorTester">
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="400" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:37Z">
- </test-method>
- <test-method status="PASS" signature="testgetAllOptions()" name="testgetAllOptions" duration-ms="1" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:37Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="111" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:38Z">
- </test-method>
- <test-method status="PASS" signature="testgetAllParameters()" name="testgetAllParameters" duration-ms="3" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:38Z">
- </test-method>
- </class>
- <class name="compbio.engine.FilePullerTester">
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1739" started-at="2010-02-17T15:34:08Z" finished-at="2010-02-17T15:34:10Z">
- </test-method>
- <test-method status="PASS" signature="loadPresets()" name="loadPresets" is-config="true" duration-ms="167" started-at="2010-02-17T15:34:10Z" finished-at="2010-02-17T15:34:10Z">
- </test-method>
- <test-method status="PASS" signature="testPull()" name="testPull" duration-ms="450" started-at="2010-02-17T15:34:10Z" finished-at="2010-02-17T15:34:11Z">
- </test-method>
- <test-method status="PASS" signature="testCache()" name="testCache" duration-ms="6006" started-at="2010-02-17T15:34:11Z" depends-on-methods="compbio.engine.FilePullerTester.testPull" finished-at="2010-02-17T15:34:17Z">
- </test-method>
- <test-method status="PASS" signature="testGetDelay()" name="testGetDelay" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- <test-method status="PASS" signature="testGet()" name="testGet" duration-ms="46" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- </class>
- <class name="compbio.runner.msa.MuscleTester">
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:59Z" finished-at="2010-02-17T15:38:59Z">
- </test-method>
- <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="932" started-at="2010-02-17T15:38:59Z" finished-at="2010-02-17T15:39:00Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:39:00Z" finished-at="2010-02-17T15:39:00Z">
- </test-method>
- <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="313" started-at="2010-02-17T15:39:00Z" finished-at="2010-02-17T15:39:00Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:39:00Z" finished-at="2010-02-17T15:39:00Z">
- </test-method>
- <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="241" started-at="2010-02-17T15:39:00Z" finished-at="2010-02-17T15:39:01Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:39:01Z" finished-at="2010-02-17T15:39:01Z">
- </test-method>
- <test-method status="PASS" signature="testRunLocally()" name="testRunLocally" duration-ms="101" started-at="2010-02-17T15:39:01Z" finished-at="2010-02-17T15:39:01Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:39:01Z" finished-at="2010-02-17T15:39:01Z">
- </test-method>
- <test-method status="PASS" signature="testRunOnCluster()" name="testRunOnCluster" duration-ms="8142" started-at="2010-02-17T15:39:01Z" finished-at="2010-02-17T15:39:09Z">
- </test-method>
- </class>
- <class name="compbio.runner.msa.TcoffeeTester">
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:42:43Z" finished-at="2010-02-17T15:42:43Z">
- </test-method>
- <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="876" started-at="2010-02-17T15:42:43Z" finished-at="2010-02-17T15:42:44Z">
- </test-method>
- <test-method status="PASS" signature="testClusterExecute()" name="testClusterExecute" duration-ms="5526" started-at="2010-02-17T15:42:44Z" finished-at="2010-02-17T15:42:50Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:44Z" finished-at="2010-02-17T15:42:44Z">
- </test-method>
- <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="99" started-at="2010-02-17T15:42:50Z" finished-at="2010-02-17T15:42:50Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:50Z" finished-at="2010-02-17T15:42:50Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:50Z" finished-at="2010-02-17T15:42:50Z">
- </test-method>
- <test-method status="PASS" signature="testExecute()" name="testExecute" duration-ms="868" started-at="2010-02-17T15:42:50Z" finished-at="2010-02-17T15:42:51Z">
- </test-method>
- <test-method status="PASS" signature="testNcore()" name="testNcore" duration-ms="1" started-at="2010-02-17T15:42:51Z" finished-at="2010-02-17T15:42:51Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:51Z" finished-at="2010-02-17T15:42:51Z">
- </test-method>
- <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="1771" started-at="2010-02-17T15:42:51Z" finished-at="2010-02-17T15:42:53Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:51Z" finished-at="2010-02-17T15:42:51Z">
- </test-method>
- </class>
- <class name="compbio.runner.msa.LimitTester">
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="61" started-at="2010-02-17T15:37:09Z" finished-at="2010-02-17T15:37:09Z">
- </test-method>
- <test-method status="PASS" signature="testLoadLimits()" name="testLoadLimits" duration-ms="0" started-at="2010-02-17T15:37:09Z" finished-at="2010-02-17T15:37:09Z">
- </test-method>
- </class>
- <class name="compbio.runner._impl.OBTester">
- <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testGetTestArgsCommand()" name="testGetTestArgsCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- </class>
- <class name="compbio.engine.local.LocalRunnerTester">
- <test-method status="PASS" signature="testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" duration-ms="336" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:37Z">
- <exception class="java.util.concurrent.CancellationException">
- <full-stacktrace>
- <![CDATA[java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
- at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="testCancelLocally()" name="testCancelLocally" duration-ms="20" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:37Z">
- <exception class="java.util.concurrent.CancellationException">
- <full-stacktrace>
- <![CDATA[java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
- at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="testMultipleCancelLocally()" name="testMultipleCancelLocally" duration-ms="58" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:37Z">
- <exception class="java.util.concurrent.CancellationException">
- <full-stacktrace>
- <![CDATA[java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
- at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- </class>
- <class name="compbio.engine.local.AsyncLocalRunnerTester">
- <test-method status="PASS" signature="testAsyncCancelOperation()" name="testAsyncCancelOperation" duration-ms="48" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:50Z">
- </test-method>
- <test-method status="PASS" signature="testAsyncRetrievOperation()" name="testAsyncRetrievOperation" duration-ms="560" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:51Z">
- </test-method>
- <test-method status="PASS" signature="testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" duration-ms="3053" started-at="2010-02-17T15:35:51Z" finished-at="2010-02-17T15:35:54Z">
- </test-method>
- <test-method status="PASS" signature="testCancelLocally()" name="testCancelLocally" duration-ms="27" started-at="2010-02-17T15:35:54Z" finished-at="2010-02-17T15:35:54Z">
- <exception class="java.util.concurrent.CancellationException">
- <full-stacktrace>
- <![CDATA[java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
- at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="21332" started-at="2010-02-17T15:35:54Z" finished-at="2010-02-17T15:36:15Z">
- </test-method>
- <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="20872" started-at="2010-02-17T15:35:54Z" finished-at="2010-02-17T15:36:15Z">
- </test-method>
- <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="40987" started-at="2010-02-17T15:35:54Z" finished-at="2010-02-17T15:36:35Z">
- </test-method>
- <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="20915" started-at="2010-02-17T15:35:54Z" finished-at="2010-02-17T15:36:15Z">
- </test-method>
- <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="20863" started-at="2010-02-17T15:36:15Z" finished-at="2010-02-17T15:36:36Z">
- </test-method>
- <test-method status="PASS" signature="testMultipleCancelLocally()" name="testMultipleCancelLocally" duration-ms="267" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:36Z">
- <exception class="java.util.concurrent.CancellationException">
- <full-stacktrace>
- <![CDATA[java.util.concurrent.CancellationException
- at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
- at java.util.concurrent.FutureTask.get(FutureTask.java:83)
- at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
- at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
- at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="634" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:37Z">
- </test-method>
- <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="220" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:36Z">
- </test-method>
- <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="125" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:36Z">
- </test-method>
- <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="482" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:36Z">
- </test-method>
- <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="176" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:36Z">
- </test-method>
- </class>
- <class name="compbio.runner._impl.Tmhmm2Tester">
- <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- </class>
- <class name="compbio.runner.msa.MafftTester">
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:37:57Z" finished-at="2010-02-17T15:37:57Z">
- </test-method>
- <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="639" started-at="2010-02-17T15:37:57Z" finished-at="2010-02-17T15:37:57Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:37:57Z" finished-at="2010-02-17T15:37:57Z">
- </test-method>
- <test-method status="PASS" signature="testClusterExecute()" name="testClusterExecute" duration-ms="11340" started-at="2010-02-17T15:37:57Z" finished-at="2010-02-17T15:38:09Z">
- </test-method>
- <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="435" started-at="2010-02-17T15:38:09Z" finished-at="2010-02-17T15:38:09Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:09Z" finished-at="2010-02-17T15:38:09Z">
- </test-method>
- <test-method status="PASS" signature="testExecute()" name="testExecute" duration-ms="428" started-at="2010-02-17T15:38:09Z" finished-at="2010-02-17T15:38:10Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:09Z" finished-at="2010-02-17T15:38:09Z">
- </test-method>
- <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="1033" started-at="2010-02-17T15:38:10Z" finished-at="2010-02-17T15:38:11Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:10Z" finished-at="2010-02-17T15:38:10Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:11Z" finished-at="2010-02-17T15:38:11Z">
- </test-method>
- <test-method status="PASS" signature="testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" duration-ms="21418" started-at="2010-02-17T15:38:11Z" finished-at="2010-02-17T15:38:32Z">
- </test-method>
- <test-method status="PASS" signature="testSetInputTester()" name="testSetInputTester" duration-ms="0" started-at="2010-02-17T15:38:32Z" finished-at="2010-02-17T15:38:32Z">
- </test-method>
- <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:32Z" finished-at="2010-02-17T15:38:32Z">
- </test-method>
- </class>
- <class name="compbio.data.sequence.ClustalAlignmentUtilTester">
- <test-method status="PASS" signature="testReadClustalFile()" name="testReadClustalFile" duration-ms="22" started-at="2010-02-17T15:34:32Z" finished-at="2010-02-17T15:34:32Z">
- </test-method>
- <test-method status="PASS" signature="testReadClustalFileLongNames()" name="testReadClustalFileLongNames" duration-ms="52" started-at="2010-02-17T15:34:32Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- <test-method status="PASS" signature="testReadClustalFileShortNames()" name="testReadClustalFileShortNames" duration-ms="54" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- </class>
- <class name="compbio.runner.msa.MuscleParametersTester">
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="85" started-at="2010-02-17T15:38:32Z" finished-at="2010-02-17T15:38:32Z">
- </test-method>
- <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="7798" started-at="2010-02-17T15:38:32Z" finished-at="2010-02-17T15:38:40Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="44" started-at="2010-02-17T15:38:40Z" finished-at="2010-02-17T15:38:40Z">
- </test-method>
- <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="0" started-at="2010-02-17T15:38:40Z" finished-at="2010-02-17T15:38:40Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="41" started-at="2010-02-17T15:38:40Z" finished-at="2010-02-17T15:38:40Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="1534" started-at="2010-02-17T15:38:40Z" finished-at="2010-02-17T15:38:42Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="44" started-at="2010-02-17T15:38:42Z" finished-at="2010-02-17T15:38:42Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="845" started-at="2010-02-17T15:38:42Z" finished-at="2010-02-17T15:38:43Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="43" started-at="2010-02-17T15:38:43Z" finished-at="2010-02-17T15:38:43Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="7603" started-at="2010-02-17T15:38:43Z" finished-at="2010-02-17T15:38:50Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="42" started-at="2010-02-17T15:38:50Z" finished-at="2010-02-17T15:38:50Z">
- </test-method>
- <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="622" started-at="2010-02-17T15:38:50Z" finished-at="2010-02-17T15:38:51Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="42" started-at="2010-02-17T15:38:51Z" finished-at="2010-02-17T15:38:51Z">
- </test-method>
- <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="2481" started-at="2010-02-17T15:38:51Z" finished-at="2010-02-17T15:38:53Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="44" started-at="2010-02-17T15:38:53Z" finished-at="2010-02-17T15:38:53Z">
- </test-method>
- <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="4773" started-at="2010-02-17T15:38:53Z" finished-at="2010-02-17T15:38:58Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="48" started-at="2010-02-17T15:38:58Z" finished-at="2010-02-17T15:38:58Z">
- </test-method>
- <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="856" started-at="2010-02-17T15:38:58Z" finished-at="2010-02-17T15:38:59Z">
- </test-method>
- </class>
- <class name="compbio.data.sequence.FastaSequenceGeneratorTester">
- <test-method status="PASS" signature="testProteinSequenceGeneration()" name="testProteinSequenceGeneration" duration-ms="8" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- </class>
- <class name="compbio.engine.cluster.drmaa.ClusterSessionTester">
- <test-method status="PASS" signature="testTaskList()" name="testTaskList" duration-ms="8964" started-at="2010-02-17T15:34:39Z" finished-at="2010-02-17T15:34:48Z">
- </test-method>
- </class>
- <class name="compbio.data.sequence.FastaSequenceTester">
- <test-method status="PASS" signature="testGetFormattedFasta()" name="testGetFormattedFasta" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- </class>
- <class name="compbio.engine.client.PathValidatorTester">
- <test-method status="PASS" signature="testGetClassPath()" name="testGetClassPath" duration-ms="234" started-at="2010-02-17T15:34:39Z" finished-at="2010-02-17T15:34:39Z">
- </test-method>
- <test-method status="PASS" signature="testIsAbsolutePath()" name="testIsAbsolutePath" duration-ms="0" started-at="2010-02-17T15:34:39Z" finished-at="2010-02-17T15:34:39Z">
- </test-method>
- </class>
- <class name="compbio.data.sequence.SequenceUtilTester">
- <test-method status="PASS" signature="testCleanSequence()" name="testCleanSequence" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- <test-method status="PASS" signature="testReadWriteFasta()" name="testReadWriteFasta" duration-ms="16" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- <test-method status="PASS" signature="testDeepCleanSequence()" name="testDeepCleanSequence" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- <test-method status="PASS" signature="testisNonAmbNucleotideSequence()" name="testisNonAmbNucleotideSequence" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- <test-method status="PASS" signature="testisProteinSequence()" name="testisProteinSequence" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
- </test-method>
- </class>
- <class name="compbio.runner.msa.TcoffeeParametersTester">
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:30Z">
- </test-method>
- <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="8765" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:39Z">
- </test-method>
- <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="0" started-at="2010-02-17T15:41:39Z" finished-at="2010-02-17T15:41:39Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:39Z" finished-at="2010-02-17T15:41:39Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:39Z" finished-at="2010-02-17T15:41:39Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="11166" started-at="2010-02-17T15:41:39Z" finished-at="2010-02-17T15:41:50Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="1" started-at="2010-02-17T15:41:50Z" finished-at="2010-02-17T15:41:50Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="5507" started-at="2010-02-17T15:41:50Z" finished-at="2010-02-17T15:41:56Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:56Z" finished-at="2010-02-17T15:41:56Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="21942" started-at="2010-02-17T15:41:56Z" finished-at="2010-02-17T15:42:18Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="1" started-at="2010-02-17T15:42:18Z" finished-at="2010-02-17T15:42:18Z">
- </test-method>
- <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="10988" started-at="2010-02-17T15:42:18Z" finished-at="2010-02-17T15:42:29Z">
- </test-method>
- <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="891" started-at="2010-02-17T15:42:29Z" finished-at="2010-02-17T15:42:30Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:29Z" finished-at="2010-02-17T15:42:29Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="1" started-at="2010-02-17T15:42:30Z" finished-at="2010-02-17T15:42:30Z">
- </test-method>
- <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="12717" started-at="2010-02-17T15:42:30Z" finished-at="2010-02-17T15:42:42Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:42Z" finished-at="2010-02-17T15:42:42Z">
- </test-method>
- <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="1094" started-at="2010-02-17T15:42:42Z" finished-at="2010-02-17T15:42:43Z">
- </test-method>
- </class>
- <class name="compbio.engine.cluster.drmaa.UtilTester">
- <test-method status="PASS" signature="testParser()" name="testParser" duration-ms="0" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- </class>
- <class name="compbio.runner.msa.ClustalWTester">
- <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="1178" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:40Z">
- </test-method>
- <test-method status="PASS" signature="readStatisticsClusterExecution()" name="readStatisticsClusterExecution" duration-ms="8121" started-at="2010-02-17T15:36:40Z" finished-at="2010-02-17T15:36:49Z">
- </test-method>
- <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="688" started-at="2010-02-17T15:36:49Z" finished-at="2010-02-17T15:36:49Z">
- </test-method>
- <test-method status="PASS" signature="testOptionsLocally()" name="testOptionsLocally" duration-ms="1932" started-at="2010-02-17T15:36:49Z" finished-at="2010-02-17T15:36:51Z">
- </test-method>
- <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="431" started-at="2010-02-17T15:36:51Z" finished-at="2010-02-17T15:36:52Z">
- </test-method>
- <test-method status="PASS" signature="testRunLocally()" name="testRunLocally" duration-ms="171" started-at="2010-02-17T15:36:52Z" finished-at="2010-02-17T15:36:52Z">
- </test-method>
- <test-method status="PASS" signature="testRunOnCluster()" name="testRunOnCluster" duration-ms="15937" started-at="2010-02-17T15:36:52Z" finished-at="2010-02-17T15:37:08Z">
- </test-method>
- <test-method status="PASS" signature="testRunWithMatrix()" name="testRunWithMatrix" duration-ms="824" started-at="2010-02-17T15:37:08Z" finished-at="2010-02-17T15:37:09Z">
- </test-method>
- </class>
- <class name="compbio.engine.conf.DirectoryManagerTester">
- <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="110" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="104" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="103" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="100" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- </class>
- <class name="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester">
- <test-method status="PASS" signature="testCancel()" name="testCancel" duration-ms="1587" started-at="2010-02-17T15:35:29Z" finished-at="2010-02-17T15:35:30Z">
- </test-method>
- <test-method status="PASS" signature="testSubmit()" name="testSubmit" duration-ms="17835" started-at="2010-02-17T15:35:30Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- </class>
- <class name="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester">
- <test-method status="PASS" signature="testCancel()" name="testCancel" duration-ms="1273" started-at="2010-02-17T15:34:48Z" finished-at="2010-02-17T15:34:49Z">
- <exception class="compbio.metadata.ResultNotAvailableException">
- <message>
- <![CDATA[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!]]>
- </message>
- <full-stacktrace>
- <![CDATA[compbio.metadata.ResultNotAvailableException: 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!
- at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
- at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
- at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
- at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-Caused by: 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!
- at compbio.runner.Util.readClustalFile(Util.java:126)
- at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
- ... 25 more
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="testGetJobStatus()" name="testGetJobStatus" duration-ms="20778" started-at="2010-02-17T15:34:49Z" finished-at="2010-02-17T15:35:10Z">
- </test-method>
- <test-method status="PASS" signature="testSubmit()" name="testSubmit" duration-ms="18714" started-at="2010-02-17T15:35:10Z" finished-at="2010-02-17T15:35:29Z">
- </test-method>
- </class>
- <class name="compbio.metadata.PresetTester">
- <test-method status="PASS" signature="marshallPreset()" name="marshallPreset" duration-ms="899" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="validatePresets()" name="validatePresets" duration-ms="1" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- </class>
- <class name="compbio.metadata.OptionMarshallerTester">
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:38Z">
- </test-method>
- <test-method status="PASS" signature="testMarshalling()" name="testMarshalling" duration-ms="58" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:38Z">
- <exception class="javax.xml.bind.MarshalException">
- <full-stacktrace>
- <![CDATA[javax.xml.bind.MarshalException
- - with linked exception:
-[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
- at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
- at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
- at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
- at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
- at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
- at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
- at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
- at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
- ... 26 more
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:38Z">
- </test-method>
- <test-method status="PASS" signature="testUnMarshalling()" name="testUnMarshalling" duration-ms="386" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:38Z">
- </test-method>
- </class>
- <class name="compbio.engine.PulledFileCacheTester">
- <test-method status="PASS" signature="test()" name="test" duration-ms="5187" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:38Z">
- </test-method>
- </class>
- <class name="compbio.runner._impl.RPSBlastTester">
- <test-method status="PASS" signature="testGetTestArgsCommand()" name="testGetTestArgsCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- </class>
- <class name="compbio.runner.msa.ClustalWParametersTester">
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="369" started-at="2010-02-17T15:34:17Z" finished-at="2010-02-17T15:34:17Z">
- </test-method>
- <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="3518" started-at="2010-02-17T15:34:17Z" finished-at="2010-02-17T15:34:20Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="33" started-at="2010-02-17T15:34:20Z" finished-at="2010-02-17T15:34:20Z">
- </test-method>
- <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="1" started-at="2010-02-17T15:34:20Z" finished-at="2010-02-17T15:34:20Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="26" started-at="2010-02-17T15:34:20Z" finished-at="2010-02-17T15:34:20Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="1835" started-at="2010-02-17T15:34:20Z" finished-at="2010-02-17T15:34:22Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="30" started-at="2010-02-17T15:34:22Z" finished-at="2010-02-17T15:34:22Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="1232" started-at="2010-02-17T15:34:22Z" finished-at="2010-02-17T15:34:24Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="61" started-at="2010-02-17T15:34:24Z" finished-at="2010-02-17T15:34:24Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="3105" started-at="2010-02-17T15:34:24Z" finished-at="2010-02-17T15:34:27Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="53" started-at="2010-02-17T15:34:27Z" finished-at="2010-02-17T15:34:27Z">
- </test-method>
- <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="502" started-at="2010-02-17T15:34:27Z" finished-at="2010-02-17T15:34:27Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="56" started-at="2010-02-17T15:34:27Z" finished-at="2010-02-17T15:34:27Z">
- </test-method>
- <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="2109" started-at="2010-02-17T15:34:27Z" finished-at="2010-02-17T15:34:29Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="54" started-at="2010-02-17T15:34:29Z" finished-at="2010-02-17T15:34:30Z">
- </test-method>
- <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="2680" started-at="2010-02-17T15:34:30Z" finished-at="2010-02-17T15:34:32Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="77" started-at="2010-02-17T15:34:32Z" finished-at="2010-02-17T15:34:32Z">
- </test-method>
- <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="177" started-at="2010-02-17T15:34:32Z" finished-at="2010-02-17T15:34:32Z">
- </test-method>
- </class>
- <class name="compbio.runner._impl.MclTester">
- <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="1" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
- </test-method>
- </class>
- <class name="compbio.engine.cluster.dundee._QueueTester">
- <test-method status="PASS" signature="testQueue()" name="testQueue" duration-ms="0" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- </class>
- <class name="compbio.runner.msa.ProbconsParametersTester">
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="50" started-at="2010-02-17T15:39:09Z" finished-at="2010-02-17T15:39:09Z">
- </test-method>
- <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="2874" started-at="2010-02-17T15:39:09Z" finished-at="2010-02-17T15:39:12Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="28" started-at="2010-02-17T15:39:12Z" finished-at="2010-02-17T15:39:12Z">
- </test-method>
- <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="1" started-at="2010-02-17T15:39:12Z" finished-at="2010-02-17T15:39:12Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="29" started-at="2010-02-17T15:39:12Z" finished-at="2010-02-17T15:39:12Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="38416" started-at="2010-02-17T15:39:12Z" finished-at="2010-02-17T15:39:50Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="38" started-at="2010-02-17T15:39:50Z" finished-at="2010-02-17T15:39:50Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="768" started-at="2010-02-17T15:39:50Z" finished-at="2010-02-17T15:39:51Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="29" started-at="2010-02-17T15:39:51Z" finished-at="2010-02-17T15:39:51Z">
- </test-method>
- <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="61881" started-at="2010-02-17T15:39:51Z" finished-at="2010-02-17T15:40:53Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="29" started-at="2010-02-17T15:40:53Z" finished-at="2010-02-17T15:40:53Z">
- </test-method>
- <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="14704" started-at="2010-02-17T15:40:53Z" finished-at="2010-02-17T15:41:08Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="28" started-at="2010-02-17T15:41:08Z" finished-at="2010-02-17T15:41:08Z">
- </test-method>
- <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="433" started-at="2010-02-17T15:41:08Z" finished-at="2010-02-17T15:41:08Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="31" started-at="2010-02-17T15:41:08Z" finished-at="2010-02-17T15:41:08Z">
- </test-method>
- <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="1321" started-at="2010-02-17T15:41:08Z" finished-at="2010-02-17T15:41:09Z">
- </test-method>
- </class>
- <class name="compbio.engine.conf.RunnerConfigMarshallerTester">
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="29" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- <test-method status="PASS" signature="testMarshalling()" name="testMarshalling" duration-ms="20" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="16" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
- </test-method>
- <test-method status="PASS" signature="testSchemaFromCodeGeneration()" name="testSchemaFromCodeGeneration" duration-ms="504" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:49Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="67" started-at="2010-02-17T15:35:49Z" finished-at="2010-02-17T15:35:49Z">
- </test-method>
- <test-method status="PASS" signature="testUnMarshalling()" name="testUnMarshalling" duration-ms="580" started-at="2010-02-17T15:35:49Z" finished-at="2010-02-17T15:35:50Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="18" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:50Z">
- </test-method>
- <test-method status="PASS" signature="testValidation()" name="testValidation" duration-ms="636" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:50Z">
- </test-method>
- <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="16" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:50Z">
- </test-method>
- <test-method status="PASS" signature="testValidationOnMarshalling()" name="testValidationOnMarshalling" duration-ms="11" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:50Z">
- <exception class="javax.xml.bind.MarshalException">
- <full-stacktrace>
- <![CDATA[javax.xml.bind.MarshalException
- - with linked exception:
-[org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
- at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
- at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
- at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
- at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
- at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
- at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
- at java.lang.reflect.Method.invoke(Method.java:597)
- at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
- at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
- at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
- at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
- at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
- at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
- at org.testng.TestRunner.runWorkers(TestRunner.java:759)
- at org.testng.TestRunner.privateRun(TestRunner.java:592)
- at org.testng.TestRunner.run(TestRunner.java:486)
- at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
- at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
- at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
- at org.testng.SuiteRunner.run(SuiteRunner.java:204)
- at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
- at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
- at org.testng.TestNG.run(TestNG.java:784)
- at org.testng.TestNG.privateMain(TestNG.java:949)
- at org.testng.TestNG.main(TestNG.java:922)
-Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
- at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
- at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
- at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
- at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
- at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
- at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
- at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
- at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
- at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
- at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
- at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
- at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
- ... 26 more
-]]>
- </full-stacktrace>
- </exception>
- </test-method>
- </class>
- </test>
- </suite>
-</testng-results>
+++ /dev/null
-.invocation-failed, .test-failed { background-color: #DD0000; }\r
-.invocation-percent, .test-percent { background-color: #006600; }\r
-.invocation-passed, .test-passed { background-color: #00AA00; }\r
-.invocation-skipped, .test-skipped { background-color: #CCCC00; }\r
-\r
-.main-page {\r
- font-size: x-large;\r
-}\r
-\r
git://source.jalview.org / jabaws.git / commitdiff