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Remove old test from web site to replace with most recent
[jabaws.git] / website / tests / Ant suite / Ant test.html
diff --git a/website/tests/Ant suite/Ant test.html b/website/tests/Ant suite/Ant test.html
deleted file mode 100644 (file)
index 98af8e8..0000000
--- a/website/tests/Ant suite/Ant test.html
+++ /dev/null
@@ -1,1621 +0,0 @@
-<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">
-.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));
-  }
-  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;
-  }
-
-}
-
-function toggleAllBoxes() {
-  if (document.getElementsByTagName) {
-    d = document.getElementsByTagName('div');
-    for (i = 0; i < d.length; i++) {
-      if (d[i].className == 'log') {
-        flip(d[i]);
-      }
-    }
-  }
-}
-
-// -->
-</script>
-
-</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>
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