website/tests/testng-results.xml

   1 <testng-results>
   2   <reporter-output>
   3   </reporter-output>
   4   <suite name="Ant suite">
   5     <groups>
   6       <group name="engine">
   7         <method signature="compbio.engine.FilePullerTester.testGetDelay()" name="testGetDelay" class="compbio.engine.FilePullerTester"/>
   8         <method signature="compbio.engine.FilePullerTester.testPull()" name="testPull" class="compbio.engine.FilePullerTester"/>
   9         <method signature="compbio.engine.FilePullerTester.testCache()" name="testCache" class="compbio.engine.FilePullerTester"/>
  10         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  11         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()" name="testGetJobStatus" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  12         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  13         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation()" name="testAsyncCancelOperation" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  14         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation()" name="testAsyncRetrievOperation" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  15         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  16         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally()" name="testCancelLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  17         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()" name="testGetStatus" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  18         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally()" name="testMultipleCancelLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  19         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()" name="testSubmitLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  20         <method signature="compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" class="compbio.engine.local.LocalRunnerTester"/>
  21         <method signature="compbio.engine.local.LocalRunnerTester.testCancelLocally()" name="testCancelLocally" class="compbio.engine.local.LocalRunnerTester"/>
  22         <method signature="compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally()" name="testMultipleCancelLocally" class="compbio.engine.local.LocalRunnerTester"/>
  23         <method signature="compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()" name="testTaskList" class="compbio.engine.cluster.drmaa.ClusterSessionTester"/>
  24         <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
  25         <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
  26       </group>
  27       <group name="cluster">
  28         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  29         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()" name="testGetJobStatus" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  30         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  31         <method signature="compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()" name="testClusterEngineConf" class="compbio.engine.conf.PropertyHelperManagerTester"/>
  32         <method signature="compbio.runner.conservation.AAConTester.testRunOnClusterAsync()" name="testRunOnClusterAsync" class="compbio.runner.conservation.AAConTester"/>
  33         <method signature="compbio.runner.disorder.DisemblTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.disorder.DisemblTester"/>
  34         <method signature="compbio.runner.disorder.DisemblTester.testRunOnClusterAsync()" name="testRunOnClusterAsync" class="compbio.runner.disorder.DisemblTester"/>
  35         <method signature="compbio.runner.disorder.GlobPlotTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.disorder.GlobPlotTester"/>
  36         <method signature="compbio.runner.disorder.GlobPlotTester.testRunOnClusterAsync()" name="testRunOnClusterAsync" class="compbio.runner.disorder.GlobPlotTester"/>
  37         <method signature="compbio.runner.disorder.IUPredTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.disorder.IUPredTester"/>
  38         <method signature="compbio.runner.disorder.IUPredTester.testRunOnClusterAsync()" name="testRunOnClusterAsync" class="compbio.runner.disorder.IUPredTester"/>
  39         <method signature="compbio.runner.disorder.JronnTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.disorder.JronnTester"/>
  40         <method signature="compbio.runner.disorder.JronnTester.testRunOnClusterAsync()" name="testRunOnClusterAsync" class="compbio.runner.disorder.JronnTester"/>
  41         <method signature="compbio.runner.msa.MafftTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.MafftTester"/>
  42         <method signature="compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" class="compbio.runner.msa.MafftTester"/>
  43         <method signature="compbio.runner.msa.MuscleTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.MuscleTester"/>
  44         <method signature="compbio.runner.msa.ProbconsTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.ProbconsTester"/>
  45         <method signature="compbio.runner.msa.TcoffeeTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.TcoffeeTester"/>
  46         <method signature="compbio.runner.msa.TcoffeeTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.TcoffeeTester"/>
  47         <method signature="compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()" name="readStatisticsClusterExecution" class="compbio.runner.msa.ClustalWTester"/>
  48         <method signature="compbio.runner.msa.ClustalWTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.ClustalWTester"/>
  49         <method signature="compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()" name="testTaskList" class="compbio.engine.cluster.drmaa.ClusterSessionTester"/>
  50         <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
  51         <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
  52       </group>
  53       <group name="runner">
  54         <method signature="compbio.runner.conservation.AAConTester.readStatistics()" name="readStatistics" class="compbio.runner.conservation.AAConTester"/>
  55         <method signature="compbio.runner.conservation.AAConTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.conservation.AAConTester"/>
  56         <method signature="compbio.runner.conservation.AAConTester.testPersistance()" name="testPersistance" class="compbio.runner.conservation.AAConTester"/>
  57         <method signature="compbio.runner.conservation.AAConTester.testRunLocally()" name="testRunLocally" class="compbio.runner.conservation.AAConTester"/>
  58         <method signature="compbio.runner.conservation.AAConTester.testRunLocallyOnTwoCpu()" name="testRunLocallyOnTwoCpu" class="compbio.runner.conservation.AAConTester"/>
  59         <method signature="compbio.runner.conservation.AAConTester.testRunLocallyWithPreset()" name="testRunLocallyWithPreset" class="compbio.runner.conservation.AAConTester"/>
  60         <method signature="compbio.runner.conservation.AAConTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.conservation.AAConTester"/>
  61         <method signature="compbio.runner.conservation.AAConTester.testRunOnClusterAsync()" name="testRunOnClusterAsync" class="compbio.runner.conservation.AAConTester"/>
  62         <method signature="compbio.runner.disorder.DisemblTester.readStatistics()" name="readStatistics" class="compbio.runner.disorder.DisemblTester"/>
  63         <method signature="compbio.runner.disorder.DisemblTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.disorder.DisemblTester"/>
  64         <method signature="compbio.runner.disorder.DisemblTester.testPersistance()" name="testPersistance" class="compbio.runner.disorder.DisemblTester"/>
  65         <method signature="compbio.runner.disorder.DisemblTester.testRunLocally()" name="testRunLocally" class="compbio.runner.disorder.DisemblTester"/>
  66         <method signature="compbio.runner.disorder.DisemblTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.disorder.DisemblTester"/>
  67         <method signature="compbio.runner.disorder.DisemblTester.testRunOnClusterAsync()" name="testRunOnClusterAsync" class="compbio.runner.disorder.DisemblTester"/>
  68         <method signature="compbio.runner.disorder.GlobPlotTester.readStatistics()" name="readStatistics" class="compbio.runner.disorder.GlobPlotTester"/>
  69         <method signature="compbio.runner.disorder.GlobPlotTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.disorder.GlobPlotTester"/>
  70         <method signature="compbio.runner.disorder.GlobPlotTester.testPersistance()" name="testPersistance" class="compbio.runner.disorder.GlobPlotTester"/>
  71         <method signature="compbio.runner.disorder.GlobPlotTester.testRunLocally()" name="testRunLocally" class="compbio.runner.disorder.GlobPlotTester"/>
  72         <method signature="compbio.runner.disorder.GlobPlotTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.disorder.GlobPlotTester"/>
  73         <method signature="compbio.runner.disorder.GlobPlotTester.testRunOnClusterAsync()" name="testRunOnClusterAsync" class="compbio.runner.disorder.GlobPlotTester"/>
  74         <method signature="compbio.runner.disorder.IUPredTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.disorder.IUPredTester"/>
  75         <method signature="compbio.runner.disorder.IUPredTester.testPersistance()" name="testPersistance" class="compbio.runner.disorder.IUPredTester"/>
  76         <method signature="compbio.runner.disorder.IUPredTester.testReadResults()" name="testReadResults" class="compbio.runner.disorder.IUPredTester"/>
  77         <method signature="compbio.runner.disorder.IUPredTester.testRunLocally()" name="testRunLocally" class="compbio.runner.disorder.IUPredTester"/>
  78         <method signature="compbio.runner.disorder.IUPredTester.testRunLocallyWithParams()" name="testRunLocallyWithParams" class="compbio.runner.disorder.IUPredTester"/>
  79         <method signature="compbio.runner.disorder.IUPredTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.disorder.IUPredTester"/>
  80         <method signature="compbio.runner.disorder.IUPredTester.testRunOnClusterAsync()" name="testRunOnClusterAsync" class="compbio.runner.disorder.IUPredTester"/>
  81         <method signature="compbio.runner.disorder.IUPredTester.testSetParameter()" name="testSetParameter" class="compbio.runner.disorder.IUPredTester"/>
  82         <method signature="compbio.runner.disorder.JronnTester.readStatistics()" name="readStatistics" class="compbio.runner.disorder.JronnTester"/>
  83         <method signature="compbio.runner.disorder.JronnTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.disorder.JronnTester"/>
  84         <method signature="compbio.runner.disorder.JronnTester.testPersistance()" name="testPersistance" class="compbio.runner.disorder.JronnTester"/>
  85         <method signature="compbio.runner.disorder.JronnTester.testRunLocally()" name="testRunLocally" class="compbio.runner.disorder.JronnTester"/>
  86         <method signature="compbio.runner.disorder.JronnTester.testRunLocallyOnTwoCpu()" name="testRunLocallyOnTwoCpu" class="compbio.runner.disorder.JronnTester"/>
  87         <method signature="compbio.runner.disorder.JronnTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.disorder.JronnTester"/>
  88         <method signature="compbio.runner.disorder.JronnTester.testRunOnClusterAsync()" name="testRunOnClusterAsync" class="compbio.runner.disorder.JronnTester"/>
  89         <method signature="compbio.runner.msa.ClustalWParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.ClustalWParametersTester"/>
  90         <method signature="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.ClustalWParametersTester"/>
  91         <method signature="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.ClustalWParametersTester"/>
  92         <method signature="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.ClustalWParametersTester"/>
  93         <method signature="compbio.runner.msa.ClustalWParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.ClustalWParametersTester"/>
  94         <method signature="compbio.runner.msa.ClustalWParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.ClustalWParametersTester"/>
  95         <method signature="compbio.runner.msa.ClustalWParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.ClustalWParametersTester"/>
  96         <method signature="compbio.runner.msa.ClustalWParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.ClustalWParametersTester"/>
  97         <method signature="compbio.runner.msa.MafftParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.MafftParametersTester"/>
  98         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.MafftParametersTester"/>
  99         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.MafftParametersTester"/>
 100         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.MafftParametersTester"/>
 101         <method signature="compbio.runner.msa.MafftParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.MafftParametersTester"/>
 102         <method signature="compbio.runner.msa.MafftParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.MafftParametersTester"/>
 103         <method signature="compbio.runner.msa.MafftParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.MafftParametersTester"/>
 104         <method signature="compbio.runner.msa.MafftParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.MafftParametersTester"/>
 105         <method signature="compbio.runner.msa.MafftTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.MafftTester"/>
 106         <method signature="compbio.runner.msa.MafftTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.MafftTester"/>
 107         <method signature="compbio.runner.msa.MafftTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.MafftTester"/>
 108         <method signature="compbio.runner.msa.MafftTester.testExecute()" name="testExecute" class="compbio.runner.msa.MafftTester"/>
 109         <method signature="compbio.runner.msa.MafftTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.MafftTester"/>
 110         <method signature="compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" class="compbio.runner.msa.MafftTester"/>
 111         <method signature="compbio.runner.msa.MafftTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.MafftTester"/>
 112         <method signature="compbio.runner.msa.MuscleParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.MuscleParametersTester"/>
 113         <method signature="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.MuscleParametersTester"/>
 114         <method signature="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.MuscleParametersTester"/>
 115         <method signature="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.MuscleParametersTester"/>
 116         <method signature="compbio.runner.msa.MuscleParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.MuscleParametersTester"/>
 117         <method signature="compbio.runner.msa.MuscleParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.MuscleParametersTester"/>
 118         <method signature="compbio.runner.msa.MuscleParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.MuscleParametersTester"/>
 119         <method signature="compbio.runner.msa.MuscleParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.MuscleParametersTester"/>
 120         <method signature="compbio.runner.msa.MuscleTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.MuscleTester"/>
 121         <method signature="compbio.runner.msa.MuscleTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.MuscleTester"/>
 122         <method signature="compbio.runner.msa.MuscleTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.MuscleTester"/>
 123         <method signature="compbio.runner.msa.MuscleTester.testRunLocally()" name="testRunLocally" class="compbio.runner.msa.MuscleTester"/>
 124         <method signature="compbio.runner.msa.MuscleTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.MuscleTester"/>
 125         <method signature="compbio.runner.msa.ProbconsParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.ProbconsParametersTester"/>
 126         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.ProbconsParametersTester"/>
 127         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.ProbconsParametersTester"/>
 128         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.ProbconsParametersTester"/>
 129         <method signature="compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
 130         <method signature="compbio.runner.msa.ProbconsParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.ProbconsParametersTester"/>
 131         <method signature="compbio.runner.msa.ProbconsParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
 132         <method signature="compbio.runner.msa.ProbconsTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.ProbconsTester"/>
 133         <method signature="compbio.runner.msa.ProbconsTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.ProbconsTester"/>
 134         <method signature="compbio.runner.msa.ProbconsTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.ProbconsTester"/>
 135         <method signature="compbio.runner.msa.ProbconsTester.testExecute()" name="testExecute" class="compbio.runner.msa.ProbconsTester"/>
 136         <method signature="compbio.runner.msa.ProbconsTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.ProbconsTester"/>
 137         <method signature="compbio.runner.msa.ProbconsTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.ProbconsTester"/>
 138         <method signature="compbio.runner.msa.TcoffeeParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.TcoffeeParametersTester"/>
 139         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 140         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 141         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 142         <method signature="compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
 143         <method signature="compbio.runner.msa.TcoffeeParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.TcoffeeParametersTester"/>
 144         <method signature="compbio.runner.msa.TcoffeeParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
 145         <method signature="compbio.runner.msa.TcoffeeParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.TcoffeeParametersTester"/>
 146         <method signature="compbio.runner.msa.TcoffeeTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.TcoffeeTester"/>
 147         <method signature="compbio.runner.msa.TcoffeeTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.TcoffeeTester"/>
 148         <method signature="compbio.runner.msa.TcoffeeTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.TcoffeeTester"/>
 149         <method signature="compbio.runner.msa.TcoffeeTester.testExecute()" name="testExecute" class="compbio.runner.msa.TcoffeeTester"/>
 150         <method signature="compbio.runner.msa.TcoffeeTester.testNcore()" name="testNcore" class="compbio.runner.msa.TcoffeeTester"/>
 151         <method signature="compbio.runner.msa.TcoffeeTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.TcoffeeTester"/>
 152         <method signature="compbio.runner.msa.ClustalWTester.testRunWithMatrix()" name="testRunWithMatrix" class="compbio.runner.msa.ClustalWTester"/>
 153         <method signature="compbio.runner.msa.ClustalWTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.ClustalWTester"/>
 154         <method signature="compbio.runner.msa.ClustalWTester.testRunLocally()" name="testRunLocally" class="compbio.runner.msa.ClustalWTester"/>
 155         <method signature="compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()" name="readStatisticsClusterExecution" class="compbio.runner.msa.ClustalWTester"/>
 156         <method signature="compbio.runner.msa.ClustalWTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.ClustalWTester"/>
 157         <method signature="compbio.runner.msa.ClustalWTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.ClustalWTester"/>
 158         <method signature="compbio.runner.msa.ClustalWTester.testOptionsLocally()" name="testOptionsLocally" class="compbio.runner.msa.ClustalWTester"/>
 159         <method signature="compbio.runner.msa.ClustalWTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.ClustalWTester"/>
 160       </group>
 161       <group name="non_windows">
 162         <method signature="compbio.runner.msa.MafftParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.MafftParametersTester"/>
 163         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.MafftParametersTester"/>
 164         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.MafftParametersTester"/>
 165         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.MafftParametersTester"/>
 166         <method signature="compbio.runner.msa.MafftParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.MafftParametersTester"/>
 167         <method signature="compbio.runner.msa.MafftParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.MafftParametersTester"/>
 168         <method signature="compbio.runner.msa.MafftParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.MafftParametersTester"/>
 169         <method signature="compbio.runner.msa.MafftParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.MafftParametersTester"/>
 170         <method signature="compbio.runner.msa.MafftTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.MafftTester"/>
 171         <method signature="compbio.runner.msa.MafftTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.MafftTester"/>
 172         <method signature="compbio.runner.msa.MafftTester.testExecute()" name="testExecute" class="compbio.runner.msa.MafftTester"/>
 173         <method signature="compbio.runner.msa.MafftTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.MafftTester"/>
 174         <method signature="compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" class="compbio.runner.msa.MafftTester"/>
 175         <method signature="compbio.runner.msa.MafftTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.MafftTester"/>
 176         <method signature="compbio.runner.msa.ProbconsParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.ProbconsParametersTester"/>
 177         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.ProbconsParametersTester"/>
 178         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.ProbconsParametersTester"/>
 179         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.ProbconsParametersTester"/>
 180         <method signature="compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
 181         <method signature="compbio.runner.msa.ProbconsParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.ProbconsParametersTester"/>
 182         <method signature="compbio.runner.msa.ProbconsParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
 183         <method signature="compbio.runner.msa.ProbconsTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.ProbconsTester"/>
 184         <method signature="compbio.runner.msa.ProbconsTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.ProbconsTester"/>
 185         <method signature="compbio.runner.msa.ProbconsTester.testExecute()" name="testExecute" class="compbio.runner.msa.ProbconsTester"/>
 186         <method signature="compbio.runner.msa.ProbconsTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.ProbconsTester"/>
 187         <method signature="compbio.runner.msa.ProbconsTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.ProbconsTester"/>
 188         <method signature="compbio.runner.msa.TcoffeeParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.TcoffeeParametersTester"/>
 189         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 190         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 191         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 192         <method signature="compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
 193         <method signature="compbio.runner.msa.TcoffeeParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.TcoffeeParametersTester"/>
 194         <method signature="compbio.runner.msa.TcoffeeParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
 195         <method signature="compbio.runner.msa.TcoffeeParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.TcoffeeParametersTester"/>
 196         <method signature="compbio.runner.msa.TcoffeeTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.TcoffeeTester"/>
 197         <method signature="compbio.runner.msa.TcoffeeTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.TcoffeeTester"/>
 198         <method signature="compbio.runner.msa.TcoffeeTester.testExecute()" name="testExecute" class="compbio.runner.msa.TcoffeeTester"/>
 199         <method signature="compbio.runner.msa.TcoffeeTester.testNcore()" name="testNcore" class="compbio.runner.msa.TcoffeeTester"/>
 200         <method signature="compbio.runner.msa.TcoffeeTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.TcoffeeTester"/>
 201       </group>
 202     </groups>
 203     <test name="Ant test">
 204       <class name="compbio.engine.client.CommandBuilderTester">
 205         <test-method status="PASS" signature="testCommandBuilding()" name="testCommandBuilding" duration-ms="1" started-at="2011-06-23T10:35:12Z" finished-at="2011-06-23T10:35:12Z">
 206         </test-method>
 207         <test-method status="PASS" signature="testOptionsToCommand()" name="testOptionsToCommand" duration-ms="40" started-at="2011-06-23T10:35:12Z" finished-at="2011-06-23T10:35:12Z">
 208         </test-method>
 209         <test-method status="PASS" signature="testSpaceDelimiterExecutable()" name="testSpaceDelimiterExecutable" duration-ms="0" started-at="2011-06-23T10:35:12Z" finished-at="2011-06-23T10:35:12Z">
 210         </test-method>
 211       </class>
 212       <class name="compbio.runner._impl.NetNglycTester">
 213         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="1" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 214         </test-method>
 215       </class>
 216       <class name="compbio.engine.EngineConfiguratorTester">
 217         <test-method status="PASS" signature="testGetAsyncEngine()" name="testGetAsyncEngine" duration-ms="12" started-at="2011-06-23T10:35:07Z" finished-at="2011-06-23T10:35:07Z">
 218         </test-method>
 219         <test-method status="PASS" signature="testGetSyncEngine()" name="testGetSyncEngine" duration-ms="1" started-at="2011-06-23T10:35:07Z" finished-at="2011-06-23T10:35:07Z">
 220         </test-method>
 221       </class>
 222       <class name="compbio.runner.disorder.GlobPlotTester">
 223         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:37Z" finished-at="2011-06-23T10:36:37Z">
 224         </test-method>
 225         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="0" started-at="2011-06-23T10:36:37Z" finished-at="2011-06-23T10:36:37Z">
 226         </test-method>
 227         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="43" started-at="2011-06-23T10:36:37Z" finished-at="2011-06-23T10:36:37Z">
 228         </test-method>
 229         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:37Z" finished-at="2011-06-23T10:36:37Z">
 230         </test-method>
 231         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:37Z" finished-at="2011-06-23T10:36:37Z">
 232         </test-method>
 233         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="980" started-at="2011-06-23T10:36:37Z" finished-at="2011-06-23T10:36:38Z">
 234         </test-method>
 235         <test-method status="PASS" signature="testRunLocally()" name="testRunLocally" duration-ms="454" started-at="2011-06-23T10:36:38Z" finished-at="2011-06-23T10:36:38Z">
 236         </test-method>
 237         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:38Z" finished-at="2011-06-23T10:36:38Z">
 238         </test-method>
 239         <test-method status="PASS" signature="testRunOnCluster()" name="testRunOnCluster" duration-ms="2503" started-at="2011-06-23T10:36:38Z" finished-at="2011-06-23T10:36:41Z">
 240         </test-method>
 241         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:38Z" finished-at="2011-06-23T10:36:38Z">
 242         </test-method>
 243         <test-method status="PASS" signature="testRunOnClusterAsync()" name="testRunOnClusterAsync" duration-ms="6021" started-at="2011-06-23T10:36:41Z" finished-at="2011-06-23T10:36:47Z">
 244         </test-method>
 245         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:41Z" finished-at="2011-06-23T10:36:41Z">
 246         </test-method>
 247       </class>
 248       <class name="compbio.stat.collector.ExecutionStatCollectorTester">
 249         <test-method status="PASS" signature="testCollectStat()" name="testCollectStat" duration-ms="271" started-at="2011-06-23T10:41:52Z" finished-at="2011-06-23T10:41:52Z">
 250         </test-method>
 251         <test-method status="PASS" signature="testHasCompleted()" name="testHasCompleted" duration-ms="1" started-at="2011-06-23T10:41:52Z" finished-at="2011-06-23T10:41:52Z">
 252         </test-method>
 253         <test-method status="PASS" signature="testUpdateStatTester()" name="testUpdateStatTester" duration-ms="35012" started-at="2011-06-23T10:41:52Z" finished-at="2011-06-23T10:42:27Z">
 254         </test-method>
 255       </class>
 256       <class name="compbio.engine.local.AsyncLocalRunnerTester">
 257         <test-method status="PASS" signature="testAsyncCancelOperation()" name="testAsyncCancelOperation" duration-ms="17" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
 258         </test-method>
 259         <test-method status="PASS" signature="testAsyncRetrievOperation()" name="testAsyncRetrievOperation" duration-ms="124" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
 260         </test-method>
 261         <test-method status="PASS" signature="testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" duration-ms="3017" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:34Z">
 262         </test-method>
 263         <test-method status="PASS" signature="testCancelLocally()" name="testCancelLocally" duration-ms="13" started-at="2011-06-23T10:35:34Z" finished-at="2011-06-23T10:35:34Z">
 264           <exception class="java.util.concurrent.CancellationException">
 265             <full-stacktrace>
 266               <![CDATA[java.util.concurrent.CancellationException
 267         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 268         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 269         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 270         at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 271         at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
 272         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 273         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 274         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 275         at java.lang.reflect.Method.invoke(Method.java:597)
 276         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 277         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 278         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 279         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 280         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 281         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 282         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 283         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 284         at org.testng.TestRunner.run(TestRunner.java:486)
 285         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 286         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 287         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 288         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 289         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 290         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 291         at org.testng.TestNG.run(TestNG.java:784)
 292         at org.testng.TestNG.privateMain(TestNG.java:949)
 293         at org.testng.TestNG.main(TestNG.java:922)
 294 ]]>
 295             </full-stacktrace>
 296           </exception>
 297         </test-method>
 298         <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="19351" started-at="2011-06-23T10:35:34Z" finished-at="2011-06-23T10:35:54Z">
 299         </test-method>
 300         <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="19362" started-at="2011-06-23T10:35:34Z" finished-at="2011-06-23T10:35:54Z">
 301         </test-method>
 302         <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="19322" started-at="2011-06-23T10:35:34Z" finished-at="2011-06-23T10:35:54Z">
 303         </test-method>
 304         <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="19358" started-at="2011-06-23T10:35:34Z" finished-at="2011-06-23T10:35:54Z">
 305         </test-method>
 306         <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="19298" started-at="2011-06-23T10:35:54Z" finished-at="2011-06-23T10:36:13Z">
 307         </test-method>
 308         <test-method status="PASS" signature="testMultipleCancelLocally()" name="testMultipleCancelLocally" duration-ms="54" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:13Z">
 309           <exception class="java.util.concurrent.CancellationException">
 310             <full-stacktrace>
 311               <![CDATA[java.util.concurrent.CancellationException
 312         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 313         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 314         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 315         at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 316         at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
 317         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 318         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 319         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 320         at java.lang.reflect.Method.invoke(Method.java:597)
 321         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 322         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 323         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 324         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 325         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 326         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 327         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 328         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 329         at org.testng.TestRunner.run(TestRunner.java:486)
 330         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 331         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 332         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 333         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 334         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 335         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 336         at org.testng.TestNG.run(TestNG.java:784)
 337         at org.testng.TestNG.privateMain(TestNG.java:949)
 338         at org.testng.TestNG.main(TestNG.java:922)
 339 ]]>
 340             </full-stacktrace>
 341           </exception>
 342         </test-method>
 343         <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="187" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:13Z">
 344         </test-method>
 345         <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="170" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:13Z">
 346         </test-method>
 347         <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="122" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:13Z">
 348         </test-method>
 349         <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="151" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:13Z">
 350         </test-method>
 351         <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="105" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:13Z">
 352         </test-method>
 353       </class>
 354       <class name="compbio.runner.msa.MafftTester">
 355         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:38:49Z" finished-at="2011-06-23T10:38:49Z">
 356         </test-method>
 357         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="516" started-at="2011-06-23T10:38:49Z" finished-at="2011-06-23T10:38:49Z">
 358         </test-method>
 359         <test-method status="PASS" signature="testClusterExecute()" name="testClusterExecute" duration-ms="1264" started-at="2011-06-23T10:38:49Z" finished-at="2011-06-23T10:38:51Z">
 360         </test-method>
 361         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:38:49Z" finished-at="2011-06-23T10:38:49Z">
 362         </test-method>
 363         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:38:51Z" finished-at="2011-06-23T10:38:51Z">
 364         </test-method>
 365         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="62" started-at="2011-06-23T10:38:51Z" finished-at="2011-06-23T10:38:51Z">
 366         </test-method>
 367         <test-method status="PASS" signature="testExecute()" name="testExecute" duration-ms="162" started-at="2011-06-23T10:38:51Z" finished-at="2011-06-23T10:38:51Z">
 368         </test-method>
 369         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:38:51Z" finished-at="2011-06-23T10:38:51Z">
 370         </test-method>
 371         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:38:51Z" finished-at="2011-06-23T10:38:51Z">
 372         </test-method>
 373         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="305" started-at="2011-06-23T10:38:51Z" finished-at="2011-06-23T10:38:51Z">
 374         </test-method>
 375         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:38:51Z" finished-at="2011-06-23T10:38:51Z">
 376         </test-method>
 377         <test-method status="PASS" signature="testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" duration-ms="5535" started-at="2011-06-23T10:38:51Z" finished-at="2011-06-23T10:38:57Z">
 378         </test-method>
 379         <test-method status="PASS" signature="testSetInputTester()" name="testSetInputTester" duration-ms="0" started-at="2011-06-23T10:38:57Z" finished-at="2011-06-23T10:38:57Z">
 380         </test-method>
 381         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:38:57Z" finished-at="2011-06-23T10:38:57Z">
 382         </test-method>
 383       </class>
 384       <class name="compbio.data.sequence.ClustalAlignmentUtilTester">
 385         <test-method status="PASS" signature="testReadClustalFile()" name="testReadClustalFile" duration-ms="12" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
 386         </test-method>
 387         <test-method status="PASS" signature="testReadClustalFileLongNames()" name="testReadClustalFileLongNames" duration-ms="19" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
 388         </test-method>
 389         <test-method status="PASS" signature="testReadClustalFileShortNames()" name="testReadClustalFileShortNames" duration-ms="14" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
 390         </test-method>
 391       </class>
 392       <class name="compbio.runner.disorder.IUPredTester">
 393         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:47Z">
 394         </test-method>
 395         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="69" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:47Z">
 396         </test-method>
 397         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:47Z">
 398         </test-method>
 399         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="308" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:47Z">
 400         </test-method>
 401         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:47Z">
 402         </test-method>
 403         <test-method status="PASS" signature="testReadResults()" name="testReadResults" duration-ms="25" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:47Z">
 404         </test-method>
 405         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:47Z">
 406         </test-method>
 407         <test-method status="PASS" signature="testRunLocally()" name="testRunLocally" duration-ms="196" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:47Z">
 408         </test-method>
 409         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:47Z">
 410         </test-method>
 411         <test-method status="PASS" signature="testRunLocallyWithParams()" name="testRunLocallyWithParams" duration-ms="71" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:47Z">
 412         </test-method>
 413         <test-method status="PASS" signature="testRunOnCluster()" name="testRunOnCluster" duration-ms="3308" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:51Z">
 414         </test-method>
 415         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:47Z" finished-at="2011-06-23T10:36:47Z">
 416         </test-method>
 417         <test-method status="PASS" signature="testRunOnClusterAsync()" name="testRunOnClusterAsync" duration-ms="6025" started-at="2011-06-23T10:36:51Z" finished-at="2011-06-23T10:36:57Z">
 418         </test-method>
 419         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:51Z" finished-at="2011-06-23T10:36:51Z">
 420         </test-method>
 421         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:57Z" finished-at="2011-06-23T10:36:57Z">
 422         </test-method>
 423         <test-method status="PASS" signature="testSetParameter()" name="testSetParameter" duration-ms="0" started-at="2011-06-23T10:36:57Z" finished-at="2011-06-23T10:36:57Z">
 424         </test-method>
 425       </class>
 426       <class name="compbio.engine.client.PathValidatorTester">
 427         <test-method status="PASS" signature="testGetClassPath()" name="testGetClassPath" duration-ms="1" started-at="2011-06-23T10:35:12Z" finished-at="2011-06-23T10:35:12Z">
 428         </test-method>
 429         <test-method status="PASS" signature="testIsAbsolutePath()" name="testIsAbsolutePath" duration-ms="0" started-at="2011-06-23T10:35:12Z" finished-at="2011-06-23T10:35:12Z">
 430         </test-method>
 431       </class>
 432       <class name="compbio.stat.collector.StatDBTester">
 433         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="11" started-at="2011-06-23T10:42:27Z" finished-at="2011-06-23T10:42:27Z">
 434         </test-method>
 435         <test-method status="PASS" signature="testVerifyJobsCount()" name="testVerifyJobsCount" duration-ms="412" started-at="2011-06-23T10:42:27Z" finished-at="2011-06-23T10:42:27Z">
 436         </test-method>
 437       </class>
 438       <class name="compbio.stat.servlet.util.StatCollectionTester">
 439         <test-method status="PASS" signature="testGetStats()" name="testGetStats" duration-ms="22" started-at="2011-06-23T10:42:27Z" finished-at="2011-06-23T10:42:27Z">
 440         </test-method>
 441       </class>
 442       <class name="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester">
 443         <test-method status="PASS" signature="testCancel()" name="testCancel" duration-ms="1538" started-at="2011-06-23T10:35:26Z" finished-at="2011-06-23T10:35:27Z">
 444         </test-method>
 445         <test-method status="PASS" signature="testSubmit()" name="testSubmit" duration-ms="3508" started-at="2011-06-23T10:35:27Z" finished-at="2011-06-23T10:35:31Z">
 446         </test-method>
 447       </class>
 448       <class name="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester">
 449         <test-method status="PASS" signature="testCancel()" name="testCancel" duration-ms="1257" started-at="2011-06-23T10:35:16Z" finished-at="2011-06-23T10:35:17Z">
 450           <exception class="compbio.metadata.ResultNotAvailableException">
 451             <message>
 452               <![CDATA[java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/jaba2/local_jobsout/ClustalW#6405924652151282 with file name TO1381.clustal.cluster.out is not found!]]>
 453             </message>
 454             <full-stacktrace>
 455               <![CDATA[compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/jaba2/local_jobsout/ClustalW#6405924652151282 with file name TO1381.clustal.cluster.out is not found!
 456         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:73)
 457         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:34)
 458         at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:207)
 459         at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
 460         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 461         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 462         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 463         at java.lang.reflect.Method.invoke(Method.java:597)
 464         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 465         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 466         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 467         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 468         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 469         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 470         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 471         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 472         at org.testng.TestRunner.run(TestRunner.java:486)
 473         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 474         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 475         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 476         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 477         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 478         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 479         at org.testng.TestNG.run(TestNG.java:784)
 480         at org.testng.TestNG.privateMain(TestNG.java:949)
 481         at org.testng.TestNG.main(TestNG.java:922)
 482 Caused by: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/jaba2/local_jobsout/ClustalW#6405924652151282 with file name TO1381.clustal.cluster.out is not found!
 483         at compbio.runner.Util.readClustalFile(Util.java:93)
 484         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:70)
 485         ... 25 more
 486 ]]>
 487             </full-stacktrace>
 488           </exception>
 489         </test-method>
 490         <test-method status="PASS" signature="testGetJobStatus()" name="testGetJobStatus" duration-ms="4765" started-at="2011-06-23T10:35:17Z" finished-at="2011-06-23T10:35:22Z">
 491         </test-method>
 492         <test-method status="PASS" signature="testSubmit()" name="testSubmit" duration-ms="3976" started-at="2011-06-23T10:35:22Z" finished-at="2011-06-23T10:35:26Z">
 493         </test-method>
 494       </class>
 495       <class name="compbio.runner.conservation.AAConTester">
 496         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 497         </test-method>
 498         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="1493" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:15Z">
 499         </test-method>
 500         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:36:15Z" finished-at="2011-06-23T10:36:15Z">
 501         </test-method>
 502         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="113" started-at="2011-06-23T10:36:15Z" finished-at="2011-06-23T10:36:15Z">
 503         </test-method>
 504         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:15Z" finished-at="2011-06-23T10:36:15Z">
 505         </test-method>
 506         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="775" started-at="2011-06-23T10:36:15Z" finished-at="2011-06-23T10:36:16Z">
 507         </test-method>
 508         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:36:16Z" finished-at="2011-06-23T10:36:16Z">
 509         </test-method>
 510         <test-method status="PASS" signature="testRunLocally()" name="testRunLocally" duration-ms="827" started-at="2011-06-23T10:36:16Z" finished-at="2011-06-23T10:36:17Z">
 511         </test-method>
 512         <test-method status="PASS" signature="testRunLocallyOnTwoCpu()" name="testRunLocallyOnTwoCpu" duration-ms="289" started-at="2011-06-23T10:36:17Z" finished-at="2011-06-23T10:36:17Z">
 513         </test-method>
 514         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:17Z" finished-at="2011-06-23T10:36:17Z">
 515         </test-method>
 516         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:36:17Z" finished-at="2011-06-23T10:36:17Z">
 517         </test-method>
 518         <test-method status="PASS" signature="testRunLocallyWithPreset()" name="testRunLocallyWithPreset" duration-ms="653" started-at="2011-06-23T10:36:17Z" finished-at="2011-06-23T10:36:18Z">
 519         </test-method>
 520         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:36:18Z" finished-at="2011-06-23T10:36:18Z">
 521         </test-method>
 522         <test-method status="PASS" signature="testRunOnCluster()" name="testRunOnCluster" duration-ms="3640" started-at="2011-06-23T10:36:18Z" finished-at="2011-06-23T10:36:22Z">
 523         </test-method>
 524         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:22Z" finished-at="2011-06-23T10:36:22Z">
 525         </test-method>
 526         <test-method status="PASS" signature="testRunOnClusterAsync()" name="testRunOnClusterAsync" duration-ms="5018" started-at="2011-06-23T10:36:22Z" finished-at="2011-06-23T10:36:27Z">
 527         </test-method>
 528       </class>
 529       <class name="compbio.runner.disorder.DisemblTester">
 530         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="44" started-at="2011-06-23T10:36:27Z" finished-at="2011-06-23T10:36:27Z">
 531         </test-method>
 532         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="0" started-at="2011-06-23T10:36:27Z" finished-at="2011-06-23T10:36:27Z">
 533         </test-method>
 534         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:27Z" finished-at="2011-06-23T10:36:27Z">
 535         </test-method>
 536         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:27Z" finished-at="2011-06-23T10:36:27Z">
 537         </test-method>
 538         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:36:27Z" finished-at="2011-06-23T10:36:27Z">
 539         </test-method>
 540         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="1297" started-at="2011-06-23T10:36:27Z" finished-at="2011-06-23T10:36:28Z">
 541         </test-method>
 542         <test-method status="PASS" signature="testRunLocally()" name="testRunLocally" duration-ms="579" started-at="2011-06-23T10:36:28Z" finished-at="2011-06-23T10:36:29Z">
 543         </test-method>
 544         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:28Z" finished-at="2011-06-23T10:36:28Z">
 545         </test-method>
 546         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:29Z" finished-at="2011-06-23T10:36:29Z">
 547         </test-method>
 548         <test-method status="PASS" signature="testRunOnCluster()" name="testRunOnCluster" duration-ms="2047" started-at="2011-06-23T10:36:29Z" finished-at="2011-06-23T10:36:31Z">
 549         </test-method>
 550         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:36:31Z" finished-at="2011-06-23T10:36:31Z">
 551         </test-method>
 552         <test-method status="PASS" signature="testRunOnClusterAsync()" name="testRunOnClusterAsync" duration-ms="6011" started-at="2011-06-23T10:36:31Z" finished-at="2011-06-23T10:36:37Z">
 553         </test-method>
 554       </class>
 555       <class name="compbio.runner._impl.RPSBlastTester">
 556         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 557         </test-method>
 558         <test-method status="PASS" signature="testGetTestArgsCommand()" name="testGetTestArgsCommand" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 559         </test-method>
 560       </class>
 561       <class name="compbio.engine.PulledFileCacheTester">
 562         <test-method status="PASS" signature="test()" name="test" duration-ms="5011" started-at="2011-06-23T10:35:07Z" finished-at="2011-06-23T10:35:12Z">
 563         </test-method>
 564       </class>
 565       <class name="compbio.runner._impl.MclTester">
 566         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 567         </test-method>
 568       </class>
 569       <class name="compbio.engine.cluster.dundee._QueueTester">
 570         <test-method status="PASS" signature="testQueue()" name="testQueue" duration-ms="0" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
 571         </test-method>
 572       </class>
 573       <class name="compbio.engine.LoadBalancerTester">
 574         <test-method status="PASS" signature="testLoadBalance()" name="testLoadBalance" duration-ms="57" started-at="2011-06-23T10:35:07Z" finished-at="2011-06-23T10:35:07Z">
 575         </test-method>
 576       </class>
 577       <class name="compbio.runner.msa.ProbconsParametersTester">
 578         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="36" started-at="2011-06-23T10:39:16Z" finished-at="2011-06-23T10:39:16Z">
 579         </test-method>
 580         <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="1819" started-at="2011-06-23T10:39:16Z" finished-at="2011-06-23T10:39:17Z">
 581         </test-method>
 582         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="22" started-at="2011-06-23T10:39:17Z" finished-at="2011-06-23T10:39:17Z">
 583         </test-method>
 584         <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="0" started-at="2011-06-23T10:39:17Z" finished-at="2011-06-23T10:39:17Z">
 585         </test-method>
 586         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="20" started-at="2011-06-23T10:39:17Z" finished-at="2011-06-23T10:39:18Z">
 587         </test-method>
 588         <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="37102" started-at="2011-06-23T10:39:18Z" finished-at="2011-06-23T10:39:55Z">
 589         </test-method>
 590         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="22" started-at="2011-06-23T10:39:55Z" finished-at="2011-06-23T10:39:55Z">
 591         </test-method>
 592         <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="768" started-at="2011-06-23T10:39:55Z" finished-at="2011-06-23T10:39:55Z">
 593         </test-method>
 594         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="22" started-at="2011-06-23T10:39:55Z" finished-at="2011-06-23T10:39:55Z">
 595         </test-method>
 596         <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="70319" started-at="2011-06-23T10:39:55Z" finished-at="2011-06-23T10:41:06Z">
 597         </test-method>
 598         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="22" started-at="2011-06-23T10:41:06Z" finished-at="2011-06-23T10:41:06Z">
 599         </test-method>
 600         <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="4845" started-at="2011-06-23T10:41:06Z" finished-at="2011-06-23T10:41:11Z">
 601         </test-method>
 602         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="21" started-at="2011-06-23T10:41:11Z" finished-at="2011-06-23T10:41:11Z">
 603         </test-method>
 604         <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="443" started-at="2011-06-23T10:41:11Z" finished-at="2011-06-23T10:41:11Z">
 605         </test-method>
 606         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="22" started-at="2011-06-23T10:41:11Z" finished-at="2011-06-23T10:41:11Z">
 607         </test-method>
 608         <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="1344" started-at="2011-06-23T10:41:11Z" finished-at="2011-06-23T10:41:12Z">
 609         </test-method>
 610       </class>
 611       <class name="compbio.metadata.RunnerConfigTester">
 612         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 613         </test-method>
 614         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 615         </test-method>
 616         <test-method status="PASS" signature="testCreateNumParameterWithoutValidValue()" name="testCreateNumParameterWithoutValidValue" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 617           <exception class="java.lang.IllegalStateException">
 618             <message>
 619               <![CDATA[Attempting to set default value for parameter: Option name: Matrix
 620 Description: DNA weight matrix
 621 URL: null
 622 Is required: false
 623
 624  Without possible values! Please define possible value first!]]>
 625             </message>
 626             <full-stacktrace>
 627               <![CDATA[java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
 628 Description: DNA weight matrix
 629 URL: null
 630 Is required: false
 631
 632  Without possible values! Please define possible value first!
 633         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
 634         at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
 635         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 636         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 637         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 638         at java.lang.reflect.Method.invoke(Method.java:597)
 639         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 640         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 641         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 642         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 643         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 644         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 645         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 646         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 647         at org.testng.TestRunner.run(TestRunner.java:486)
 648         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 649         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 650         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 651         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 652         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 653         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 654         at org.testng.TestNG.run(TestNG.java:784)
 655         at org.testng.TestNG.privateMain(TestNG.java:949)
 656         at org.testng.TestNG.main(TestNG.java:922)
 657 ]]>
 658             </full-stacktrace>
 659           </exception>
 660         </test-method>
 661         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 662         </test-method>
 663         <test-method status="PASS" signature="testCreateParameter()" name="testCreateParameter" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 664           <exception class="compbio.metadata.WrongParameterException">
 665             <message>
 666               <![CDATA[Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
 667 Description: Protein weight matrix
 668 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 669 Is required: true
 670 Option Names:
 671 --AAMATRIX
 672 POSSIBLE VALUES:
 673 BLOSUM
 674 GONNET
 675 ID
 676 PAM
 677
 678 ]]>
 679             </message>
 680             <full-stacktrace>
 681               <![CDATA[compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
 682 Description: Protein weight matrix
 683 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 684 Is required: true
 685 Option Names:
 686 --AAMATRIX
 687 POSSIBLE VALUES:
 688 BLOSUM
 689 GONNET
 690 ID
 691 PAM
 692
 693
 694         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
 695         at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
 696         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 697         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 698         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 699         at java.lang.reflect.Method.invoke(Method.java:597)
 700         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 701         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 702         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 703         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 704         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 705         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 706         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 707         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 708         at org.testng.TestRunner.run(TestRunner.java:486)
 709         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 710         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 711         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 712         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 713         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 714         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 715         at org.testng.TestNG.run(TestNG.java:784)
 716         at org.testng.TestNG.privateMain(TestNG.java:949)
 717         at org.testng.TestNG.main(TestNG.java:922)
 718 ]]>
 719             </full-stacktrace>
 720           </exception>
 721         </test-method>
 722         <test-method status="PASS" signature="testCreateParameterWithValidValueConstrain()" name="testCreateParameterWithValidValueConstrain" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 723         </test-method>
 724         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 725         </test-method>
 726         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 727         </test-method>
 728         <test-method status="PASS" signature="testOptionNoDefaultValidate()" name="testOptionNoDefaultValidate" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 729           <exception class="javax.xml.bind.ValidationException">
 730             <message>
 731               <![CDATA[Default value is required as multiple optionNames are defined for option: Option name: Matrix1
 732 Description: Protein weight matrix
 733 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 734 Is required: true
 735 Option Names:
 736 --AAMATRIX
 737 --ABMAT
 738 --BBBB
 739 ]]>
 740             </message>
 741             <full-stacktrace>
 742               <![CDATA[javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
 743 Description: Protein weight matrix
 744 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 745 Is required: true
 746 Option Names:
 747 --AAMATRIX
 748 --ABMAT
 749 --BBBB
 750
 751         at compbio.metadata.Option.validate(Option.java:317)
 752         at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
 753         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 754         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 755         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 756         at java.lang.reflect.Method.invoke(Method.java:597)
 757         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 758         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 759         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 760         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 761         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 762         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 763         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 764         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 765         at org.testng.TestRunner.run(TestRunner.java:486)
 766         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 767         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 768         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 769         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 770         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 771         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 772         at org.testng.TestNG.run(TestNG.java:784)
 773         at org.testng.TestNG.privateMain(TestNG.java:949)
 774         at org.testng.TestNG.main(TestNG.java:922)
 775 ]]>
 776             </full-stacktrace>
 777           </exception>
 778         </test-method>
 779         <test-method status="PASS" signature="testOptionSetInvalidValue()" name="testOptionSetInvalidValue" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 780           <exception class="compbio.metadata.WrongParameterException">
 781             <message>
 782               <![CDATA[Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
 783 Description: Protein weight matrix
 784 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 785 Is required: true
 786 Option Names:
 787 --AAMATRIX
 788 --ABMAT
 789 --BBBB
 790 ]]>
 791             </message>
 792             <full-stacktrace>
 793               <![CDATA[compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
 794 Description: Protein weight matrix
 795 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 796 Is required: true
 797 Option Names:
 798 --AAMATRIX
 799 --ABMAT
 800 --BBBB
 801
 802         at compbio.metadata.Option.setDefaultValue(Option.java:130)
 803         at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
 804         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 805         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 806         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 807         at java.lang.reflect.Method.invoke(Method.java:597)
 808         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 809         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 810         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 811         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 812         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 813         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 814         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 815         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 816         at org.testng.TestRunner.run(TestRunner.java:486)
 817         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 818         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 819         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 820         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 821         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 822         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 823         at org.testng.TestNG.run(TestNG.java:784)
 824         at org.testng.TestNG.privateMain(TestNG.java:949)
 825         at org.testng.TestNG.main(TestNG.java:922)
 826 ]]>
 827             </full-stacktrace>
 828           </exception>
 829         </test-method>
 830         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="13" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 831         </test-method>
 832         <test-method status="PASS" signature="testOptionToCommand()" name="testOptionToCommand" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 833         </test-method>
 834         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="13" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 835         </test-method>
 836         <test-method status="PASS" signature="testParameterToCommand()" name="testParameterToCommand" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 837         </test-method>
 838         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="13" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 839         </test-method>
 840         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 841         </test-method>
 842         <test-method status="PASS" signature="testValidate()" name="testValidate" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 843         </test-method>
 844         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="13" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 845         </test-method>
 846         <test-method status="PASS" signature="testValidateBoundaryConstrainCheck()" name="testValidateBoundaryConstrainCheck" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 847         </test-method>
 848         <test-method status="PASS" signature="testValidateLowerBoundaryConstrainCheck()" name="testValidateLowerBoundaryConstrainCheck" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 849           <exception class="compbio.metadata.WrongParameterException">
 850             <message>
 851               <![CDATA[Attempting to set default value outside boundaries defined by the constraint: Type: Float
 852 Min: -10.12
 853 Max: 0
 854
 855  For parameter: Option name: Matrix1
 856 Description: Protein weight matrix
 857 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 858 Is required: true
 859 Option Names:
 860 --AAMATRIX
 861 Type: Float
 862 Min: -10.12
 863 Max: 0
 864
 865 ]]>
 866             </message>
 867             <full-stacktrace>
 868               <![CDATA[compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
 869 Min: -10.12
 870 Max: 0
 871
 872  For parameter: Option name: Matrix1
 873 Description: Protein weight matrix
 874 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 875 Is required: true
 876 Option Names:
 877 --AAMATRIX
 878 Type: Float
 879 Min: -10.12
 880 Max: 0
 881
 882
 883         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
 884         at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
 885         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 886         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 887         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 888         at java.lang.reflect.Method.invoke(Method.java:597)
 889         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 890         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 891         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 892         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 893         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 894         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 895         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 896         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 897         at org.testng.TestRunner.run(TestRunner.java:486)
 898         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 899         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 900         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 901         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 902         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 903         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 904         at org.testng.TestNG.run(TestNG.java:784)
 905         at org.testng.TestNG.privateMain(TestNG.java:949)
 906         at org.testng.TestNG.main(TestNG.java:922)
 907 ]]>
 908             </full-stacktrace>
 909           </exception>
 910         </test-method>
 911         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="13" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 912         </test-method>
 913         <test-method status="PASS" signature="testValidateUpperBoundaryConstrainCheck()" name="testValidateUpperBoundaryConstrainCheck" duration-ms="1" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 914           <exception class="compbio.metadata.WrongParameterException">
 915             <message>
 916               <![CDATA[Attempting to set default value outside boundaries defined by the constraint: Type: Float
 917 Min: -10.12
 918 Max: 0
 919
 920  For parameter: Option name: Matrix1
 921 Description: Protein weight matrix
 922 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 923 Is required: true
 924 Option Names:
 925 --AAMATRIX
 926 Type: Float
 927 Min: -10.12
 928 Max: 0
 929
 930 ]]>
 931             </message>
 932             <full-stacktrace>
 933               <![CDATA[compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
 934 Min: -10.12
 935 Max: 0
 936
 937  For parameter: Option name: Matrix1
 938 Description: Protein weight matrix
 939 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 940 Is required: true
 941 Option Names:
 942 --AAMATRIX
 943 Type: Float
 944 Min: -10.12
 945 Max: 0
 946
 947
 948         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
 949         at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
 950         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 951         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 952         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 953         at java.lang.reflect.Method.invoke(Method.java:597)
 954         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 955         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 956         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 957         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 958         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 959         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 960         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 961         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 962         at org.testng.TestRunner.run(TestRunner.java:486)
 963         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 964         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 965         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 966         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 967         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 968         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 969         at org.testng.TestNG.run(TestNG.java:784)
 970         at org.testng.TestNG.privateMain(TestNG.java:949)
 971         at org.testng.TestNG.main(TestNG.java:922)
 972 ]]>
 973             </full-stacktrace>
 974           </exception>
 975         </test-method>
 976         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="13" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 977         </test-method>
 978         <test-method status="PASS" signature="testValidateValueConstrain()" name="testValidateValueConstrain" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
 979           <exception class="javax.xml.bind.ValidationException">
 980             <message>
 981               <![CDATA[Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
 982 ]]>
 983             </message>
 984             <full-stacktrace>
 985               <![CDATA[javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
 986
 987         at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
 988         at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
 989         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 990         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 991         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 992         at java.lang.reflect.Method.invoke(Method.java:597)
 993         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 994         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 995         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 996         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 997         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 998         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 999         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1000         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1001         at org.testng.TestRunner.run(TestRunner.java:486)
1002         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1003         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1004         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1005         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1006         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1007         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1008         at org.testng.TestNG.run(TestNG.java:784)
1009         at org.testng.TestNG.privateMain(TestNG.java:949)
1010         at org.testng.TestNG.main(TestNG.java:922)
1011 ]]>
1012             </full-stacktrace>
1013           </exception>
1014         </test-method>
1015       </class>
1016       <class name="compbio.runner.msa.MafftParametersTester">
1017         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="39" started-at="2011-06-23T10:38:32Z" finished-at="2011-06-23T10:38:32Z">
1018         </test-method>
1019         <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="3027" started-at="2011-06-23T10:38:32Z" finished-at="2011-06-23T10:38:35Z">
1020         </test-method>
1021         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="67" started-at="2011-06-23T10:38:35Z" finished-at="2011-06-23T10:38:35Z">
1022         </test-method>
1023         <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="0" started-at="2011-06-23T10:38:35Z" finished-at="2011-06-23T10:38:35Z">
1024         </test-method>
1025         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="37" started-at="2011-06-23T10:38:35Z" finished-at="2011-06-23T10:38:35Z">
1026         </test-method>
1027         <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="1461" started-at="2011-06-23T10:38:35Z" finished-at="2011-06-23T10:38:37Z">
1028         </test-method>
1029         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="38" started-at="2011-06-23T10:38:37Z" finished-at="2011-06-23T10:38:37Z">
1030         </test-method>
1031         <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="886" started-at="2011-06-23T10:38:37Z" finished-at="2011-06-23T10:38:37Z">
1032         </test-method>
1033         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="37" started-at="2011-06-23T10:38:37Z" finished-at="2011-06-23T10:38:38Z">
1034         </test-method>
1035         <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="3530" started-at="2011-06-23T10:38:38Z" finished-at="2011-06-23T10:38:41Z">
1036         </test-method>
1037         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="37" started-at="2011-06-23T10:38:41Z" finished-at="2011-06-23T10:38:41Z">
1038         </test-method>
1039         <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="4507" started-at="2011-06-23T10:38:41Z" finished-at="2011-06-23T10:38:46Z">
1040         </test-method>
1041         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="34" started-at="2011-06-23T10:38:46Z" finished-at="2011-06-23T10:38:46Z">
1042         </test-method>
1043         <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="971" started-at="2011-06-23T10:38:46Z" finished-at="2011-06-23T10:38:47Z">
1044         </test-method>
1045         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="40" started-at="2011-06-23T10:38:47Z" finished-at="2011-06-23T10:38:47Z">
1046         </test-method>
1047         <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="1179" started-at="2011-06-23T10:38:47Z" finished-at="2011-06-23T10:38:48Z">
1048         </test-method>
1049         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="36" started-at="2011-06-23T10:38:48Z" finished-at="2011-06-23T10:38:48Z">
1050         </test-method>
1051         <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="965" started-at="2011-06-23T10:38:48Z" finished-at="2011-06-23T10:38:49Z">
1052         </test-method>
1053       </class>
1054       <class name="compbio.runner.disorder.JronnTester">
1055         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:57Z" finished-at="2011-06-23T10:36:57Z">
1056         </test-method>
1057         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="18639" started-at="2011-06-23T10:36:57Z" finished-at="2011-06-23T10:37:15Z">
1058         </test-method>
1059         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="45" started-at="2011-06-23T10:37:15Z" finished-at="2011-06-23T10:37:15Z">
1060         </test-method>
1061         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:37:15Z" finished-at="2011-06-23T10:37:15Z">
1062         </test-method>
1063         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:37:15Z" finished-at="2011-06-23T10:37:15Z">
1064         </test-method>
1065         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="18613" started-at="2011-06-23T10:37:15Z" finished-at="2011-06-23T10:37:34Z">
1066         </test-method>
1067         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:37:34Z" finished-at="2011-06-23T10:37:34Z">
1068         </test-method>
1069         <test-method status="PASS" signature="testRunLocally()" name="testRunLocally" duration-ms="18541" started-at="2011-06-23T10:37:34Z" finished-at="2011-06-23T10:37:52Z">
1070         </test-method>
1071         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:37:52Z" finished-at="2011-06-23T10:37:52Z">
1072         </test-method>
1073         <test-method status="PASS" signature="testRunLocallyOnTwoCpu()" name="testRunLocallyOnTwoCpu" duration-ms="7131" started-at="2011-06-23T10:37:52Z" finished-at="2011-06-23T10:38:00Z">
1074         </test-method>
1075         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:38:00Z" finished-at="2011-06-23T10:38:00Z">
1076         </test-method>
1077         <test-method status="PASS" signature="testRunOnCluster()" name="testRunOnCluster" duration-ms="13058" started-at="2011-06-23T10:38:00Z" finished-at="2011-06-23T10:38:13Z">
1078         </test-method>
1079         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:38:13Z" finished-at="2011-06-23T10:38:13Z">
1080         </test-method>
1081         <test-method status="PASS" signature="testRunOnClusterAsync()" name="testRunOnClusterAsync" duration-ms="11022" started-at="2011-06-23T10:38:13Z" finished-at="2011-06-23T10:38:24Z">
1082         </test-method>
1083       </class>
1084       <class name="compbio.runner._impl.RonnTester">
1085         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1086         </test-method>
1087       </class>
1088       <class name="compbio.runner.msa.ProbconsTester">
1089         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="455" started-at="2011-06-23T10:41:12Z" finished-at="2011-06-23T10:41:13Z">
1090         </test-method>
1091         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:12Z" finished-at="2011-06-23T10:41:12Z">
1092         </test-method>
1093         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:13Z" finished-at="2011-06-23T10:41:13Z">
1094         </test-method>
1095         <test-method status="PASS" signature="testClusterExecute()" name="testClusterExecute" duration-ms="2710" started-at="2011-06-23T10:41:13Z" finished-at="2011-06-23T10:41:16Z">
1096         </test-method>
1097         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:16Z" finished-at="2011-06-23T10:41:16Z">
1098         </test-method>
1099         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="89" started-at="2011-06-23T10:41:16Z" finished-at="2011-06-23T10:41:16Z">
1100         </test-method>
1101         <test-method status="PASS" signature="testExecute()" name="testExecute" duration-ms="455" started-at="2011-06-23T10:41:16Z" finished-at="2011-06-23T10:41:16Z">
1102         </test-method>
1103         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:16Z" finished-at="2011-06-23T10:41:16Z">
1104         </test-method>
1105         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:41:16Z" finished-at="2011-06-23T10:41:16Z">
1106         </test-method>
1107         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="527" started-at="2011-06-23T10:41:16Z" finished-at="2011-06-23T10:41:17Z">
1108         </test-method>
1109         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:41:17Z" finished-at="2011-06-23T10:41:17Z">
1110         </test-method>
1111         <test-method status="PASS" signature="testSetInputTester()" name="testSetInputTester" duration-ms="0" started-at="2011-06-23T10:41:17Z" finished-at="2011-06-23T10:41:17Z">
1112         </test-method>
1113       </class>
1114       <class name="compbio.engine.conf.PropertyHelperManagerTester">
1115         <test-method status="PASS" signature="testLoadResources()" name="testLoadResources" is-config="true" duration-ms="3" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1116         </test-method>
1117         <test-method status="PASS" signature="testClusterEngineConf()" name="testClusterEngineConf" duration-ms="1" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1118         </test-method>
1119         <test-method status="PASS" signature="validateClustalConfiguration()" name="validateClustalConfiguration" duration-ms="0" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1120         </test-method>
1121         <test-method status="PASS" signature="validateMafftConfiguration()" name="validateMafftConfiguration" duration-ms="2" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1122         </test-method>
1123         <test-method status="PASS" signature="validateMuscleConfiguration()" name="validateMuscleConfiguration" duration-ms="0" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1124         </test-method>
1125         <test-method status="PASS" signature="validateTcoffeeConfiguration()" name="validateTcoffeeConfiguration" duration-ms="0" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1126         </test-method>
1127       </class>
1128       <class name="compbio.metadata.OptionCombinatorTester">
1129         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="109" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:13Z">
1130         </test-method>
1131         <test-method status="PASS" signature="testgetAllOptions()" name="testgetAllOptions" duration-ms="1" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:13Z">
1132         </test-method>
1133         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="101" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:14Z">
1134         </test-method>
1135         <test-method status="PASS" signature="testgetAllParameters()" name="testgetAllParameters" duration-ms="3" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1136         </test-method>
1137       </class>
1138       <class name="compbio.engine.FilePullerTester">
1139         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="298" started-at="2011-06-23T10:34:54Z" finished-at="2011-06-23T10:34:54Z">
1140         </test-method>
1141         <test-method status="PASS" signature="loadPresets()" name="loadPresets" is-config="true" duration-ms="62" started-at="2011-06-23T10:34:54Z" finished-at="2011-06-23T10:34:54Z">
1142         </test-method>
1143         <test-method status="PASS" signature="testPull()" name="testPull" duration-ms="14" started-at="2011-06-23T10:34:54Z" finished-at="2011-06-23T10:34:54Z">
1144         </test-method>
1145         <test-method status="PASS" signature="testCache()" name="testCache" duration-ms="6008" started-at="2011-06-23T10:34:54Z" depends-on-methods="compbio.engine.FilePullerTester.testPull" finished-at="2011-06-23T10:35:00Z">
1146         </test-method>
1147         <test-method status="PASS" signature="testGetDelay()" name="testGetDelay" duration-ms="0" started-at="2011-06-23T10:35:07Z" finished-at="2011-06-23T10:35:07Z">
1148         </test-method>
1149         <test-method status="PASS" signature="testGet()" name="testGet" duration-ms="2" started-at="2011-06-23T10:35:07Z" finished-at="2011-06-23T10:35:07Z">
1150         </test-method>
1151       </class>
1152       <class name="compbio.runner.msa.MuscleTester">
1153         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:39:11Z" finished-at="2011-06-23T10:39:11Z">
1154         </test-method>
1155         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="520" started-at="2011-06-23T10:39:11Z" finished-at="2011-06-23T10:39:11Z">
1156         </test-method>
1157         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:39:11Z" finished-at="2011-06-23T10:39:11Z">
1158         </test-method>
1159         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="43" started-at="2011-06-23T10:39:11Z" finished-at="2011-06-23T10:39:11Z">
1160         </test-method>
1161         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:39:11Z" finished-at="2011-06-23T10:39:11Z">
1162         </test-method>
1163         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="233" started-at="2011-06-23T10:39:11Z" finished-at="2011-06-23T10:39:12Z">
1164         </test-method>
1165         <test-method status="PASS" signature="testRunLocally()" name="testRunLocally" duration-ms="100" started-at="2011-06-23T10:39:12Z" finished-at="2011-06-23T10:39:12Z">
1166         </test-method>
1167         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:39:12Z" finished-at="2011-06-23T10:39:12Z">
1168         </test-method>
1169         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:39:12Z" finished-at="2011-06-23T10:39:12Z">
1170         </test-method>
1171         <test-method status="PASS" signature="testRunOnCluster()" name="testRunOnCluster" duration-ms="3867" started-at="2011-06-23T10:39:12Z" finished-at="2011-06-23T10:39:16Z">
1172         </test-method>
1173       </class>
1174       <class name="compbio.runner.msa.TcoffeeTester">
1175         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:45Z" finished-at="2011-06-23T10:41:45Z">
1176         </test-method>
1177         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="516" started-at="2011-06-23T10:41:45Z" finished-at="2011-06-23T10:41:46Z">
1178         </test-method>
1179         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:41:46Z" finished-at="2011-06-23T10:41:46Z">
1180         </test-method>
1181         <test-method status="PASS" signature="testClusterExecute()" name="testClusterExecute" duration-ms="5084" started-at="2011-06-23T10:41:46Z" finished-at="2011-06-23T10:41:51Z">
1182         </test-method>
1183         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2011-06-23T10:41:51Z" finished-at="2011-06-23T10:41:51Z">
1184         </test-method>
1185         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="39" started-at="2011-06-23T10:41:51Z" finished-at="2011-06-23T10:41:51Z">
1186         </test-method>
1187         <test-method status="PASS" signature="testExecute()" name="testExecute" duration-ms="364" started-at="2011-06-23T10:41:51Z" finished-at="2011-06-23T10:41:51Z">
1188         </test-method>
1189         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:51Z" finished-at="2011-06-23T10:41:51Z">
1190         </test-method>
1191         <test-method status="PASS" signature="testNcore()" name="testNcore" duration-ms="0" started-at="2011-06-23T10:41:51Z" finished-at="2011-06-23T10:41:51Z">
1192         </test-method>
1193         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:51Z" finished-at="2011-06-23T10:41:51Z">
1194         </test-method>
1195         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:51Z" finished-at="2011-06-23T10:41:51Z">
1196         </test-method>
1197         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="769" started-at="2011-06-23T10:41:51Z" finished-at="2011-06-23T10:41:52Z">
1198         </test-method>
1199       </class>
1200       <class name="compbio.runner.msa.LimitTester">
1201         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="22" started-at="2011-06-23T10:38:32Z" finished-at="2011-06-23T10:38:32Z">
1202         </test-method>
1203         <test-method status="PASS" signature="testLimitExceeded()" name="testLimitExceeded" duration-ms="14" started-at="2011-06-23T10:38:32Z" finished-at="2011-06-23T10:38:32Z">
1204         </test-method>
1205         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="18" started-at="2011-06-23T10:38:32Z" finished-at="2011-06-23T10:38:32Z">
1206         </test-method>
1207         <test-method status="PASS" signature="testLoadLimits()" name="testLoadLimits" duration-ms="0" started-at="2011-06-23T10:38:32Z" finished-at="2011-06-23T10:38:32Z">
1208         </test-method>
1209       </class>
1210       <class name="compbio.runner._impl.OBTester">
1211         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1212         </test-method>
1213         <test-method status="PASS" signature="testGetTestArgsCommand()" name="testGetTestArgsCommand" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1214         </test-method>
1215       </class>
1216       <class name="compbio.engine.local.LocalRunnerTester">
1217         <test-method status="PASS" signature="testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" duration-ms="49" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:13Z">
1218           <exception class="java.util.concurrent.CancellationException">
1219             <full-stacktrace>
1220               <![CDATA[java.util.concurrent.CancellationException
1221         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
1222         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
1223         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
1224         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
1225         at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
1226         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1227         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1228         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1229         at java.lang.reflect.Method.invoke(Method.java:597)
1230         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1231         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1232         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1233         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1234         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1235         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1236         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1237         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1238         at org.testng.TestRunner.run(TestRunner.java:486)
1239         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1240         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1241         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1242         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1243         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1244         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1245         at org.testng.TestNG.run(TestNG.java:784)
1246         at org.testng.TestNG.privateMain(TestNG.java:949)
1247         at org.testng.TestNG.main(TestNG.java:922)
1248 ]]>
1249             </full-stacktrace>
1250           </exception>
1251         </test-method>
1252         <test-method status="PASS" signature="testCancelLocally()" name="testCancelLocally" duration-ms="17" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:13Z">
1253           <exception class="java.util.concurrent.CancellationException">
1254             <full-stacktrace>
1255               <![CDATA[java.util.concurrent.CancellationException
1256         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
1257         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
1258         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
1259         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
1260         at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
1261         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1262         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1263         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1264         at java.lang.reflect.Method.invoke(Method.java:597)
1265         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1266         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1267         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1268         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1269         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1270         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1271         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1272         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1273         at org.testng.TestRunner.run(TestRunner.java:486)
1274         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1275         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1276         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1277         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1278         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1279         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1280         at org.testng.TestNG.run(TestNG.java:784)
1281         at org.testng.TestNG.privateMain(TestNG.java:949)
1282         at org.testng.TestNG.main(TestNG.java:922)
1283 ]]>
1284             </full-stacktrace>
1285           </exception>
1286         </test-method>
1287         <test-method status="PASS" signature="testMultipleCancelLocally()" name="testMultipleCancelLocally" duration-ms="44" started-at="2011-06-23T10:36:13Z" finished-at="2011-06-23T10:36:13Z">
1288           <exception class="java.util.concurrent.CancellationException">
1289             <full-stacktrace>
1290               <![CDATA[java.util.concurrent.CancellationException
1291         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
1292         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
1293         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
1294         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
1295         at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
1296         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1297         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1298         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1299         at java.lang.reflect.Method.invoke(Method.java:597)
1300         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1301         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1302         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1303         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1304         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1305         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1306         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1307         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1308         at org.testng.TestRunner.run(TestRunner.java:486)
1309         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1310         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1311         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1312         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1313         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1314         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1315         at org.testng.TestNG.run(TestNG.java:784)
1316         at org.testng.TestNG.privateMain(TestNG.java:949)
1317         at org.testng.TestNG.main(TestNG.java:922)
1318 ]]>
1319             </full-stacktrace>
1320           </exception>
1321         </test-method>
1322       </class>
1323       <class name="compbio.runner._impl.Tmhmm2Tester">
1324         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1325         </test-method>
1326       </class>
1327       <class name="compbio.runner.msa.MuscleParametersTester">
1328         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="48" started-at="2011-06-23T10:38:57Z" finished-at="2011-06-23T10:38:57Z">
1329         </test-method>
1330         <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="4387" started-at="2011-06-23T10:38:57Z" finished-at="2011-06-23T10:39:01Z">
1331         </test-method>
1332         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="37" started-at="2011-06-23T10:39:01Z" finished-at="2011-06-23T10:39:01Z">
1333         </test-method>
1334         <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="1" started-at="2011-06-23T10:39:01Z" finished-at="2011-06-23T10:39:01Z">
1335         </test-method>
1336         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="34" started-at="2011-06-23T10:39:01Z" finished-at="2011-06-23T10:39:01Z">
1337         </test-method>
1338         <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="1977" started-at="2011-06-23T10:39:01Z" finished-at="2011-06-23T10:39:03Z">
1339         </test-method>
1340         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="36" started-at="2011-06-23T10:39:03Z" finished-at="2011-06-23T10:39:03Z">
1341         </test-method>
1342         <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="1112" started-at="2011-06-23T10:39:03Z" finished-at="2011-06-23T10:39:04Z">
1343         </test-method>
1344         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="35" started-at="2011-06-23T10:39:04Z" finished-at="2011-06-23T10:39:04Z">
1345         </test-method>
1346         <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="2749" started-at="2011-06-23T10:39:04Z" finished-at="2011-06-23T10:39:07Z">
1347         </test-method>
1348         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="34" started-at="2011-06-23T10:39:07Z" finished-at="2011-06-23T10:39:07Z">
1349         </test-method>
1350         <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="100" started-at="2011-06-23T10:39:07Z" finished-at="2011-06-23T10:39:07Z">
1351         </test-method>
1352         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="35" started-at="2011-06-23T10:39:07Z" finished-at="2011-06-23T10:39:07Z">
1353         </test-method>
1354         <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="1360" started-at="2011-06-23T10:39:07Z" finished-at="2011-06-23T10:39:09Z">
1355         </test-method>
1356         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="35" started-at="2011-06-23T10:39:09Z" finished-at="2011-06-23T10:39:09Z">
1357         </test-method>
1358         <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="1919" started-at="2011-06-23T10:39:09Z" finished-at="2011-06-23T10:39:11Z">
1359         </test-method>
1360         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="36" started-at="2011-06-23T10:39:11Z" finished-at="2011-06-23T10:39:11Z">
1361         </test-method>
1362         <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="242" started-at="2011-06-23T10:39:11Z" finished-at="2011-06-23T10:39:11Z">
1363         </test-method>
1364       </class>
1365       <class name="compbio.data.sequence.FastaSequenceGeneratorTester">
1366         <test-method status="PASS" signature="testProteinSequenceGeneration()" name="testProteinSequenceGeneration" duration-ms="7" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1367         </test-method>
1368       </class>
1369       <class name="compbio.engine.cluster.drmaa.ClusterSessionTester">
1370         <test-method status="PASS" signature="testTaskList()" name="testTaskList" duration-ms="3953" started-at="2011-06-23T10:35:12Z" finished-at="2011-06-23T10:35:16Z">
1371         </test-method>
1372       </class>
1373       <class name="compbio.data.sequence.FastaReaderTester">
1374         <test-method status="PASS" signature="test()" name="test" duration-ms="18" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1375         </test-method>
1376       </class>
1377       <class name="compbio.data.sequence.FastaSequenceTester">
1378         <test-method status="PASS" signature="testGetFormattedFasta()" name="testGetFormattedFasta" duration-ms="0" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1379         </test-method>
1380       </class>
1381       <class name="compbio.data.sequence.SequenceUtilTester">
1382         <test-method status="PASS" signature="loadJronnFile()" name="loadJronnFile" duration-ms="27" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1383         </test-method>
1384         <test-method status="PASS" signature="testCleanProteinSequence()" name="testCleanProteinSequence" duration-ms="1" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1385         </test-method>
1386         <test-method status="PASS" signature="testDeepCleanSequence()" name="testDeepCleanSequence" duration-ms="0" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1387         </test-method>
1388         <test-method status="PASS" signature="testReadAAConResults()" name="testReadAAConResults" duration-ms="269" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1389         </test-method>
1390         <test-method status="PASS" signature="testCleanSequence()" name="testCleanSequence" duration-ms="0" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1391         </test-method>
1392         <test-method status="PASS" signature="testReadDisemblResults()" name="testReadDisemblResults" duration-ms="125" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1393         </test-method>
1394         <test-method status="PASS" signature="testReadGlobPlotResults()" name="testReadGlobPlotResults" duration-ms="104" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1395         </test-method>
1396         <test-method status="PASS" signature="testReadIUPredForGlobDomain()" name="testReadIUPredForGlobDomain" duration-ms="6" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1397         </test-method>
1398         <test-method status="PASS" signature="testReadIUPredForShortAndLongDisorder()" name="testReadIUPredForShortAndLongDisorder" duration-ms="36" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1399         </test-method>
1400         <test-method status="PASS" signature="testReadWriteFasta()" name="testReadWriteFasta" duration-ms="8" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:07Z">
1401         </test-method>
1402         <test-method status="PASS" signature="testisNonAmbNucleotideSequence()" name="testisNonAmbNucleotideSequence" duration-ms="1" started-at="2011-06-23T10:35:07Z" finished-at="2011-06-23T10:35:07Z">
1403         </test-method>
1404         <test-method status="PASS" signature="testisProteinSequence()" name="testisProteinSequence" duration-ms="0" started-at="2011-06-23T10:35:07Z" finished-at="2011-06-23T10:35:07Z">
1405         </test-method>
1406       </class>
1407       <class name="compbio.runner.msa.TcoffeeParametersTester">
1408         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:17Z" finished-at="2011-06-23T10:41:17Z">
1409         </test-method>
1410         <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="4098" started-at="2011-06-23T10:41:17Z" finished-at="2011-06-23T10:41:21Z">
1411         </test-method>
1412         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:21Z" finished-at="2011-06-23T10:41:21Z">
1413         </test-method>
1414         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:21Z" finished-at="2011-06-23T10:41:21Z">
1415         </test-method>
1416         <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="0" started-at="2011-06-23T10:41:21Z" finished-at="2011-06-23T10:41:21Z">
1417         </test-method>
1418         <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="4319" started-at="2011-06-23T10:41:21Z" finished-at="2011-06-23T10:41:25Z">
1419         </test-method>
1420         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="1" started-at="2011-06-23T10:41:25Z" finished-at="2011-06-23T10:41:25Z">
1421         </test-method>
1422         <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="2887" started-at="2011-06-23T10:41:25Z" finished-at="2011-06-23T10:41:28Z">
1423         </test-method>
1424         <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="8762" started-at="2011-06-23T10:41:28Z" finished-at="2011-06-23T10:41:37Z">
1425         </test-method>
1426         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:28Z" finished-at="2011-06-23T10:41:28Z">
1427         </test-method>
1428         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:37Z" finished-at="2011-06-23T10:41:37Z">
1429         </test-method>
1430         <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="3850" started-at="2011-06-23T10:41:37Z" finished-at="2011-06-23T10:41:41Z">
1431         </test-method>
1432         <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="377" started-at="2011-06-23T10:41:41Z" finished-at="2011-06-23T10:41:41Z">
1433         </test-method>
1434         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:41Z" finished-at="2011-06-23T10:41:41Z">
1435         </test-method>
1436         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:41Z" finished-at="2011-06-23T10:41:41Z">
1437         </test-method>
1438         <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="3800" started-at="2011-06-23T10:41:41Z" finished-at="2011-06-23T10:41:45Z">
1439         </test-method>
1440         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2011-06-23T10:41:45Z" finished-at="2011-06-23T10:41:45Z">
1441         </test-method>
1442         <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="214" started-at="2011-06-23T10:41:45Z" finished-at="2011-06-23T10:41:45Z">
1443         </test-method>
1444       </class>
1445       <class name="compbio.runner.msa.ClustalWTester">
1446         <test-method status="PASS" signature="testRunWithMatrix()" name="testRunWithMatrix" duration-ms="130" started-at="2011-06-23T10:38:24Z" finished-at="2011-06-23T10:38:24Z">
1447         </test-method>
1448         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="46" started-at="2011-06-23T10:38:24Z" finished-at="2011-06-23T10:38:24Z">
1449         </test-method>
1450         <test-method status="PASS" signature="testRunLocally()" name="testRunLocally" duration-ms="132" started-at="2011-06-23T10:38:24Z" finished-at="2011-06-23T10:38:24Z">
1451         </test-method>
1452         <test-method status="PASS" signature="readStatisticsClusterExecution()" name="readStatisticsClusterExecution" duration-ms="1640" started-at="2011-06-23T10:38:24Z" finished-at="2011-06-23T10:38:26Z">
1453         </test-method>
1454         <test-method status="PASS" signature="testRunOnCluster()" name="testRunOnCluster" duration-ms="5003" started-at="2011-06-23T10:38:26Z" finished-at="2011-06-23T10:38:31Z">
1455         </test-method>
1456         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="518" started-at="2011-06-23T10:38:31Z" finished-at="2011-06-23T10:38:31Z">
1457         </test-method>
1458         <test-method status="PASS" signature="testOptionsLocally()" name="testOptionsLocally" duration-ms="429" started-at="2011-06-23T10:38:31Z" finished-at="2011-06-23T10:38:32Z">
1459         </test-method>
1460         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="303" started-at="2011-06-23T10:38:32Z" finished-at="2011-06-23T10:38:32Z">
1461         </test-method>
1462       </class>
1463       <class name="compbio.engine.cluster.drmaa.UtilTester">
1464         <test-method status="PASS" signature="testParser()" name="testParser" duration-ms="1" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1465         </test-method>
1466       </class>
1467       <class name="compbio.engine.conf.DirectoryManagerTester">
1468         <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="104" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1469         </test-method>
1470         <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="101" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1471         </test-method>
1472         <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="98" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1473         </test-method>
1474         <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="97" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1475         </test-method>
1476       </class>
1477       <class name="compbio.metadata.PresetTester">
1478         <test-method status="PASS" signature="marshallPreset()" name="marshallPreset" duration-ms="14" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1479         </test-method>
1480         <test-method status="PASS" signature="testPresetWithMuptiOptions()" name="testPresetWithMuptiOptions" duration-ms="1" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1481         </test-method>
1482         <test-method status="PASS" signature="validatePresets()" name="validatePresets" duration-ms="1" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1483         </test-method>
1484       </class>
1485       <class name="compbio.metadata.OptionMarshallerTester">
1486         <test-method status="PASS" signature="testMarshalling()" name="testMarshalling" duration-ms="33" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1487           <exception class="javax.xml.bind.MarshalException">
1488             <full-stacktrace>
1489               <![CDATA[javax.xml.bind.MarshalException
1490  - with linked exception:
1491 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
1492         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:323)
1493         at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
1494         at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
1495         at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
1496         at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
1497         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1498         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1499         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1500         at java.lang.reflect.Method.invoke(Method.java:597)
1501         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1502         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1503         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1504         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1505         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1506         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1507         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1508         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1509         at org.testng.TestRunner.run(TestRunner.java:486)
1510         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1511         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1512         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1513         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1514         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1515         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1516         at org.testng.TestNG.run(TestNG.java:784)
1517         at org.testng.TestNG.privateMain(TestNG.java:949)
1518         at org.testng.TestNG.main(TestNG.java:922)
1519 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.
1520         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
1521         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
1522         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
1523         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
1524         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
1525         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
1526         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
1527         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
1528         at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
1529         at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
1530         at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:128)
1531         at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:106)
1532         at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:310)
1533         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:699)
1534         at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:69)
1535         at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:172)
1536         at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:159)
1537         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:344)
1538         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:597)
1539         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:328)
1540         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:498)
1541         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:320)
1542         ... 26 more
1543 ]]>
1544             </full-stacktrace>
1545           </exception>
1546         </test-method>
1547         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1548         </test-method>
1549         <test-method status="PASS" signature="testUnMarshalling()" name="testUnMarshalling" duration-ms="65" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1550         </test-method>
1551         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2011-06-23T10:36:14Z" finished-at="2011-06-23T10:36:14Z">
1552         </test-method>
1553       </class>
1554       <class name="compbio.runner.msa.ClustalWParametersTester">
1555         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="52" started-at="2011-06-23T10:35:00Z" finished-at="2011-06-23T10:35:00Z">
1556         </test-method>
1557         <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="1649" started-at="2011-06-23T10:35:00Z" finished-at="2011-06-23T10:35:02Z">
1558         </test-method>
1559         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="53" started-at="2011-06-23T10:35:02Z" finished-at="2011-06-23T10:35:02Z">
1560         </test-method>
1561         <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="1" started-at="2011-06-23T10:35:02Z" finished-at="2011-06-23T10:35:02Z">
1562         </test-method>
1563         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="55" started-at="2011-06-23T10:35:02Z" finished-at="2011-06-23T10:35:02Z">
1564         </test-method>
1565         <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="678" started-at="2011-06-23T10:35:02Z" finished-at="2011-06-23T10:35:02Z">
1566         </test-method>
1567         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="51" started-at="2011-06-23T10:35:02Z" finished-at="2011-06-23T10:35:03Z">
1568         </test-method>
1569         <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="682" started-at="2011-06-23T10:35:03Z" finished-at="2011-06-23T10:35:03Z">
1570         </test-method>
1571         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="56" started-at="2011-06-23T10:35:03Z" finished-at="2011-06-23T10:35:03Z">
1572         </test-method>
1573         <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="672" started-at="2011-06-23T10:35:03Z" finished-at="2011-06-23T10:35:04Z">
1574         </test-method>
1575         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="48" started-at="2011-06-23T10:35:04Z" finished-at="2011-06-23T10:35:04Z">
1576         </test-method>
1577         <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="129" started-at="2011-06-23T10:35:04Z" finished-at="2011-06-23T10:35:04Z">
1578         </test-method>
1579         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="48" started-at="2011-06-23T10:35:04Z" finished-at="2011-06-23T10:35:04Z">
1580         </test-method>
1581         <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="396" started-at="2011-06-23T10:35:04Z" finished-at="2011-06-23T10:35:05Z">
1582         </test-method>
1583         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="48" started-at="2011-06-23T10:35:05Z" finished-at="2011-06-23T10:35:05Z">
1584         </test-method>
1585         <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="1074" started-at="2011-06-23T10:35:05Z" finished-at="2011-06-23T10:35:06Z">
1586         </test-method>
1587         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="49" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1588         </test-method>
1589         <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="129" started-at="2011-06-23T10:35:06Z" finished-at="2011-06-23T10:35:06Z">
1590         </test-method>
1591       </class>
1592       <class name="compbio.engine.conf.RunnerConfigMarshallerTester">
1593         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1594         </test-method>
1595         <test-method status="PASS" signature="testMarshalling()" name="testMarshalling" duration-ms="4" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1596         </test-method>
1597         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="13" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1598         </test-method>
1599         <test-method status="PASS" signature="testSchemaFromCodeGeneration()" name="testSchemaFromCodeGeneration" duration-ms="130" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1600         </test-method>
1601         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1602         </test-method>
1603         <test-method status="PASS" signature="testUnMarshalling()" name="testUnMarshalling" duration-ms="17" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1604         </test-method>
1605         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1606         </test-method>
1607         <test-method status="PASS" signature="testValidation()" name="testValidation" duration-ms="82" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1608         </test-method>
1609         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1610         </test-method>
1611         <test-method status="PASS" signature="testValidationOnMarshalling()" name="testValidationOnMarshalling" duration-ms="10" started-at="2011-06-23T10:35:31Z" finished-at="2011-06-23T10:35:31Z">
1612           <exception class="javax.xml.bind.MarshalException">
1613             <full-stacktrace>
1614               <![CDATA[javax.xml.bind.MarshalException
1615  - with linked exception:
1616 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
1617         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:323)
1618         at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
1619         at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
1620         at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
1621         at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:259)
1622         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1623         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1624         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1625         at java.lang.reflect.Method.invoke(Method.java:597)
1626         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1627         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1628         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1629         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1630         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1631         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1632         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1633         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1634         at org.testng.TestRunner.run(TestRunner.java:486)
1635         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1636         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1637         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1638         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1639         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1640         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1641         at org.testng.TestNG.run(TestNG.java:784)
1642         at org.testng.TestNG.privateMain(TestNG.java:949)
1643         at org.testng.TestNG.main(TestNG.java:922)
1644 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.
1645         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
1646         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
1647         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
1648         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
1649         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
1650         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
1651         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
1652         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
1653         at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
1654         at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
1655         at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:128)
1656         at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:106)
1657         at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:310)
1658         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:699)
1659         at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:69)
1660         at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:172)
1661         at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:159)
1662         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:344)
1663         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:597)
1664         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:328)
1665         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:498)
1666         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:320)
1667         ... 26 more
1668 ]]>
1669             </full-stacktrace>
1670           </exception>
1671         </test-method>
1672       </class>
1673     </test>
1674   </suite>
1675 </testng-results>