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.ClusterSessionTester.testTaskList()" name="testTaskList" class="compbio.engine.cluster.drmaa.ClusterSessionTester"/>
  11         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  12         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()" name="testGetJobStatus" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  13         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  14         <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
  15         <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
  16         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation()" name="testAsyncCancelOperation" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  17         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation()" name="testAsyncRetrievOperation" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  18         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  19         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally()" name="testCancelLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  20         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()" name="testGetStatus" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  21         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally()" name="testMultipleCancelLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  22         <method signature="compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()" name="testSubmitLocally" class="compbio.engine.local.AsyncLocalRunnerTester"/>
  23         <method signature="compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" class="compbio.engine.local.LocalRunnerTester"/>
  24         <method signature="compbio.engine.local.LocalRunnerTester.testCancelLocally()" name="testCancelLocally" class="compbio.engine.local.LocalRunnerTester"/>
  25         <method signature="compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally()" name="testMultipleCancelLocally" class="compbio.engine.local.LocalRunnerTester"/>
  26       </group>
  27       <group name="cluster">
  28         <method signature="compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()" name="testTaskList" class="compbio.engine.cluster.drmaa.ClusterSessionTester"/>
  29         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  30         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()" name="testGetJobStatus" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  31         <method signature="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester"/>
  32         <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()" name="testCancel" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
  33         <method signature="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()" name="testSubmit" class="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester"/>
  34         <method signature="compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()" name="testClusterEngineConf" class="compbio.engine.conf.PropertyHelperManagerTester"/>
  35         <method signature="compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()" name="readStatisticsClusterExecution" class="compbio.runner.msa.ClustalWTester"/>
  36         <method signature="compbio.runner.msa.ClustalWTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.ClustalWTester"/>
  37         <method signature="compbio.runner.msa.MafftTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.MafftTester"/>
  38         <method signature="compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" class="compbio.runner.msa.MafftTester"/>
  39         <method signature="compbio.runner.msa.MuscleTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.MuscleTester"/>
  40         <method signature="compbio.runner.msa.ProbconsTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.ProbconsTester"/>
  41         <method signature="compbio.runner.msa.TcoffeeTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.TcoffeeTester"/>
  42         <method signature="compbio.runner.msa.TcoffeeTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.TcoffeeTester"/>
  43       </group>
  44       <group name="runner">
  45         <method signature="compbio.runner.msa.ClustalWParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.ClustalWParametersTester"/>
  46         <method signature="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.ClustalWParametersTester"/>
  47         <method signature="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.ClustalWParametersTester"/>
  48         <method signature="compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.ClustalWParametersTester"/>
  49         <method signature="compbio.runner.msa.ClustalWParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.ClustalWParametersTester"/>
  50         <method signature="compbio.runner.msa.ClustalWParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.ClustalWParametersTester"/>
  51         <method signature="compbio.runner.msa.ClustalWParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.ClustalWParametersTester"/>
  52         <method signature="compbio.runner.msa.ClustalWParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.ClustalWParametersTester"/>
  53         <method signature="compbio.runner.msa.ClustalWTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.ClustalWTester"/>
  54         <method signature="compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()" name="readStatisticsClusterExecution" class="compbio.runner.msa.ClustalWTester"/>
  55         <method signature="compbio.runner.msa.ClustalWTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.ClustalWTester"/>
  56         <method signature="compbio.runner.msa.ClustalWTester.testOptionsLocally()" name="testOptionsLocally" class="compbio.runner.msa.ClustalWTester"/>
  57         <method signature="compbio.runner.msa.ClustalWTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.ClustalWTester"/>
  58         <method signature="compbio.runner.msa.ClustalWTester.testRunLocally()" name="testRunLocally" class="compbio.runner.msa.ClustalWTester"/>
  59         <method signature="compbio.runner.msa.ClustalWTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.ClustalWTester"/>
  60         <method signature="compbio.runner.msa.ClustalWTester.testRunWithMatrix()" name="testRunWithMatrix" class="compbio.runner.msa.ClustalWTester"/>
  61         <method signature="compbio.runner.msa.MafftParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.MafftParametersTester"/>
  62         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.MafftParametersTester"/>
  63         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.MafftParametersTester"/>
  64         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.MafftParametersTester"/>
  65         <method signature="compbio.runner.msa.MafftParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.MafftParametersTester"/>
  66         <method signature="compbio.runner.msa.MafftParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.MafftParametersTester"/>
  67         <method signature="compbio.runner.msa.MafftParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.MafftParametersTester"/>
  68         <method signature="compbio.runner.msa.MafftParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.MafftParametersTester"/>
  69         <method signature="compbio.runner.msa.MafftTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.MafftTester"/>
  70         <method signature="compbio.runner.msa.MafftTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.MafftTester"/>
  71         <method signature="compbio.runner.msa.MafftTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.MafftTester"/>
  72         <method signature="compbio.runner.msa.MafftTester.testExecute()" name="testExecute" class="compbio.runner.msa.MafftTester"/>
  73         <method signature="compbio.runner.msa.MafftTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.MafftTester"/>
  74         <method signature="compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" class="compbio.runner.msa.MafftTester"/>
  75         <method signature="compbio.runner.msa.MafftTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.MafftTester"/>
  76         <method signature="compbio.runner.msa.MuscleParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.MuscleParametersTester"/>
  77         <method signature="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.MuscleParametersTester"/>
  78         <method signature="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.MuscleParametersTester"/>
  79         <method signature="compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.MuscleParametersTester"/>
  80         <method signature="compbio.runner.msa.MuscleParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.MuscleParametersTester"/>
  81         <method signature="compbio.runner.msa.MuscleParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.MuscleParametersTester"/>
  82         <method signature="compbio.runner.msa.MuscleParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.MuscleParametersTester"/>
  83         <method signature="compbio.runner.msa.MuscleParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.MuscleParametersTester"/>
  84         <method signature="compbio.runner.msa.MuscleTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.MuscleTester"/>
  85         <method signature="compbio.runner.msa.MuscleTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.MuscleTester"/>
  86         <method signature="compbio.runner.msa.MuscleTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.MuscleTester"/>
  87         <method signature="compbio.runner.msa.MuscleTester.testRunLocally()" name="testRunLocally" class="compbio.runner.msa.MuscleTester"/>
  88         <method signature="compbio.runner.msa.MuscleTester.testRunOnCluster()" name="testRunOnCluster" class="compbio.runner.msa.MuscleTester"/>
  89         <method signature="compbio.runner.msa.ProbconsParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.ProbconsParametersTester"/>
  90         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.ProbconsParametersTester"/>
  91         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.ProbconsParametersTester"/>
  92         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.ProbconsParametersTester"/>
  93         <method signature="compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
  94         <method signature="compbio.runner.msa.ProbconsParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.ProbconsParametersTester"/>
  95         <method signature="compbio.runner.msa.ProbconsParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
  96         <method signature="compbio.runner.msa.ProbconsTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.ProbconsTester"/>
  97         <method signature="compbio.runner.msa.ProbconsTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.ProbconsTester"/>
  98         <method signature="compbio.runner.msa.ProbconsTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.ProbconsTester"/>
  99         <method signature="compbio.runner.msa.ProbconsTester.testExecute()" name="testExecute" class="compbio.runner.msa.ProbconsTester"/>
 100         <method signature="compbio.runner.msa.ProbconsTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.ProbconsTester"/>
 101         <method signature="compbio.runner.msa.ProbconsTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.ProbconsTester"/>
 102         <method signature="compbio.runner.msa.TcoffeeParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.TcoffeeParametersTester"/>
 103         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 104         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 105         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 106         <method signature="compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
 107         <method signature="compbio.runner.msa.TcoffeeParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.TcoffeeParametersTester"/>
 108         <method signature="compbio.runner.msa.TcoffeeParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
 109         <method signature="compbio.runner.msa.TcoffeeParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.TcoffeeParametersTester"/>
 110         <method signature="compbio.runner.msa.TcoffeeTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.TcoffeeTester"/>
 111         <method signature="compbio.runner.msa.TcoffeeTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.TcoffeeTester"/>
 112         <method signature="compbio.runner.msa.TcoffeeTester.testConfigurationLoading()" name="testConfigurationLoading" class="compbio.runner.msa.TcoffeeTester"/>
 113         <method signature="compbio.runner.msa.TcoffeeTester.testExecute()" name="testExecute" class="compbio.runner.msa.TcoffeeTester"/>
 114         <method signature="compbio.runner.msa.TcoffeeTester.testNcore()" name="testNcore" class="compbio.runner.msa.TcoffeeTester"/>
 115         <method signature="compbio.runner.msa.TcoffeeTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.TcoffeeTester"/>
 116       </group>
 117       <group name="non_windows">
 118         <method signature="compbio.runner.msa.MafftParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.MafftParametersTester"/>
 119         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.MafftParametersTester"/>
 120         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.MafftParametersTester"/>
 121         <method signature="compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.MafftParametersTester"/>
 122         <method signature="compbio.runner.msa.MafftParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.MafftParametersTester"/>
 123         <method signature="compbio.runner.msa.MafftParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.MafftParametersTester"/>
 124         <method signature="compbio.runner.msa.MafftParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.MafftParametersTester"/>
 125         <method signature="compbio.runner.msa.MafftParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.MafftParametersTester"/>
 126         <method signature="compbio.runner.msa.MafftTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.MafftTester"/>
 127         <method signature="compbio.runner.msa.MafftTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.MafftTester"/>
 128         <method signature="compbio.runner.msa.MafftTester.testExecute()" name="testExecute" class="compbio.runner.msa.MafftTester"/>
 129         <method signature="compbio.runner.msa.MafftTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.MafftTester"/>
 130         <method signature="compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" class="compbio.runner.msa.MafftTester"/>
 131         <method signature="compbio.runner.msa.MafftTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.MafftTester"/>
 132         <method signature="compbio.runner.msa.ProbconsParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.ProbconsParametersTester"/>
 133         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.ProbconsParametersTester"/>
 134         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.ProbconsParametersTester"/>
 135         <method signature="compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.ProbconsParametersTester"/>
 136         <method signature="compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
 137         <method signature="compbio.runner.msa.ProbconsParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.ProbconsParametersTester"/>
 138         <method signature="compbio.runner.msa.ProbconsParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.ProbconsParametersTester"/>
 139         <method signature="compbio.runner.msa.ProbconsTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.ProbconsTester"/>
 140         <method signature="compbio.runner.msa.ProbconsTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.ProbconsTester"/>
 141         <method signature="compbio.runner.msa.ProbconsTester.testExecute()" name="testExecute" class="compbio.runner.msa.ProbconsTester"/>
 142         <method signature="compbio.runner.msa.ProbconsTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.ProbconsTester"/>
 143         <method signature="compbio.runner.msa.ProbconsTester.testSetInputTester()" name="testSetInputTester" class="compbio.runner.msa.ProbconsTester"/>
 144         <method signature="compbio.runner.msa.TcoffeeParametersTester.testArguments()" name="testArguments" class="compbio.runner.msa.TcoffeeParametersTester"/>
 145         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 146         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 147         <method signature="compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" class="compbio.runner.msa.TcoffeeParametersTester"/>
 148         <method signature="compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()" name="testDefaultParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
 149         <method signature="compbio.runner.msa.TcoffeeParametersTester.testOptions()" name="testOptions" class="compbio.runner.msa.TcoffeeParametersTester"/>
 150         <method signature="compbio.runner.msa.TcoffeeParametersTester.testParameters()" name="testParameters" class="compbio.runner.msa.TcoffeeParametersTester"/>
 151         <method signature="compbio.runner.msa.TcoffeeParametersTester.testPresets()" name="testPresets" class="compbio.runner.msa.TcoffeeParametersTester"/>
 152         <method signature="compbio.runner.msa.TcoffeeTester.readStatistics()" name="readStatistics" class="compbio.runner.msa.TcoffeeTester"/>
 153         <method signature="compbio.runner.msa.TcoffeeTester.testClusterExecute()" name="testClusterExecute" class="compbio.runner.msa.TcoffeeTester"/>
 154         <method signature="compbio.runner.msa.TcoffeeTester.testExecute()" name="testExecute" class="compbio.runner.msa.TcoffeeTester"/>
 155         <method signature="compbio.runner.msa.TcoffeeTester.testNcore()" name="testNcore" class="compbio.runner.msa.TcoffeeTester"/>
 156         <method signature="compbio.runner.msa.TcoffeeTester.testPersistance()" name="testPersistance" class="compbio.runner.msa.TcoffeeTester"/>
 157       </group>
 158     </groups>
 159     <test name="Ant test">
 160       <class name="compbio.engine.client.CommandBuilderTester">
 161         <test-method status="PASS" signature="testCommandBuilding()" name="testCommandBuilding" duration-ms="1" started-at="2010-02-17T15:34:38Z" finished-at="2010-02-17T15:34:38Z">
 162         </test-method>
 163         <test-method status="PASS" signature="testOptionsToCommand()" name="testOptionsToCommand" duration-ms="567" started-at="2010-02-17T15:34:38Z" finished-at="2010-02-17T15:34:39Z">
 164         </test-method>
 165         <test-method status="PASS" signature="testSpaceDelimiterExecutable()" name="testSpaceDelimiterExecutable" duration-ms="0" started-at="2010-02-17T15:34:39Z" finished-at="2010-02-17T15:34:39Z">
 166         </test-method>
 167       </class>
 168       <class name="compbio.metadata.RunnerConfigTester">
 169         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="34" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 170         </test-method>
 171         <test-method status="PASS" signature="testCreateNumParameterWithoutValidValue()" name="testCreateNumParameterWithoutValidValue" duration-ms="1" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 172           <exception class="java.lang.IllegalStateException">
 173             <message>
 174               <![CDATA[Attempting to set default value for parameter: Option name: Matrix
 175 Description: DNA weight matrix
 176 URL: null
 177 Is required: false
 178
 179  Without possible values! Please define possible value first!]]>
 180             </message>
 181             <full-stacktrace>
 182               <![CDATA[java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
 183 Description: DNA weight matrix
 184 URL: null
 185 Is required: false
 186
 187  Without possible values! Please define possible value first!
 188         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
 189         at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
 190         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 191         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 192         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 193         at java.lang.reflect.Method.invoke(Method.java:597)
 194         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 195         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 196         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 197         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 198         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 199         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 200         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 201         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 202         at org.testng.TestRunner.run(TestRunner.java:486)
 203         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 204         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 205         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 206         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 207         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 208         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 209         at org.testng.TestNG.run(TestNG.java:784)
 210         at org.testng.TestNG.privateMain(TestNG.java:949)
 211         at org.testng.TestNG.main(TestNG.java:922)
 212 ]]>
 213             </full-stacktrace>
 214           </exception>
 215         </test-method>
 216         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 217         </test-method>
 218         <test-method status="PASS" signature="testCreateParameter()" name="testCreateParameter" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 219           <exception class="compbio.metadata.WrongParameterException">
 220             <message>
 221               <![CDATA[Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
 222 Description: Protein weight matrix
 223 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 224 Is required: true
 225 Option Names:
 226 --AAMATRIX
 227 POSSIBLE VALUES:
 228 BLOSUM
 229 GONNET
 230 ID
 231 PAM
 232
 233 ]]>
 234             </message>
 235             <full-stacktrace>
 236               <![CDATA[compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
 237 Description: Protein weight matrix
 238 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 239 Is required: true
 240 Option Names:
 241 --AAMATRIX
 242 POSSIBLE VALUES:
 243 BLOSUM
 244 GONNET
 245 ID
 246 PAM
 247
 248
 249         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
 250         at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
 251         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 252         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 253         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 254         at java.lang.reflect.Method.invoke(Method.java:597)
 255         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 256         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 257         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 258         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 259         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 260         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 261         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 262         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 263         at org.testng.TestRunner.run(TestRunner.java:486)
 264         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 265         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 266         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 267         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 268         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 269         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 270         at org.testng.TestNG.run(TestNG.java:784)
 271         at org.testng.TestNG.privateMain(TestNG.java:949)
 272         at org.testng.TestNG.main(TestNG.java:922)
 273 ]]>
 274             </full-stacktrace>
 275           </exception>
 276         </test-method>
 277         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 278         </test-method>
 279         <test-method status="PASS" signature="testCreateParameterWithValidValueConstrain()" name="testCreateParameterWithValidValueConstrain" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 280         </test-method>
 281         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 282         </test-method>
 283         <test-method status="PASS" signature="testOptionNoDefaultValidate()" name="testOptionNoDefaultValidate" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 284           <exception class="javax.xml.bind.ValidationException">
 285             <message>
 286               <![CDATA[Default value is required as multiple optionNames are defined for option: Option name: Matrix1
 287 Description: Protein weight matrix
 288 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 289 Is required: true
 290 Option Names:
 291 --AAMATRIX
 292 --ABMAT
 293 --BBBB
 294 ]]>
 295             </message>
 296             <full-stacktrace>
 297               <![CDATA[javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
 298 Description: Protein weight matrix
 299 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 300 Is required: true
 301 Option Names:
 302 --AAMATRIX
 303 --ABMAT
 304 --BBBB
 305
 306         at compbio.metadata.Option.validate(Option.java:317)
 307         at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
 308         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 309         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 310         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 311         at java.lang.reflect.Method.invoke(Method.java:597)
 312         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 313         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 314         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 315         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 316         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 317         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 318         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 319         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 320         at org.testng.TestRunner.run(TestRunner.java:486)
 321         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 322         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 323         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 324         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 325         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 326         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 327         at org.testng.TestNG.run(TestNG.java:784)
 328         at org.testng.TestNG.privateMain(TestNG.java:949)
 329         at org.testng.TestNG.main(TestNG.java:922)
 330 ]]>
 331             </full-stacktrace>
 332           </exception>
 333         </test-method>
 334         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="14" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 335         </test-method>
 336         <test-method status="PASS" signature="testOptionSetInvalidValue()" name="testOptionSetInvalidValue" duration-ms="1" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 337           <exception class="compbio.metadata.WrongParameterException">
 338             <message>
 339               <![CDATA[Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
 340 Description: Protein weight matrix
 341 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 342 Is required: true
 343 Option Names:
 344 --AAMATRIX
 345 --ABMAT
 346 --BBBB
 347 ]]>
 348             </message>
 349             <full-stacktrace>
 350               <![CDATA[compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
 351 Description: Protein weight matrix
 352 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 353 Is required: true
 354 Option Names:
 355 --AAMATRIX
 356 --ABMAT
 357 --BBBB
 358
 359         at compbio.metadata.Option.setDefaultValue(Option.java:130)
 360         at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
 361         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 362         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 363         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 364         at java.lang.reflect.Method.invoke(Method.java:597)
 365         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 366         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 367         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 368         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 369         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 370         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 371         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 372         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 373         at org.testng.TestRunner.run(TestRunner.java:486)
 374         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 375         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 376         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 377         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 378         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 379         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 380         at org.testng.TestNG.run(TestNG.java:784)
 381         at org.testng.TestNG.privateMain(TestNG.java:949)
 382         at org.testng.TestNG.main(TestNG.java:922)
 383 ]]>
 384             </full-stacktrace>
 385           </exception>
 386         </test-method>
 387         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 388         </test-method>
 389         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 390         </test-method>
 391         <test-method status="PASS" signature="testOptionToCommand()" name="testOptionToCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 392         </test-method>
 393         <test-method status="PASS" signature="testParameterToCommand()" name="testParameterToCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 394         </test-method>
 395         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 396         </test-method>
 397         <test-method status="PASS" signature="testValidate()" name="testValidate" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 398         </test-method>
 399         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="203" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 400         </test-method>
 401         <test-method status="PASS" signature="testValidateBoundaryConstrainCheck()" name="testValidateBoundaryConstrainCheck" duration-ms="1" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 402         </test-method>
 403         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 404         </test-method>
 405         <test-method status="PASS" signature="testValidateLowerBoundaryConstrainCheck()" name="testValidateLowerBoundaryConstrainCheck" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 406           <exception class="compbio.metadata.WrongParameterException">
 407             <message>
 408               <![CDATA[Attempting to set default value outside boundaries defined by the constraint: Type: Float
 409 Min: -10.12
 410 Max: 0
 411
 412  For parameter: Option name: Matrix1
 413 Description: Protein weight matrix
 414 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 415 Is required: true
 416 Option Names:
 417 --AAMATRIX
 418 Type: Float
 419 Min: -10.12
 420 Max: 0
 421
 422 ]]>
 423             </message>
 424             <full-stacktrace>
 425               <![CDATA[compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
 426 Min: -10.12
 427 Max: 0
 428
 429  For parameter: Option name: Matrix1
 430 Description: Protein weight matrix
 431 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 432 Is required: true
 433 Option Names:
 434 --AAMATRIX
 435 Type: Float
 436 Min: -10.12
 437 Max: 0
 438
 439
 440         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
 441         at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
 442         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 443         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 444         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 445         at java.lang.reflect.Method.invoke(Method.java:597)
 446         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 447         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 448         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 449         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 450         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 451         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 452         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 453         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 454         at org.testng.TestRunner.run(TestRunner.java:486)
 455         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 456         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 457         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 458         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 459         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 460         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 461         at org.testng.TestNG.run(TestNG.java:784)
 462         at org.testng.TestNG.privateMain(TestNG.java:949)
 463         at org.testng.TestNG.main(TestNG.java:922)
 464 ]]>
 465             </full-stacktrace>
 466           </exception>
 467         </test-method>
 468         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 469         </test-method>
 470         <test-method status="PASS" signature="testValidateUpperBoundaryConstrainCheck()" name="testValidateUpperBoundaryConstrainCheck" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 471           <exception class="compbio.metadata.WrongParameterException">
 472             <message>
 473               <![CDATA[Attempting to set default value outside boundaries defined by the constraint: Type: Float
 474 Min: -10.12
 475 Max: 0
 476
 477  For parameter: Option name: Matrix1
 478 Description: Protein weight matrix
 479 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 480 Is required: true
 481 Option Names:
 482 --AAMATRIX
 483 Type: Float
 484 Min: -10.12
 485 Max: 0
 486
 487 ]]>
 488             </message>
 489             <full-stacktrace>
 490               <![CDATA[compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
 491 Min: -10.12
 492 Max: 0
 493
 494  For parameter: Option name: Matrix1
 495 Description: Protein weight matrix
 496 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 497 Is required: true
 498 Option Names:
 499 --AAMATRIX
 500 Type: Float
 501 Min: -10.12
 502 Max: 0
 503
 504
 505         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
 506         at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
 507         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 508         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 509         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 510         at java.lang.reflect.Method.invoke(Method.java:597)
 511         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 512         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 513         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 514         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 515         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 516         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 517         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 518         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 519         at org.testng.TestRunner.run(TestRunner.java:486)
 520         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 521         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 522         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 523         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 524         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 525         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 526         at org.testng.TestNG.run(TestNG.java:784)
 527         at org.testng.TestNG.privateMain(TestNG.java:949)
 528         at org.testng.TestNG.main(TestNG.java:922)
 529 ]]>
 530             </full-stacktrace>
 531           </exception>
 532         </test-method>
 533         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="15" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 534         </test-method>
 535         <test-method status="PASS" signature="testValidateValueConstrain()" name="testValidateValueConstrain" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 536           <exception class="javax.xml.bind.ValidationException">
 537             <message>
 538               <![CDATA[Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
 539 ]]>
 540             </message>
 541             <full-stacktrace>
 542               <![CDATA[javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
 543
 544         at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
 545         at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
 546         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 547         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 548         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 549         at java.lang.reflect.Method.invoke(Method.java:597)
 550         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 551         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 552         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 553         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 554         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 555         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 556         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 557         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 558         at org.testng.TestRunner.run(TestRunner.java:486)
 559         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 560         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 561         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 562         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 563         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 564         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 565         at org.testng.TestNG.run(TestNG.java:784)
 566         at org.testng.TestNG.privateMain(TestNG.java:949)
 567         at org.testng.TestNG.main(TestNG.java:922)
 568 ]]>
 569             </full-stacktrace>
 570           </exception>
 571         </test-method>
 572       </class>
 573       <class name="compbio.runner._impl.NetNglycTester">
 574         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 575         </test-method>
 576       </class>
 577       <class name="compbio.engine.EngineConfiguratorTester">
 578         <test-method status="PASS" signature="testGetAsyncEngine()" name="testGetAsyncEngine" duration-ms="296" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
 579         </test-method>
 580         <test-method status="PASS" signature="testGetSyncEngine()" name="testGetSyncEngine" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
 581         </test-method>
 582       </class>
 583       <class name="compbio.runner.msa.MafftParametersTester">
 584         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="47" started-at="2010-02-17T15:37:09Z" finished-at="2010-02-17T15:37:09Z">
 585         </test-method>
 586         <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="6103" started-at="2010-02-17T15:37:09Z" finished-at="2010-02-17T15:37:15Z">
 587         </test-method>
 588         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="54" started-at="2010-02-17T15:37:15Z" finished-at="2010-02-17T15:37:15Z">
 589         </test-method>
 590         <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="1" started-at="2010-02-17T15:37:15Z" finished-at="2010-02-17T15:37:15Z">
 591         </test-method>
 592         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="44" started-at="2010-02-17T15:37:15Z" finished-at="2010-02-17T15:37:15Z">
 593         </test-method>
 594         <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="3235" started-at="2010-02-17T15:37:15Z" finished-at="2010-02-17T15:37:18Z">
 595         </test-method>
 596         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="47" started-at="2010-02-17T15:37:18Z" finished-at="2010-02-17T15:37:18Z">
 597         </test-method>
 598         <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="1326" started-at="2010-02-17T15:37:18Z" finished-at="2010-02-17T15:37:19Z">
 599         </test-method>
 600         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="45" started-at="2010-02-17T15:37:19Z" finished-at="2010-02-17T15:37:20Z">
 601         </test-method>
 602         <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="7672" started-at="2010-02-17T15:37:20Z" finished-at="2010-02-17T15:37:27Z">
 603         </test-method>
 604         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="47" started-at="2010-02-17T15:37:27Z" finished-at="2010-02-17T15:37:27Z">
 605         </test-method>
 606         <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="20463" started-at="2010-02-17T15:37:27Z" finished-at="2010-02-17T15:37:48Z">
 607         </test-method>
 608         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="55" started-at="2010-02-17T15:37:48Z" finished-at="2010-02-17T15:37:48Z">
 609         </test-method>
 610         <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="4449" started-at="2010-02-17T15:37:48Z" finished-at="2010-02-17T15:37:52Z">
 611         </test-method>
 612         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="52" started-at="2010-02-17T15:37:52Z" finished-at="2010-02-17T15:37:52Z">
 613         </test-method>
 614         <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="2422" started-at="2010-02-17T15:37:52Z" finished-at="2010-02-17T15:37:55Z">
 615         </test-method>
 616         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="47" started-at="2010-02-17T15:37:55Z" finished-at="2010-02-17T15:37:55Z">
 617         </test-method>
 618         <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="2136" started-at="2010-02-17T15:37:55Z" finished-at="2010-02-17T15:37:57Z">
 619         </test-method>
 620       </class>
 621       <class name="compbio.runner._impl.RonnTester">
 622         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 623         </test-method>
 624       </class>
 625       <class name="compbio.runner.msa.ProbconsTester">
 626         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:09Z" finished-at="2010-02-17T15:41:09Z">
 627         </test-method>
 628         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="441" started-at="2010-02-17T15:41:09Z" finished-at="2010-02-17T15:41:10Z">
 629         </test-method>
 630         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:41:10Z" finished-at="2010-02-17T15:41:10Z">
 631         </test-method>
 632         <test-method status="PASS" signature="testClusterExecute()" name="testClusterExecute" duration-ms="19326" started-at="2010-02-17T15:41:10Z" finished-at="2010-02-17T15:41:29Z">
 633         </test-method>
 634         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="107" started-at="2010-02-17T15:41:29Z" finished-at="2010-02-17T15:41:29Z">
 635         </test-method>
 636         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:29Z" finished-at="2010-02-17T15:41:29Z">
 637         </test-method>
 638         <test-method status="PASS" signature="testExecute()" name="testExecute" duration-ms="436" started-at="2010-02-17T15:41:29Z" finished-at="2010-02-17T15:41:30Z">
 639         </test-method>
 640         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:29Z" finished-at="2010-02-17T15:41:29Z">
 641         </test-method>
 642         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:30Z">
 643         </test-method>
 644         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="509" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:30Z">
 645         </test-method>
 646         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:30Z">
 647         </test-method>
 648         <test-method status="PASS" signature="testSetInputTester()" name="testSetInputTester" duration-ms="0" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:30Z">
 649         </test-method>
 650       </class>
 651       <class name="compbio.engine.conf.PropertyHelperManagerTester">
 652         <test-method status="PASS" signature="testLoadResources()" name="testLoadResources" is-config="true" duration-ms="2" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
 653         </test-method>
 654         <test-method status="PASS" signature="testClusterEngineConf()" name="testClusterEngineConf" duration-ms="104" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
 655         </test-method>
 656         <test-method status="PASS" signature="validateClustalConfiguration()" name="validateClustalConfiguration" duration-ms="43" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
 657         </test-method>
 658         <test-method status="PASS" signature="validateMafftConfiguration()" name="validateMafftConfiguration" duration-ms="1" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
 659         </test-method>
 660         <test-method status="PASS" signature="validateMuscleConfiguration()" name="validateMuscleConfiguration" duration-ms="4" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
 661         </test-method>
 662         <test-method status="PASS" signature="validateTcoffeeConfiguration()" name="validateTcoffeeConfiguration" duration-ms="4" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
 663         </test-method>
 664       </class>
 665       <class name="compbio.metadata.OptionCombinatorTester">
 666         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="400" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:37Z">
 667         </test-method>
 668         <test-method status="PASS" signature="testgetAllOptions()" name="testgetAllOptions" duration-ms="1" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:37Z">
 669         </test-method>
 670         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="111" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:38Z">
 671         </test-method>
 672         <test-method status="PASS" signature="testgetAllParameters()" name="testgetAllParameters" duration-ms="3" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:38Z">
 673         </test-method>
 674       </class>
 675       <class name="compbio.engine.FilePullerTester">
 676         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1739" started-at="2010-02-17T15:34:08Z" finished-at="2010-02-17T15:34:10Z">
 677         </test-method>
 678         <test-method status="PASS" signature="loadPresets()" name="loadPresets" is-config="true" duration-ms="167" started-at="2010-02-17T15:34:10Z" finished-at="2010-02-17T15:34:10Z">
 679         </test-method>
 680         <test-method status="PASS" signature="testPull()" name="testPull" duration-ms="450" started-at="2010-02-17T15:34:10Z" finished-at="2010-02-17T15:34:11Z">
 681         </test-method>
 682         <test-method status="PASS" signature="testCache()" name="testCache" duration-ms="6006" started-at="2010-02-17T15:34:11Z" depends-on-methods="compbio.engine.FilePullerTester.testPull" finished-at="2010-02-17T15:34:17Z">
 683         </test-method>
 684         <test-method status="PASS" signature="testGetDelay()" name="testGetDelay" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
 685         </test-method>
 686         <test-method status="PASS" signature="testGet()" name="testGet" duration-ms="46" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
 687         </test-method>
 688       </class>
 689       <class name="compbio.runner.msa.MuscleTester">
 690         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:59Z" finished-at="2010-02-17T15:38:59Z">
 691         </test-method>
 692         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="932" started-at="2010-02-17T15:38:59Z" finished-at="2010-02-17T15:39:00Z">
 693         </test-method>
 694         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:39:00Z" finished-at="2010-02-17T15:39:00Z">
 695         </test-method>
 696         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="313" started-at="2010-02-17T15:39:00Z" finished-at="2010-02-17T15:39:00Z">
 697         </test-method>
 698         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:39:00Z" finished-at="2010-02-17T15:39:00Z">
 699         </test-method>
 700         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="241" started-at="2010-02-17T15:39:00Z" finished-at="2010-02-17T15:39:01Z">
 701         </test-method>
 702         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:39:01Z" finished-at="2010-02-17T15:39:01Z">
 703         </test-method>
 704         <test-method status="PASS" signature="testRunLocally()" name="testRunLocally" duration-ms="101" started-at="2010-02-17T15:39:01Z" finished-at="2010-02-17T15:39:01Z">
 705         </test-method>
 706         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:39:01Z" finished-at="2010-02-17T15:39:01Z">
 707         </test-method>
 708         <test-method status="PASS" signature="testRunOnCluster()" name="testRunOnCluster" duration-ms="8142" started-at="2010-02-17T15:39:01Z" finished-at="2010-02-17T15:39:09Z">
 709         </test-method>
 710       </class>
 711       <class name="compbio.runner.msa.TcoffeeTester">
 712         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="1" started-at="2010-02-17T15:42:43Z" finished-at="2010-02-17T15:42:43Z">
 713         </test-method>
 714         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="876" started-at="2010-02-17T15:42:43Z" finished-at="2010-02-17T15:42:44Z">
 715         </test-method>
 716         <test-method status="PASS" signature="testClusterExecute()" name="testClusterExecute" duration-ms="5526" started-at="2010-02-17T15:42:44Z" finished-at="2010-02-17T15:42:50Z">
 717         </test-method>
 718         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:44Z" finished-at="2010-02-17T15:42:44Z">
 719         </test-method>
 720         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="99" started-at="2010-02-17T15:42:50Z" finished-at="2010-02-17T15:42:50Z">
 721         </test-method>
 722         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:50Z" finished-at="2010-02-17T15:42:50Z">
 723         </test-method>
 724         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:50Z" finished-at="2010-02-17T15:42:50Z">
 725         </test-method>
 726         <test-method status="PASS" signature="testExecute()" name="testExecute" duration-ms="868" started-at="2010-02-17T15:42:50Z" finished-at="2010-02-17T15:42:51Z">
 727         </test-method>
 728         <test-method status="PASS" signature="testNcore()" name="testNcore" duration-ms="1" started-at="2010-02-17T15:42:51Z" finished-at="2010-02-17T15:42:51Z">
 729         </test-method>
 730         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:51Z" finished-at="2010-02-17T15:42:51Z">
 731         </test-method>
 732         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="1771" started-at="2010-02-17T15:42:51Z" finished-at="2010-02-17T15:42:53Z">
 733         </test-method>
 734         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:51Z" finished-at="2010-02-17T15:42:51Z">
 735         </test-method>
 736       </class>
 737       <class name="compbio.runner.msa.LimitTester">
 738         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="61" started-at="2010-02-17T15:37:09Z" finished-at="2010-02-17T15:37:09Z">
 739         </test-method>
 740         <test-method status="PASS" signature="testLoadLimits()" name="testLoadLimits" duration-ms="0" started-at="2010-02-17T15:37:09Z" finished-at="2010-02-17T15:37:09Z">
 741         </test-method>
 742       </class>
 743       <class name="compbio.runner._impl.OBTester">
 744         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 745         </test-method>
 746         <test-method status="PASS" signature="testGetTestArgsCommand()" name="testGetTestArgsCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 747         </test-method>
 748       </class>
 749       <class name="compbio.engine.local.LocalRunnerTester">
 750         <test-method status="PASS" signature="testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" duration-ms="336" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:37Z">
 751           <exception class="java.util.concurrent.CancellationException">
 752             <full-stacktrace>
 753               <![CDATA[java.util.concurrent.CancellationException
 754         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 755         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 756         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 757         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 758         at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
 759         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 760         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 761         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 762         at java.lang.reflect.Method.invoke(Method.java:597)
 763         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 764         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 765         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 766         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 767         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 768         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 769         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 770         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 771         at org.testng.TestRunner.run(TestRunner.java:486)
 772         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 773         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 774         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 775         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 776         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 777         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 778         at org.testng.TestNG.run(TestNG.java:784)
 779         at org.testng.TestNG.privateMain(TestNG.java:949)
 780         at org.testng.TestNG.main(TestNG.java:922)
 781 ]]>
 782             </full-stacktrace>
 783           </exception>
 784         </test-method>
 785         <test-method status="PASS" signature="testCancelLocally()" name="testCancelLocally" duration-ms="20" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:37Z">
 786           <exception class="java.util.concurrent.CancellationException">
 787             <full-stacktrace>
 788               <![CDATA[java.util.concurrent.CancellationException
 789         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 790         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 791         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 792         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 793         at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
 794         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 795         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 796         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 797         at java.lang.reflect.Method.invoke(Method.java:597)
 798         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 799         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 800         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 801         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 802         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 803         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 804         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 805         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 806         at org.testng.TestRunner.run(TestRunner.java:486)
 807         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 808         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 809         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 810         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 811         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 812         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 813         at org.testng.TestNG.run(TestNG.java:784)
 814         at org.testng.TestNG.privateMain(TestNG.java:949)
 815         at org.testng.TestNG.main(TestNG.java:922)
 816 ]]>
 817             </full-stacktrace>
 818           </exception>
 819         </test-method>
 820         <test-method status="PASS" signature="testMultipleCancelLocally()" name="testMultipleCancelLocally" duration-ms="58" started-at="2010-02-17T15:36:37Z" finished-at="2010-02-17T15:36:37Z">
 821           <exception class="java.util.concurrent.CancellationException">
 822             <full-stacktrace>
 823               <![CDATA[java.util.concurrent.CancellationException
 824         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 825         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 826         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 827         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 828         at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
 829         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 830         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 831         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 832         at java.lang.reflect.Method.invoke(Method.java:597)
 833         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 834         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 835         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 836         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 837         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 838         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 839         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 840         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 841         at org.testng.TestRunner.run(TestRunner.java:486)
 842         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 843         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 844         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 845         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 846         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 847         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 848         at org.testng.TestNG.run(TestNG.java:784)
 849         at org.testng.TestNG.privateMain(TestNG.java:949)
 850         at org.testng.TestNG.main(TestNG.java:922)
 851 ]]>
 852             </full-stacktrace>
 853           </exception>
 854         </test-method>
 855       </class>
 856       <class name="compbio.engine.local.AsyncLocalRunnerTester">
 857         <test-method status="PASS" signature="testAsyncCancelOperation()" name="testAsyncCancelOperation" duration-ms="48" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:50Z">
 858         </test-method>
 859         <test-method status="PASS" signature="testAsyncRetrievOperation()" name="testAsyncRetrievOperation" duration-ms="560" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:51Z">
 860         </test-method>
 861         <test-method status="PASS" signature="testCancelCompletedTaskLocally()" name="testCancelCompletedTaskLocally" duration-ms="3053" started-at="2010-02-17T15:35:51Z" finished-at="2010-02-17T15:35:54Z">
 862         </test-method>
 863         <test-method status="PASS" signature="testCancelLocally()" name="testCancelLocally" duration-ms="27" started-at="2010-02-17T15:35:54Z" finished-at="2010-02-17T15:35:54Z">
 864           <exception class="java.util.concurrent.CancellationException">
 865             <full-stacktrace>
 866               <![CDATA[java.util.concurrent.CancellationException
 867         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 868         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 869         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 870         at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 871         at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
 872         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 873         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 874         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 875         at java.lang.reflect.Method.invoke(Method.java:597)
 876         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 877         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 878         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 879         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 880         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 881         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 882         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 883         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 884         at org.testng.TestRunner.run(TestRunner.java:486)
 885         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 886         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 887         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 888         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 889         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 890         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 891         at org.testng.TestNG.run(TestNG.java:784)
 892         at org.testng.TestNG.privateMain(TestNG.java:949)
 893         at org.testng.TestNG.main(TestNG.java:922)
 894 ]]>
 895             </full-stacktrace>
 896           </exception>
 897         </test-method>
 898         <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="21332" started-at="2010-02-17T15:35:54Z" finished-at="2010-02-17T15:36:15Z">
 899         </test-method>
 900         <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="20872" started-at="2010-02-17T15:35:54Z" finished-at="2010-02-17T15:36:15Z">
 901         </test-method>
 902         <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="40987" started-at="2010-02-17T15:35:54Z" finished-at="2010-02-17T15:36:35Z">
 903         </test-method>
 904         <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="20915" started-at="2010-02-17T15:35:54Z" finished-at="2010-02-17T15:36:15Z">
 905         </test-method>
 906         <test-method status="PASS" signature="testGetStatus()" name="testGetStatus" duration-ms="20863" started-at="2010-02-17T15:36:15Z" finished-at="2010-02-17T15:36:36Z">
 907         </test-method>
 908         <test-method status="PASS" signature="testMultipleCancelLocally()" name="testMultipleCancelLocally" duration-ms="267" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:36Z">
 909           <exception class="java.util.concurrent.CancellationException">
 910             <full-stacktrace>
 911               <![CDATA[java.util.concurrent.CancellationException
 912         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 913         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 914         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 915         at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 916         at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
 917         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 918         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 919         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 920         at java.lang.reflect.Method.invoke(Method.java:597)
 921         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 922         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 923         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 924         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 925         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 926         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 927         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 928         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 929         at org.testng.TestRunner.run(TestRunner.java:486)
 930         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 931         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 932         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 933         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 934         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 935         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 936         at org.testng.TestNG.run(TestNG.java:784)
 937         at org.testng.TestNG.privateMain(TestNG.java:949)
 938         at org.testng.TestNG.main(TestNG.java:922)
 939 ]]>
 940             </full-stacktrace>
 941           </exception>
 942         </test-method>
 943         <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="634" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:37Z">
 944         </test-method>
 945         <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="220" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:36Z">
 946         </test-method>
 947         <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="125" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:36Z">
 948         </test-method>
 949         <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="482" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:36Z">
 950         </test-method>
 951         <test-method status="PASS" signature="testSubmitLocally()" name="testSubmitLocally" duration-ms="176" started-at="2010-02-17T15:36:36Z" finished-at="2010-02-17T15:36:36Z">
 952         </test-method>
 953       </class>
 954       <class name="compbio.runner._impl.Tmhmm2Tester">
 955         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
 956         </test-method>
 957       </class>
 958       <class name="compbio.runner.msa.MafftTester">
 959         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:37:57Z" finished-at="2010-02-17T15:37:57Z">
 960         </test-method>
 961         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="639" started-at="2010-02-17T15:37:57Z" finished-at="2010-02-17T15:37:57Z">
 962         </test-method>
 963         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:37:57Z" finished-at="2010-02-17T15:37:57Z">
 964         </test-method>
 965         <test-method status="PASS" signature="testClusterExecute()" name="testClusterExecute" duration-ms="11340" started-at="2010-02-17T15:37:57Z" finished-at="2010-02-17T15:38:09Z">
 966         </test-method>
 967         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="435" started-at="2010-02-17T15:38:09Z" finished-at="2010-02-17T15:38:09Z">
 968         </test-method>
 969         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:09Z" finished-at="2010-02-17T15:38:09Z">
 970         </test-method>
 971         <test-method status="PASS" signature="testExecute()" name="testExecute" duration-ms="428" started-at="2010-02-17T15:38:09Z" finished-at="2010-02-17T15:38:10Z">
 972         </test-method>
 973         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:09Z" finished-at="2010-02-17T15:38:09Z">
 974         </test-method>
 975         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="1033" started-at="2010-02-17T15:38:10Z" finished-at="2010-02-17T15:38:11Z">
 976         </test-method>
 977         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:10Z" finished-at="2010-02-17T15:38:10Z">
 978         </test-method>
 979         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:11Z" finished-at="2010-02-17T15:38:11Z">
 980         </test-method>
 981         <test-method status="PASS" signature="testRunOnClusterAsyncCheckStatusLongPoolingTime()" name="testRunOnClusterAsyncCheckStatusLongPoolingTime" duration-ms="21418" started-at="2010-02-17T15:38:11Z" finished-at="2010-02-17T15:38:32Z">
 982         </test-method>
 983         <test-method status="PASS" signature="testSetInputTester()" name="testSetInputTester" duration-ms="0" started-at="2010-02-17T15:38:32Z" finished-at="2010-02-17T15:38:32Z">
 984         </test-method>
 985         <test-method status="PASS" signature="init()" name="init" is-config="true" duration-ms="0" started-at="2010-02-17T15:38:32Z" finished-at="2010-02-17T15:38:32Z">
 986         </test-method>
 987       </class>
 988       <class name="compbio.data.sequence.ClustalAlignmentUtilTester">
 989         <test-method status="PASS" signature="testReadClustalFile()" name="testReadClustalFile" duration-ms="22" started-at="2010-02-17T15:34:32Z" finished-at="2010-02-17T15:34:32Z">
 990         </test-method>
 991         <test-method status="PASS" signature="testReadClustalFileLongNames()" name="testReadClustalFileLongNames" duration-ms="52" started-at="2010-02-17T15:34:32Z" finished-at="2010-02-17T15:34:33Z">
 992         </test-method>
 993         <test-method status="PASS" signature="testReadClustalFileShortNames()" name="testReadClustalFileShortNames" duration-ms="54" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
 994         </test-method>
 995       </class>
 996       <class name="compbio.runner.msa.MuscleParametersTester">
 997         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="85" started-at="2010-02-17T15:38:32Z" finished-at="2010-02-17T15:38:32Z">
 998         </test-method>
 999         <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="7798" started-at="2010-02-17T15:38:32Z" finished-at="2010-02-17T15:38:40Z">
1000         </test-method>
1001         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="44" started-at="2010-02-17T15:38:40Z" finished-at="2010-02-17T15:38:40Z">
1002         </test-method>
1003         <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="0" started-at="2010-02-17T15:38:40Z" finished-at="2010-02-17T15:38:40Z">
1004         </test-method>
1005         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="41" started-at="2010-02-17T15:38:40Z" finished-at="2010-02-17T15:38:40Z">
1006         </test-method>
1007         <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="1534" started-at="2010-02-17T15:38:40Z" finished-at="2010-02-17T15:38:42Z">
1008         </test-method>
1009         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="44" started-at="2010-02-17T15:38:42Z" finished-at="2010-02-17T15:38:42Z">
1010         </test-method>
1011         <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="845" started-at="2010-02-17T15:38:42Z" finished-at="2010-02-17T15:38:43Z">
1012         </test-method>
1013         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="43" started-at="2010-02-17T15:38:43Z" finished-at="2010-02-17T15:38:43Z">
1014         </test-method>
1015         <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="7603" started-at="2010-02-17T15:38:43Z" finished-at="2010-02-17T15:38:50Z">
1016         </test-method>
1017         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="42" started-at="2010-02-17T15:38:50Z" finished-at="2010-02-17T15:38:50Z">
1018         </test-method>
1019         <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="622" started-at="2010-02-17T15:38:50Z" finished-at="2010-02-17T15:38:51Z">
1020         </test-method>
1021         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="42" started-at="2010-02-17T15:38:51Z" finished-at="2010-02-17T15:38:51Z">
1022         </test-method>
1023         <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="2481" started-at="2010-02-17T15:38:51Z" finished-at="2010-02-17T15:38:53Z">
1024         </test-method>
1025         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="44" started-at="2010-02-17T15:38:53Z" finished-at="2010-02-17T15:38:53Z">
1026         </test-method>
1027         <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="4773" started-at="2010-02-17T15:38:53Z" finished-at="2010-02-17T15:38:58Z">
1028         </test-method>
1029         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="48" started-at="2010-02-17T15:38:58Z" finished-at="2010-02-17T15:38:58Z">
1030         </test-method>
1031         <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="856" started-at="2010-02-17T15:38:58Z" finished-at="2010-02-17T15:38:59Z">
1032         </test-method>
1033       </class>
1034       <class name="compbio.data.sequence.FastaSequenceGeneratorTester">
1035         <test-method status="PASS" signature="testProteinSequenceGeneration()" name="testProteinSequenceGeneration" duration-ms="8" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
1036         </test-method>
1037       </class>
1038       <class name="compbio.engine.cluster.drmaa.ClusterSessionTester">
1039         <test-method status="PASS" signature="testTaskList()" name="testTaskList" duration-ms="8964" started-at="2010-02-17T15:34:39Z" finished-at="2010-02-17T15:34:48Z">
1040         </test-method>
1041       </class>
1042       <class name="compbio.data.sequence.FastaSequenceTester">
1043         <test-method status="PASS" signature="testGetFormattedFasta()" name="testGetFormattedFasta" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
1044         </test-method>
1045       </class>
1046       <class name="compbio.engine.client.PathValidatorTester">
1047         <test-method status="PASS" signature="testGetClassPath()" name="testGetClassPath" duration-ms="234" started-at="2010-02-17T15:34:39Z" finished-at="2010-02-17T15:34:39Z">
1048         </test-method>
1049         <test-method status="PASS" signature="testIsAbsolutePath()" name="testIsAbsolutePath" duration-ms="0" started-at="2010-02-17T15:34:39Z" finished-at="2010-02-17T15:34:39Z">
1050         </test-method>
1051       </class>
1052       <class name="compbio.data.sequence.SequenceUtilTester">
1053         <test-method status="PASS" signature="testCleanSequence()" name="testCleanSequence" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
1054         </test-method>
1055         <test-method status="PASS" signature="testReadWriteFasta()" name="testReadWriteFasta" duration-ms="16" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
1056         </test-method>
1057         <test-method status="PASS" signature="testDeepCleanSequence()" name="testDeepCleanSequence" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
1058         </test-method>
1059         <test-method status="PASS" signature="testisNonAmbNucleotideSequence()" name="testisNonAmbNucleotideSequence" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
1060         </test-method>
1061         <test-method status="PASS" signature="testisProteinSequence()" name="testisProteinSequence" duration-ms="0" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:33Z">
1062         </test-method>
1063       </class>
1064       <class name="compbio.runner.msa.TcoffeeParametersTester">
1065         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:30Z">
1066         </test-method>
1067         <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="8765" started-at="2010-02-17T15:41:30Z" finished-at="2010-02-17T15:41:39Z">
1068         </test-method>
1069         <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="0" started-at="2010-02-17T15:41:39Z" finished-at="2010-02-17T15:41:39Z">
1070         </test-method>
1071         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:39Z" finished-at="2010-02-17T15:41:39Z">
1072         </test-method>
1073         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:39Z" finished-at="2010-02-17T15:41:39Z">
1074         </test-method>
1075         <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="11166" started-at="2010-02-17T15:41:39Z" finished-at="2010-02-17T15:41:50Z">
1076         </test-method>
1077         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="1" started-at="2010-02-17T15:41:50Z" finished-at="2010-02-17T15:41:50Z">
1078         </test-method>
1079         <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="5507" started-at="2010-02-17T15:41:50Z" finished-at="2010-02-17T15:41:56Z">
1080         </test-method>
1081         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:41:56Z" finished-at="2010-02-17T15:41:56Z">
1082         </test-method>
1083         <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="21942" started-at="2010-02-17T15:41:56Z" finished-at="2010-02-17T15:42:18Z">
1084         </test-method>
1085         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="1" started-at="2010-02-17T15:42:18Z" finished-at="2010-02-17T15:42:18Z">
1086         </test-method>
1087         <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="10988" started-at="2010-02-17T15:42:18Z" finished-at="2010-02-17T15:42:29Z">
1088         </test-method>
1089         <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="891" started-at="2010-02-17T15:42:29Z" finished-at="2010-02-17T15:42:30Z">
1090         </test-method>
1091         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:29Z" finished-at="2010-02-17T15:42:29Z">
1092         </test-method>
1093         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="1" started-at="2010-02-17T15:42:30Z" finished-at="2010-02-17T15:42:30Z">
1094         </test-method>
1095         <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="12717" started-at="2010-02-17T15:42:30Z" finished-at="2010-02-17T15:42:42Z">
1096         </test-method>
1097         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:42:42Z" finished-at="2010-02-17T15:42:42Z">
1098         </test-method>
1099         <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="1094" started-at="2010-02-17T15:42:42Z" finished-at="2010-02-17T15:42:43Z">
1100         </test-method>
1101       </class>
1102       <class name="compbio.engine.cluster.drmaa.UtilTester">
1103         <test-method status="PASS" signature="testParser()" name="testParser" duration-ms="0" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
1104         </test-method>
1105       </class>
1106       <class name="compbio.runner.msa.ClustalWTester">
1107         <test-method status="PASS" signature="readStatistics()" name="readStatistics" duration-ms="1178" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:40Z">
1108         </test-method>
1109         <test-method status="PASS" signature="readStatisticsClusterExecution()" name="readStatisticsClusterExecution" duration-ms="8121" started-at="2010-02-17T15:36:40Z" finished-at="2010-02-17T15:36:49Z">
1110         </test-method>
1111         <test-method status="PASS" signature="testConfigurationLoading()" name="testConfigurationLoading" duration-ms="688" started-at="2010-02-17T15:36:49Z" finished-at="2010-02-17T15:36:49Z">
1112         </test-method>
1113         <test-method status="PASS" signature="testOptionsLocally()" name="testOptionsLocally" duration-ms="1932" started-at="2010-02-17T15:36:49Z" finished-at="2010-02-17T15:36:51Z">
1114         </test-method>
1115         <test-method status="PASS" signature="testPersistance()" name="testPersistance" duration-ms="431" started-at="2010-02-17T15:36:51Z" finished-at="2010-02-17T15:36:52Z">
1116         </test-method>
1117         <test-method status="PASS" signature="testRunLocally()" name="testRunLocally" duration-ms="171" started-at="2010-02-17T15:36:52Z" finished-at="2010-02-17T15:36:52Z">
1118         </test-method>
1119         <test-method status="PASS" signature="testRunOnCluster()" name="testRunOnCluster" duration-ms="15937" started-at="2010-02-17T15:36:52Z" finished-at="2010-02-17T15:37:08Z">
1120         </test-method>
1121         <test-method status="PASS" signature="testRunWithMatrix()" name="testRunWithMatrix" duration-ms="824" started-at="2010-02-17T15:37:08Z" finished-at="2010-02-17T15:37:09Z">
1122         </test-method>
1123       </class>
1124       <class name="compbio.engine.conf.DirectoryManagerTester">
1125         <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="110" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
1126         </test-method>
1127         <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="104" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
1128         </test-method>
1129         <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="103" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
1130         </test-method>
1131         <test-method status="PASS" signature="testGetDirectory()" name="testGetDirectory" duration-ms="100" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
1132         </test-method>
1133       </class>
1134       <class name="compbio.engine.cluster.drmaa.DrmaaClusterEngineTester">
1135         <test-method status="PASS" signature="testCancel()" name="testCancel" duration-ms="1587" started-at="2010-02-17T15:35:29Z" finished-at="2010-02-17T15:35:30Z">
1136         </test-method>
1137         <test-method status="PASS" signature="testSubmit()" name="testSubmit" duration-ms="17835" started-at="2010-02-17T15:35:30Z" finished-at="2010-02-17T15:35:48Z">
1138         </test-method>
1139       </class>
1140       <class name="compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester">
1141         <test-method status="PASS" signature="testCancel()" name="testCancel" duration-ms="1273" started-at="2010-02-17T15:34:48Z" finished-at="2010-02-17T15:34:49Z">
1142           <exception class="compbio.metadata.ResultNotAvailableException">
1143             <message>
1144               <![CDATA[java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!]]>
1145             </message>
1146             <full-stacktrace>
1147               <![CDATA[compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
1148         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
1149         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
1150         at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
1151         at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
1152         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1153         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1154         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1155         at java.lang.reflect.Method.invoke(Method.java:597)
1156         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1157         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1158         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1159         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1160         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1161         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1162         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1163         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1164         at org.testng.TestRunner.run(TestRunner.java:486)
1165         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1166         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1167         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1168         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1169         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1170         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1171         at org.testng.TestNG.run(TestNG.java:784)
1172         at org.testng.TestNG.privateMain(TestNG.java:949)
1173         at org.testng.TestNG.main(TestNG.java:922)
1174 Caused by: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
1175         at compbio.runner.Util.readClustalFile(Util.java:126)
1176         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
1177         ... 25 more
1178 ]]>
1179             </full-stacktrace>
1180           </exception>
1181         </test-method>
1182         <test-method status="PASS" signature="testGetJobStatus()" name="testGetJobStatus" duration-ms="20778" started-at="2010-02-17T15:34:49Z" finished-at="2010-02-17T15:35:10Z">
1183         </test-method>
1184         <test-method status="PASS" signature="testSubmit()" name="testSubmit" duration-ms="18714" started-at="2010-02-17T15:35:10Z" finished-at="2010-02-17T15:35:29Z">
1185         </test-method>
1186       </class>
1187       <class name="compbio.metadata.PresetTester">
1188         <test-method status="PASS" signature="marshallPreset()" name="marshallPreset" duration-ms="899" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:39Z">
1189         </test-method>
1190         <test-method status="PASS" signature="validatePresets()" name="validatePresets" duration-ms="1" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
1191         </test-method>
1192       </class>
1193       <class name="compbio.metadata.OptionMarshallerTester">
1194         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:38Z">
1195         </test-method>
1196         <test-method status="PASS" signature="testMarshalling()" name="testMarshalling" duration-ms="58" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:38Z">
1197           <exception class="javax.xml.bind.MarshalException">
1198             <full-stacktrace>
1199               <![CDATA[javax.xml.bind.MarshalException
1200  - with linked exception:
1201 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
1202         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
1203         at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
1204         at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
1205         at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
1206         at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
1207         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1208         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1209         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1210         at java.lang.reflect.Method.invoke(Method.java:597)
1211         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1212         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1213         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1214         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1215         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1216         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1217         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1218         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1219         at org.testng.TestRunner.run(TestRunner.java:486)
1220         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1221         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1222         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1223         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1224         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1225         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1226         at org.testng.TestNG.run(TestNG.java:784)
1227         at org.testng.TestNG.privateMain(TestNG.java:949)
1228         at org.testng.TestNG.main(TestNG.java:922)
1229 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.
1230         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
1231         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
1232         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
1233         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
1234         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
1235         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
1236         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
1237         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
1238         at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
1239         at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
1240         at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
1241         at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
1242         at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
1243         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
1244         at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
1245         at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
1246         at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
1247         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
1248         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
1249         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
1250         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
1251         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
1252         ... 26 more
1253 ]]>
1254             </full-stacktrace>
1255           </exception>
1256         </test-method>
1257         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="0" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:38Z">
1258         </test-method>
1259         <test-method status="PASS" signature="testUnMarshalling()" name="testUnMarshalling" duration-ms="386" started-at="2010-02-17T15:36:38Z" finished-at="2010-02-17T15:36:38Z">
1260         </test-method>
1261       </class>
1262       <class name="compbio.engine.PulledFileCacheTester">
1263         <test-method status="PASS" signature="test()" name="test" duration-ms="5187" started-at="2010-02-17T15:34:33Z" finished-at="2010-02-17T15:34:38Z">
1264         </test-method>
1265       </class>
1266       <class name="compbio.runner._impl.RPSBlastTester">
1267         <test-method status="PASS" signature="testGetTestArgsCommand()" name="testGetTestArgsCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
1268         </test-method>
1269         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="0" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
1270         </test-method>
1271       </class>
1272       <class name="compbio.runner.msa.ClustalWParametersTester">
1273         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="369" started-at="2010-02-17T15:34:17Z" finished-at="2010-02-17T15:34:17Z">
1274         </test-method>
1275         <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="3518" started-at="2010-02-17T15:34:17Z" finished-at="2010-02-17T15:34:20Z">
1276         </test-method>
1277         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="33" started-at="2010-02-17T15:34:20Z" finished-at="2010-02-17T15:34:20Z">
1278         </test-method>
1279         <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="1" started-at="2010-02-17T15:34:20Z" finished-at="2010-02-17T15:34:20Z">
1280         </test-method>
1281         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="26" started-at="2010-02-17T15:34:20Z" finished-at="2010-02-17T15:34:20Z">
1282         </test-method>
1283         <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="1835" started-at="2010-02-17T15:34:20Z" finished-at="2010-02-17T15:34:22Z">
1284         </test-method>
1285         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="30" started-at="2010-02-17T15:34:22Z" finished-at="2010-02-17T15:34:22Z">
1286         </test-method>
1287         <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="1232" started-at="2010-02-17T15:34:22Z" finished-at="2010-02-17T15:34:24Z">
1288         </test-method>
1289         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="61" started-at="2010-02-17T15:34:24Z" finished-at="2010-02-17T15:34:24Z">
1290         </test-method>
1291         <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="3105" started-at="2010-02-17T15:34:24Z" finished-at="2010-02-17T15:34:27Z">
1292         </test-method>
1293         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="53" started-at="2010-02-17T15:34:27Z" finished-at="2010-02-17T15:34:27Z">
1294         </test-method>
1295         <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="502" started-at="2010-02-17T15:34:27Z" finished-at="2010-02-17T15:34:27Z">
1296         </test-method>
1297         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="56" started-at="2010-02-17T15:34:27Z" finished-at="2010-02-17T15:34:27Z">
1298         </test-method>
1299         <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="2109" started-at="2010-02-17T15:34:27Z" finished-at="2010-02-17T15:34:29Z">
1300         </test-method>
1301         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="54" started-at="2010-02-17T15:34:29Z" finished-at="2010-02-17T15:34:30Z">
1302         </test-method>
1303         <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="2680" started-at="2010-02-17T15:34:30Z" finished-at="2010-02-17T15:34:32Z">
1304         </test-method>
1305         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="77" started-at="2010-02-17T15:34:32Z" finished-at="2010-02-17T15:34:32Z">
1306         </test-method>
1307         <test-method status="PASS" signature="testPresets()" name="testPresets" duration-ms="177" started-at="2010-02-17T15:34:32Z" finished-at="2010-02-17T15:34:32Z">
1308         </test-method>
1309       </class>
1310       <class name="compbio.runner._impl.MclTester">
1311         <test-method status="PASS" signature="testGetTestCommand()" name="testGetTestCommand" duration-ms="1" started-at="2010-02-17T15:36:39Z" finished-at="2010-02-17T15:36:39Z">
1312         </test-method>
1313       </class>
1314       <class name="compbio.engine.cluster.dundee._QueueTester">
1315         <test-method status="PASS" signature="testQueue()" name="testQueue" duration-ms="0" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
1316         </test-method>
1317       </class>
1318       <class name="compbio.runner.msa.ProbconsParametersTester">
1319         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="50" started-at="2010-02-17T15:39:09Z" finished-at="2010-02-17T15:39:09Z">
1320         </test-method>
1321         <test-method status="PASS" signature="testArguments()" name="testArguments" duration-ms="2874" started-at="2010-02-17T15:39:09Z" finished-at="2010-02-17T15:39:12Z">
1322         </test-method>
1323         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="28" started-at="2010-02-17T15:39:12Z" finished-at="2010-02-17T15:39:12Z">
1324         </test-method>
1325         <test-method status="PASS" signature="testConfiguration()" name="testConfiguration" duration-ms="1" started-at="2010-02-17T15:39:12Z" finished-at="2010-02-17T15:39:12Z">
1326         </test-method>
1327         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="29" started-at="2010-02-17T15:39:12Z" finished-at="2010-02-17T15:39:12Z">
1328         </test-method>
1329         <test-method status="PASS" signature="testConstrainedParametersMaxValues()" name="testConstrainedParametersMaxValues" duration-ms="38416" started-at="2010-02-17T15:39:12Z" finished-at="2010-02-17T15:39:50Z">
1330         </test-method>
1331         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="38" started-at="2010-02-17T15:39:50Z" finished-at="2010-02-17T15:39:50Z">
1332         </test-method>
1333         <test-method status="PASS" signature="testConstrainedParametersMinValues()" name="testConstrainedParametersMinValues" duration-ms="768" started-at="2010-02-17T15:39:50Z" finished-at="2010-02-17T15:39:51Z">
1334         </test-method>
1335         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="29" started-at="2010-02-17T15:39:51Z" finished-at="2010-02-17T15:39:51Z">
1336         </test-method>
1337         <test-method status="PASS" signature="testConstrainedParametersRandomValues()" name="testConstrainedParametersRandomValues" duration-ms="61881" started-at="2010-02-17T15:39:51Z" finished-at="2010-02-17T15:40:53Z">
1338         </test-method>
1339         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="29" started-at="2010-02-17T15:40:53Z" finished-at="2010-02-17T15:40:53Z">
1340         </test-method>
1341         <test-method status="PASS" signature="testDefaultParameters()" name="testDefaultParameters" duration-ms="14704" started-at="2010-02-17T15:40:53Z" finished-at="2010-02-17T15:41:08Z">
1342         </test-method>
1343         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="28" started-at="2010-02-17T15:41:08Z" finished-at="2010-02-17T15:41:08Z">
1344         </test-method>
1345         <test-method status="PASS" signature="testOptions()" name="testOptions" duration-ms="433" started-at="2010-02-17T15:41:08Z" finished-at="2010-02-17T15:41:08Z">
1346         </test-method>
1347         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="31" started-at="2010-02-17T15:41:08Z" finished-at="2010-02-17T15:41:08Z">
1348         </test-method>
1349         <test-method status="PASS" signature="testParameters()" name="testParameters" duration-ms="1321" started-at="2010-02-17T15:41:08Z" finished-at="2010-02-17T15:41:09Z">
1350         </test-method>
1351       </class>
1352       <class name="compbio.engine.conf.RunnerConfigMarshallerTester">
1353         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="29" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
1354         </test-method>
1355         <test-method status="PASS" signature="testMarshalling()" name="testMarshalling" duration-ms="20" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
1356         </test-method>
1357         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="16" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:48Z">
1358         </test-method>
1359         <test-method status="PASS" signature="testSchemaFromCodeGeneration()" name="testSchemaFromCodeGeneration" duration-ms="504" started-at="2010-02-17T15:35:48Z" finished-at="2010-02-17T15:35:49Z">
1360         </test-method>
1361         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="67" started-at="2010-02-17T15:35:49Z" finished-at="2010-02-17T15:35:49Z">
1362         </test-method>
1363         <test-method status="PASS" signature="testUnMarshalling()" name="testUnMarshalling" duration-ms="580" started-at="2010-02-17T15:35:49Z" finished-at="2010-02-17T15:35:50Z">
1364         </test-method>
1365         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="18" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:50Z">
1366         </test-method>
1367         <test-method status="PASS" signature="testValidation()" name="testValidation" duration-ms="636" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:50Z">
1368         </test-method>
1369         <test-method status="PASS" signature="setup()" name="setup" is-config="true" duration-ms="16" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:50Z">
1370         </test-method>
1371         <test-method status="PASS" signature="testValidationOnMarshalling()" name="testValidationOnMarshalling" duration-ms="11" started-at="2010-02-17T15:35:50Z" finished-at="2010-02-17T15:35:50Z">
1372           <exception class="javax.xml.bind.MarshalException">
1373             <full-stacktrace>
1374               <![CDATA[javax.xml.bind.MarshalException
1375  - with linked exception:
1376 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
1377         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
1378         at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
1379         at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
1380         at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
1381         at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
1382         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1383         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1384         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1385         at java.lang.reflect.Method.invoke(Method.java:597)
1386         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1387         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1388         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1389         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1390         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1391         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1392         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1393         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1394         at org.testng.TestRunner.run(TestRunner.java:486)
1395         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1396         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1397         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1398         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1399         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1400         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1401         at org.testng.TestNG.run(TestNG.java:784)
1402         at org.testng.TestNG.privateMain(TestNG.java:949)
1403         at org.testng.TestNG.main(TestNG.java:922)
1404 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.
1405         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
1406         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
1407         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
1408         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
1409         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
1410         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
1411         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
1412         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
1413         at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
1414         at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
1415         at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
1416         at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
1417         at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
1418         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
1419         at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
1420         at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
1421         at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
1422         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
1423         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
1424         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
1425         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
1426         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
1427         ... 26 more
1428 ]]>
1429             </full-stacktrace>
1430           </exception>
1431         </test-method>
1432       </class>
1433     </test>
1434   </suite>
1435 </testng-results>