website/tests/Ant suite/Ant test.html

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  55 <body>
  56 <h2 align='center'>Ant test</h2><table border='1' align="center">
  57 <tr>
  58 <td>Tests passed/Failed/Skipped:</td><td>165/0/0</td>
  59 </tr><tr>
  60 <td>Started on:</td><td>Wed Feb 17 15:34:08 GMT 2010</td>
  61 </tr>
  62 <tr><td>Total time:</td><td>524 seconds (524407 ms)</td>
  63 </tr><tr>
  64 <td>Included groups:</td><td></td>
  65 </tr><tr>
  66 <td>Excluded groups:</td><td>performance </td>
  67 </tr>
  68 </table><p/>
  69 <small><i>(Hover the method name to see the test class name)</i></small><p/>
  70 <table width='100%' border='1' class='invocation-passed'>
  71 <tr><td colspan='4' align='center'><b>PASSED TESTS</b></td></tr>
  72 <tr><td><b>Test method</b></td>
  73 <td><b>Instance</b></td>
  74 <td width="10%"><b>Time (seconds)</b></td>
  75 <td width="30%"><b>Exception</b></td>
  76 </tr>
  77 <tr>
  78 <td title='compbio.metadata.PresetTester.marshallPreset()'><b>marshallPreset</b><br>Test class:Ant test</td>
  79 <td>compbio.metadata.PresetTester@50009f0d</td><td>0</td>
  80 <td></td>
  81 </tr>
  82 <tr>
  83 <td title='compbio.runner.msa.ClustalWTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
  84 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>1</td>
  85 <td></td>
  86 </tr>
  87 <tr>
  88 <td title='compbio.runner.msa.MafftTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
  89 <td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
  90 <td></td>
  91 </tr>
  92 <tr>
  93 <td title='compbio.runner.msa.MuscleTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
  94 <td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
  95 <td></td>
  96 </tr>
  97 <tr>
  98 <td title='compbio.runner.msa.ProbconsTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
  99 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
 100 <td></td>
 101 </tr>
 102 <tr>
 103 <td title='compbio.runner.msa.TcoffeeTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
 104 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
 105 <td></td>
 106 </tr>
 107 <tr>
 108 <td title='compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()'><b>readStatisticsClusterExecution</b><br>Test class:Ant test</td>
 109 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>8</td>
 110 <td></td>
 111 </tr>
 112 <tr>
 113 <td title='compbio.engine.PulledFileCacheTester.test()'><b>test</b><br>Test class:Ant test</td>
 114 <td>compbio.engine.PulledFileCacheTester@1164b9b6</td><td>5</td>
 115 <td></td>
 116 </tr>
 117 <tr>
 118 <td title='compbio.runner.msa.ClustalWParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
 119 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>3</td>
 120 <td></td>
 121 </tr>
 122 <tr>
 123 <td title='compbio.runner.msa.MafftParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
 124 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>6</td>
 125 <td></td>
 126 </tr>
 127 <tr>
 128 <td title='compbio.runner.msa.MuscleParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
 129 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>7</td>
 130 <td></td>
 131 </tr>
 132 <tr>
 133 <td title='compbio.runner.msa.ProbconsParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
 134 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>2</td>
 135 <td></td>
 136 </tr>
 137 <tr>
 138 <td title='compbio.runner.msa.TcoffeeParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
 139 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>8</td>
 140 <td></td>
 141 </tr>
 142 <tr>
 143 <td title='compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation()'><b>testAsyncCancelOperation</b><br>Test class:Ant test</td>
 144 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
 145 <td></td>
 146 </tr>
 147 <tr>
 148 <td title='compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation()'><b>testAsyncRetrievOperation</b><br>Test class:Ant test</td>
 149 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
 150 <td></td>
 151 </tr>
 152 <tr>
 153 <td title='compbio.engine.FilePullerTester.testCache()'><b>testCache</b><br>Test class:Ant test</td>
 154 <td>compbio.engine.FilePullerTester@5fa80aea</td><td>6</td>
 155 <td></td>
 156 </tr>
 157 <tr>
 158 <td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()'><b>testCancel</b><br>Test class:Ant test</td>
 159 <td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18</td><td>1</td>
 160 <td><div><pre>compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
 161         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
 162         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
 163         at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
 164         at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
 165 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!
 166         at compbio.runner.Util.readClustalFile(Util.java:126)
 167         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
 168         ... 25 more
 169 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1915626539", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
 170 <div class='stack-trace' id='stack-trace1915626539'><pre>compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
 171         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
 172         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
 173         at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
 174         at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
 175         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 176         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 177         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 178         at java.lang.reflect.Method.invoke(Method.java:597)
 179         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 180         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 181         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 182         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 183         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 184         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 185         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 186         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 187         at org.testng.TestRunner.run(TestRunner.java:486)
 188         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 189         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 190         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 191         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 192         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 193         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 194         at org.testng.TestNG.run(TestNG.java:784)
 195         at org.testng.TestNG.privateMain(TestNG.java:949)
 196         at org.testng.TestNG.main(TestNG.java:922)
 197 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!
 198         at compbio.runner.Util.readClustalFile(Util.java:126)
 199         at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
 200         ... 25 more
 201 </pre></div></td>
 202 </tr>
 203 <tr>
 204 <td title='compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()'><b>testCancel</b><br>Test class:Ant test</td>
 205 <td>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@4301ac93</td><td>1</td>
 206 <td></td>
 207 </tr>
 208 <tr>
 209 <td title='compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally()'><b>testCancelCompletedTaskLocally</b><br>Test class:Ant test</td>
 210 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>3</td>
 211 <td></td>
 212 </tr>
 213 <tr>
 214 <td title='compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally()'><b>testCancelCompletedTaskLocally</b><br>Test class:Ant test</td>
 215 <td>compbio.engine.local.LocalRunnerTester@4b2922f6</td><td>0</td>
 216 <td><div><pre>java.util.concurrent.CancellationException
 217         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 218         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 219         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 220         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 221         at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
 222 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1132612908", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
 223 <div class='stack-trace' id='stack-trace1132612908'><pre>java.util.concurrent.CancellationException
 224         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 225         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 226         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 227         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 228         at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
 229         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 230         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 231         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 232         at java.lang.reflect.Method.invoke(Method.java:597)
 233         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 234         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 235         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 236         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 237         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 238         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 239         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 240         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 241         at org.testng.TestRunner.run(TestRunner.java:486)
 242         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 243         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 244         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 245         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 246         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 247         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 248         at org.testng.TestNG.run(TestNG.java:784)
 249         at org.testng.TestNG.privateMain(TestNG.java:949)
 250         at org.testng.TestNG.main(TestNG.java:922)
 251 </pre></div></td>
 252 </tr>
 253 <tr>
 254 <td title='compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally()'><b>testCancelLocally</b><br>Test class:Ant test</td>
 255 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
 256 <td><div><pre>java.util.concurrent.CancellationException
 257         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 258         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 259         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 260         at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 261         at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
 262 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1931494437", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
 263 <div class='stack-trace' id='stack-trace1931494437'><pre>java.util.concurrent.CancellationException
 264         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 265         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 266         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 267         at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 268         at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
 269         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 270         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 271         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 272         at java.lang.reflect.Method.invoke(Method.java:597)
 273         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 274         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 275         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 276         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 277         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 278         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 279         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 280         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 281         at org.testng.TestRunner.run(TestRunner.java:486)
 282         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 283         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 284         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 285         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 286         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 287         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 288         at org.testng.TestNG.run(TestNG.java:784)
 289         at org.testng.TestNG.privateMain(TestNG.java:949)
 290         at org.testng.TestNG.main(TestNG.java:922)
 291 </pre></div></td>
 292 </tr>
 293 <tr>
 294 <td title='compbio.engine.local.LocalRunnerTester.testCancelLocally()'><b>testCancelLocally</b><br>Test class:Ant test</td>
 295 <td>compbio.engine.local.LocalRunnerTester@4b2922f6</td><td>0</td>
 296 <td><div><pre>java.util.concurrent.CancellationException
 297         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 298         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 299         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 300         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 301         at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
 302 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1100010806", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
 303 <div class='stack-trace' id='stack-trace1100010806'><pre>java.util.concurrent.CancellationException
 304         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 305         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 306         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 307         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 308         at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
 309         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 310         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 311         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 312         at java.lang.reflect.Method.invoke(Method.java:597)
 313         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 314         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 315         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 316         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 317         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 318         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 319         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 320         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 321         at org.testng.TestRunner.run(TestRunner.java:486)
 322         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 323         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 324         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 325         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 326         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 327         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 328         at org.testng.TestNG.run(TestNG.java:784)
 329         at org.testng.TestNG.privateMain(TestNG.java:949)
 330         at org.testng.TestNG.main(TestNG.java:922)
 331 </pre></div></td>
 332 </tr>
 333 <tr>
 334 <td title='compbio.data.sequence.SequenceUtilTester.testCleanSequence()'><b>testCleanSequence</b><br>Test class:Ant test</td>
 335 <td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
 336 <td></td>
 337 </tr>
 338 <tr>
 339 <td title='compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()'><b>testClusterEngineConf</b><br>Test class:Ant test</td>
 340 <td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
 341 <td></td>
 342 </tr>
 343 <tr>
 344 <td title='compbio.runner.msa.MafftTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
 345 <td>compbio.runner.msa.MafftTester@259a8416</td><td>11</td>
 346 <td></td>
 347 </tr>
 348 <tr>
 349 <td title='compbio.runner.msa.ProbconsTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
 350 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>19</td>
 351 <td></td>
 352 </tr>
 353 <tr>
 354 <td title='compbio.runner.msa.TcoffeeTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
 355 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>5</td>
 356 <td></td>
 357 </tr>
 358 <tr>
 359 <td title='compbio.engine.client.CommandBuilderTester.testCommandBuilding()'><b>testCommandBuilding</b><br>Test class:Ant test</td>
 360 <td>compbio.engine.client.CommandBuilderTester@6bdc64a5</td><td>0</td>
 361 <td></td>
 362 </tr>
 363 <tr>
 364 <td title='compbio.runner.msa.ClustalWParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
 365 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>0</td>
 366 <td></td>
 367 </tr>
 368 <tr>
 369 <td title='compbio.runner.msa.MafftParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
 370 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>0</td>
 371 <td></td>
 372 </tr>
 373 <tr>
 374 <td title='compbio.runner.msa.MuscleParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
 375 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
 376 <td></td>
 377 </tr>
 378 <tr>
 379 <td title='compbio.runner.msa.ProbconsParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
 380 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>0</td>
 381 <td></td>
 382 </tr>
 383 <tr>
 384 <td title='compbio.runner.msa.TcoffeeParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
 385 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>0</td>
 386 <td></td>
 387 </tr>
 388 <tr>
 389 <td title='compbio.runner.msa.ClustalWTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
 390 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
 391 <td></td>
 392 </tr>
 393 <tr>
 394 <td title='compbio.runner.msa.MafftTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
 395 <td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
 396 <td></td>
 397 </tr>
 398 <tr>
 399 <td title='compbio.runner.msa.MuscleTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
 400 <td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
 401 <td></td>
 402 </tr>
 403 <tr>
 404 <td title='compbio.runner.msa.ProbconsTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
 405 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
 406 <td></td>
 407 </tr>
 408 <tr>
 409 <td title='compbio.runner.msa.TcoffeeTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
 410 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
 411 <td></td>
 412 </tr>
 413 <tr>
 414 <td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
 415 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>1</td>
 416 <td></td>
 417 </tr>
 418 <tr>
 419 <td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
 420 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>3</td>
 421 <td></td>
 422 </tr>
 423 <tr>
 424 <td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
 425 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>1</td>
 426 <td></td>
 427 </tr>
 428 <tr>
 429 <td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
 430 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>38</td>
 431 <td></td>
 432 </tr>
 433 <tr>
 434 <td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
 435 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>11</td>
 436 <td></td>
 437 </tr>
 438 <tr>
 439 <td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
 440 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>1</td>
 441 <td></td>
 442 </tr>
 443 <tr>
 444 <td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
 445 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>1</td>
 446 <td></td>
 447 </tr>
 448 <tr>
 449 <td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
 450 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
 451 <td></td>
 452 </tr>
 453 <tr>
 454 <td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
 455 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>0</td>
 456 <td></td>
 457 </tr>
 458 <tr>
 459 <td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
 460 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>5</td>
 461 <td></td>
 462 </tr>
 463 <tr>
 464 <td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
 465 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>3</td>
 466 <td></td>
 467 </tr>
 468 <tr>
 469 <td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
 470 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>7</td>
 471 <td></td>
 472 </tr>
 473 <tr>
 474 <td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
 475 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>7</td>
 476 <td></td>
 477 </tr>
 478 <tr>
 479 <td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
 480 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>61</td>
 481 <td></td>
 482 </tr>
 483 <tr>
 484 <td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
 485 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>21</td>
 486 <td></td>
 487 </tr>
 488 <tr>
 489 <td title='compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue()'><b>testCreateNumParameterWithoutValidValue</b><br>Test class:Ant test</td>
 490 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
 491 <td><div><pre>java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
 492 Description: DNA weight matrix
 493 URL: null
 494 Is required: false
 495
 496  Without possible values! Please define possible value first!
 497         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
 498         at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
 499 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace713889609", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
 500 <div class='stack-trace' id='stack-trace713889609'><pre>java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
 501 Description: DNA weight matrix
 502 URL: null
 503 Is required: false
 504
 505  Without possible values! Please define possible value first!
 506         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
 507         at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
 508         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 509         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 510         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 511         at java.lang.reflect.Method.invoke(Method.java:597)
 512         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 513         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 514         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 515         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 516         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 517         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 518         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 519         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 520         at org.testng.TestRunner.run(TestRunner.java:486)
 521         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 522         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 523         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 524         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 525         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 526         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 527         at org.testng.TestNG.run(TestNG.java:784)
 528         at org.testng.TestNG.privateMain(TestNG.java:949)
 529         at org.testng.TestNG.main(TestNG.java:922)
 530 </pre></div></td>
 531 </tr>
 532 <tr>
 533 <td title='compbio.metadata.RunnerConfigTester.testCreateParameter()'><b>testCreateParameter</b><br>Test class:Ant test</td>
 534 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
 535 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
 536 Description: Protein weight matrix
 537 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 538 Is required: true
 539 Option Names:
 540 --AAMATRIX
 541 POSSIBLE VALUES:
 542 BLOSUM
 543 GONNET
 544 ID
 545 PAM
 546
 547
 548         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
 549         at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
 550 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace321958204", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
 551 <div class='stack-trace' id='stack-trace321958204'><pre>compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
 552 Description: Protein weight matrix
 553 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 554 Is required: true
 555 Option Names:
 556 --AAMATRIX
 557 POSSIBLE VALUES:
 558 BLOSUM
 559 GONNET
 560 ID
 561 PAM
 562
 563
 564         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
 565         at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
 566         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 567         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 568         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 569         at java.lang.reflect.Method.invoke(Method.java:597)
 570         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 571         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 572         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 573         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 574         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 575         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 576         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 577         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 578         at org.testng.TestRunner.run(TestRunner.java:486)
 579         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 580         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 581         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 582         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 583         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 584         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 585         at org.testng.TestNG.run(TestNG.java:784)
 586         at org.testng.TestNG.privateMain(TestNG.java:949)
 587         at org.testng.TestNG.main(TestNG.java:922)
 588 </pre></div></td>
 589 </tr>
 590 <tr>
 591 <td title='compbio.metadata.RunnerConfigTester.testCreateParameterWithValidValueConstrain()'><b>testCreateParameterWithValidValueConstrain</b><br>Test class:Ant test</td>
 592 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
 593 <td></td>
 594 </tr>
 595 <tr>
 596 <td title='compbio.data.sequence.SequenceUtilTester.testDeepCleanSequence()'><b>testDeepCleanSequence</b><br>Test class:Ant test</td>
 597 <td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
 598 <td></td>
 599 </tr>
 600 <tr>
 601 <td title='compbio.runner.msa.ClustalWParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
 602 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>0</td>
 603 <td></td>
 604 </tr>
 605 <tr>
 606 <td title='compbio.runner.msa.MafftParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
 607 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>20</td>
 608 <td></td>
 609 </tr>
 610 <tr>
 611 <td title='compbio.runner.msa.MuscleParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
 612 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
 613 <td></td>
 614 </tr>
 615 <tr>
 616 <td title='compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
 617 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>14</td>
 618 <td></td>
 619 </tr>
 620 <tr>
 621 <td title='compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
 622 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>10</td>
 623 <td></td>
 624 </tr>
 625 <tr>
 626 <td title='compbio.runner.msa.MafftTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
 627 <td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
 628 <td></td>
 629 </tr>
 630 <tr>
 631 <td title='compbio.runner.msa.ProbconsTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
 632 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
 633 <td></td>
 634 </tr>
 635 <tr>
 636 <td title='compbio.runner.msa.TcoffeeTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
 637 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
 638 <td></td>
 639 </tr>
 640 <tr>
 641 <td title='compbio.engine.FilePullerTester.testGet()'><b>testGet</b><br>Test class:Ant test</td>
 642 <td>compbio.engine.FilePullerTester@5fa80aea</td><td>0</td>
 643 <td></td>
 644 </tr>
 645 <tr>
 646 <td title='compbio.engine.EngineConfiguratorTester.testGetAsyncEngine()'><b>testGetAsyncEngine</b><br>Test class:Ant test</td>
 647 <td>compbio.engine.EngineConfiguratorTester@31f9338f</td><td>0</td>
 648 <td></td>
 649 </tr>
 650 <tr>
 651 <td title='compbio.engine.client.PathValidatorTester.testGetClassPath()'><b>testGetClassPath</b><br>Test class:Ant test</td>
 652 <td>compbio.engine.client.PathValidatorTester@5253c3f5</td><td>0</td>
 653 <td></td>
 654 </tr>
 655 <tr>
 656 <td title='compbio.engine.FilePullerTester.testGetDelay()'><b>testGetDelay</b><br>Test class:Ant test</td>
 657 <td>compbio.engine.FilePullerTester@5fa80aea</td><td>0</td>
 658 <td></td>
 659 </tr>
 660 <tr>
 661 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
 662 <td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
 663 <td></td>
 664 </tr>
 665 <tr>
 666 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
 667 <td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
 668 <td></td>
 669 </tr>
 670 <tr>
 671 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
 672 <td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
 673 <td></td>
 674 </tr>
 675 <tr>
 676 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
 677 <td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
 678 <td></td>
 679 </tr>
 680 <tr>
 681 <td title='compbio.data.sequence.FastaSequenceTester.testGetFormattedFasta()'><b>testGetFormattedFasta</b><br>Test class:Ant test</td>
 682 <td>compbio.data.sequence.FastaSequenceTester@ec0a9f9</td><td>0</td>
 683 <td></td>
 684 </tr>
 685 <tr>
 686 <td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()'><b>testGetJobStatus</b><br>Test class:Ant test</td>
 687 <td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18</td><td>20</td>
 688 <td></td>
 689 </tr>
 690 <tr>
 691 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
 692 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>20</td>
 693 <td></td>
 694 </tr>
 695 <tr>
 696 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
 697 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>20</td>
 698 <td></td>
 699 </tr>
 700 <tr>
 701 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
 702 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>21</td>
 703 <td></td>
 704 </tr>
 705 <tr>
 706 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
 707 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>40</td>
 708 <td></td>
 709 </tr>
 710 <tr>
 711 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
 712 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>20</td>
 713 <td></td>
 714 </tr>
 715 <tr>
 716 <td title='compbio.engine.EngineConfiguratorTester.testGetSyncEngine()'><b>testGetSyncEngine</b><br>Test class:Ant test</td>
 717 <td>compbio.engine.EngineConfiguratorTester@31f9338f</td><td>0</td>
 718 <td></td>
 719 </tr>
 720 <tr>
 721 <td title='compbio.runner._impl.OBTester.testGetTestArgsCommand()'><b>testGetTestArgsCommand</b><br>Test class:Ant test</td>
 722 <td>compbio.runner._impl.OBTester@327124af</td><td>0</td>
 723 <td></td>
 724 </tr>
 725 <tr>
 726 <td title='compbio.runner._impl.RPSBlastTester.testGetTestArgsCommand()'><b>testGetTestArgsCommand</b><br>Test class:Ant test</td>
 727 <td>compbio.runner._impl.RPSBlastTester@221f7708</td><td>0</td>
 728 <td></td>
 729 </tr>
 730 <tr>
 731 <td title='compbio.runner._impl.MclTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
 732 <td>compbio.runner._impl.MclTester@4402a6ff</td><td>0</td>
 733 <td></td>
 734 </tr>
 735 <tr>
 736 <td title='compbio.runner._impl.NetNglycTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
 737 <td>compbio.runner._impl.NetNglycTester@a21d23b</td><td>0</td>
 738 <td></td>
 739 </tr>
 740 <tr>
 741 <td title='compbio.runner._impl.OBTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
 742 <td>compbio.runner._impl.OBTester@327124af</td><td>0</td>
 743 <td></td>
 744 </tr>
 745 <tr>
 746 <td title='compbio.runner._impl.RPSBlastTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
 747 <td>compbio.runner._impl.RPSBlastTester@221f7708</td><td>0</td>
 748 <td></td>
 749 </tr>
 750 <tr>
 751 <td title='compbio.runner._impl.RonnTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
 752 <td>compbio.runner._impl.RonnTester@3fbfbfb8</td><td>0</td>
 753 <td></td>
 754 </tr>
 755 <tr>
 756 <td title='compbio.runner._impl.Tmhmm2Tester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
 757 <td>compbio.runner._impl.Tmhmm2Tester@45c3e9ba</td><td>0</td>
 758 <td></td>
 759 </tr>
 760 <tr>
 761 <td title='compbio.engine.client.PathValidatorTester.testIsAbsolutePath()'><b>testIsAbsolutePath</b><br>Test class:Ant test</td>
 762 <td>compbio.engine.client.PathValidatorTester@5253c3f5</td><td>0</td>
 763 <td></td>
 764 </tr>
 765 <tr>
 766 <td title='compbio.runner.msa.LimitTester.testLoadLimits()'><b>testLoadLimits</b><br>Test class:Ant test</td>
 767 <td>compbio.runner.msa.LimitTester@1b0c6cfc</td><td>0</td>
 768 <td></td>
 769 </tr>
 770 <tr>
 771 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testMarshalling()'><b>testMarshalling</b><br>Test class:Ant test</td>
 772 <td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
 773 <td></td>
 774 </tr>
 775 <tr>
 776 <td title='compbio.metadata.OptionMarshallerTester.testMarshalling()'><b>testMarshalling</b><br>Test class:Ant test</td>
 777 <td>compbio.metadata.OptionMarshallerTester@372c9557</td><td>0</td>
 778 <td><div><pre>javax.xml.bind.MarshalException
 779  - with linked exception:
 780 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
 781         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
 782         at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
 783         at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
 784         at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
 785         at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
 786 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.
 787         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
 788         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
 789         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
 790         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
 791         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
 792         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
 793         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
 794         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
 795         at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
 796         at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
 797         at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
 798         at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
 799         at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
 800         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
 801         at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
 802         at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
 803         at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
 804         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
 805         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
 806         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
 807         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
 808         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
 809         ... 26 more
 810 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1691463635", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
 811 <div class='stack-trace' id='stack-trace1691463635'><pre>javax.xml.bind.MarshalException
 812  - with linked exception:
 813 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
 814         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
 815         at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
 816         at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
 817         at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
 818         at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
 819         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 820         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 821         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 822         at java.lang.reflect.Method.invoke(Method.java:597)
 823         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 824         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 825         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 826         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 827         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 828         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 829         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 830         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 831         at org.testng.TestRunner.run(TestRunner.java:486)
 832         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 833         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 834         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 835         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 836         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 837         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 838         at org.testng.TestNG.run(TestNG.java:784)
 839         at org.testng.TestNG.privateMain(TestNG.java:949)
 840         at org.testng.TestNG.main(TestNG.java:922)
 841 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.
 842         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
 843         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
 844         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
 845         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
 846         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
 847         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
 848         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
 849         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
 850         at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
 851         at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
 852         at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
 853         at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
 854         at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
 855         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
 856         at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
 857         at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
 858         at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
 859         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
 860         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
 861         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
 862         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
 863         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
 864         ... 26 more
 865 </pre></div></td>
 866 </tr>
 867 <tr>
 868 <td title='compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally()'><b>testMultipleCancelLocally</b><br>Test class:Ant test</td>
 869 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
 870 <td><div><pre>java.util.concurrent.CancellationException
 871         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 872         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 873         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 874         at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 875         at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
 876 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1281054121", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
 877 <div class='stack-trace' id='stack-trace1281054121'><pre>java.util.concurrent.CancellationException
 878         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 879         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 880         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 881         at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
 882         at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
 883         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 884         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 885         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 886         at java.lang.reflect.Method.invoke(Method.java:597)
 887         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 888         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 889         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 890         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 891         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 892         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 893         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 894         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 895         at org.testng.TestRunner.run(TestRunner.java:486)
 896         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 897         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 898         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 899         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 900         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 901         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 902         at org.testng.TestNG.run(TestNG.java:784)
 903         at org.testng.TestNG.privateMain(TestNG.java:949)
 904         at org.testng.TestNG.main(TestNG.java:922)
 905 </pre></div></td>
 906 </tr>
 907 <tr>
 908 <td title='compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally()'><b>testMultipleCancelLocally</b><br>Test class:Ant test</td>
 909 <td>compbio.engine.local.LocalRunnerTester@4b2922f6</td><td>0</td>
 910 <td><div><pre>java.util.concurrent.CancellationException
 911         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 912         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 913         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 914         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 915         at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
 916 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace764924063", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
 917 <div class='stack-trace' id='stack-trace764924063'><pre>java.util.concurrent.CancellationException
 918         at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
 919         at java.util.concurrent.FutureTask.get(FutureTask.java:83)
 920         at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
 921         at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
 922         at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
 923         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 924         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 925         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 926         at java.lang.reflect.Method.invoke(Method.java:597)
 927         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 928         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 929         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 930         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 931         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 932         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 933         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 934         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 935         at org.testng.TestRunner.run(TestRunner.java:486)
 936         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 937         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 938         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 939         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 940         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 941         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 942         at org.testng.TestNG.run(TestNG.java:784)
 943         at org.testng.TestNG.privateMain(TestNG.java:949)
 944         at org.testng.TestNG.main(TestNG.java:922)
 945 </pre></div></td>
 946 </tr>
 947 <tr>
 948 <td title='compbio.runner.msa.TcoffeeTester.testNcore()'><b>testNcore</b><br>Test class:Ant test</td>
 949 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
 950 <td></td>
 951 </tr>
 952 <tr>
 953 <td title='compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate()'><b>testOptionNoDefaultValidate</b><br>Test class:Ant test</td>
 954 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
 955 <td><div><pre>javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
 956 Description: Protein weight matrix
 957 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 958 Is required: true
 959 Option Names:
 960 --AAMATRIX
 961 --ABMAT
 962 --BBBB
 963
 964         at compbio.metadata.Option.validate(Option.java:317)
 965         at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
 966 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace283755922", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
 967 <div class='stack-trace' id='stack-trace283755922'><pre>javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
 968 Description: Protein weight matrix
 969 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
 970 Is required: true
 971 Option Names:
 972 --AAMATRIX
 973 --ABMAT
 974 --BBBB
 975
 976         at compbio.metadata.Option.validate(Option.java:317)
 977         at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
 978         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
 979         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
 980         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
 981         at java.lang.reflect.Method.invoke(Method.java:597)
 982         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
 983         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
 984         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
 985         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
 986         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
 987         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
 988         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
 989         at org.testng.TestRunner.privateRun(TestRunner.java:592)
 990         at org.testng.TestRunner.run(TestRunner.java:486)
 991         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
 992         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
 993         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
 994         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
 995         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
 996         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
 997         at org.testng.TestNG.run(TestNG.java:784)
 998         at org.testng.TestNG.privateMain(TestNG.java:949)
 999         at org.testng.TestNG.main(TestNG.java:922)
1000 </pre></div></td>
1001 </tr>
1002 <tr>
1003 <td title='compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue()'><b>testOptionSetInvalidValue</b><br>Test class:Ant test</td>
1004 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1005 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
1006 Description: Protein weight matrix
1007 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1008 Is required: true
1009 Option Names:
1010 --AAMATRIX
1011 --ABMAT
1012 --BBBB
1013
1014         at compbio.metadata.Option.setDefaultValue(Option.java:130)
1015         at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
1016 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1260681385", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1017 <div class='stack-trace' id='stack-trace1260681385'><pre>compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
1018 Description: Protein weight matrix
1019 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1020 Is required: true
1021 Option Names:
1022 --AAMATRIX
1023 --ABMAT
1024 --BBBB
1025
1026         at compbio.metadata.Option.setDefaultValue(Option.java:130)
1027         at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
1028         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1029         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1030         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1031         at java.lang.reflect.Method.invoke(Method.java:597)
1032         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1033         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1034         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1035         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1036         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1037         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1038         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1039         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1040         at org.testng.TestRunner.run(TestRunner.java:486)
1041         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1042         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1043         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1044         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1045         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1046         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1047         at org.testng.TestNG.run(TestNG.java:784)
1048         at org.testng.TestNG.privateMain(TestNG.java:949)
1049         at org.testng.TestNG.main(TestNG.java:922)
1050 </pre></div></td>
1051 </tr>
1052 <tr>
1053 <td title='compbio.metadata.RunnerConfigTester.testOptionToCommand()'><b>testOptionToCommand</b><br>Test class:Ant test</td>
1054 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1055 <td></td>
1056 </tr>
1057 <tr>
1058 <td title='compbio.runner.msa.ClustalWParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1059 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>2</td>
1060 <td></td>
1061 </tr>
1062 <tr>
1063 <td title='compbio.runner.msa.MafftParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1064 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>4</td>
1065 <td></td>
1066 </tr>
1067 <tr>
1068 <td title='compbio.runner.msa.MuscleParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1069 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>2</td>
1070 <td></td>
1071 </tr>
1072 <tr>
1073 <td title='compbio.runner.msa.ProbconsParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1074 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>0</td>
1075 <td></td>
1076 </tr>
1077 <tr>
1078 <td title='compbio.runner.msa.TcoffeeParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1079 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>0</td>
1080 <td></td>
1081 </tr>
1082 <tr>
1083 <td title='compbio.runner.msa.ClustalWTester.testOptionsLocally()'><b>testOptionsLocally</b><br>Test class:Ant test</td>
1084 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>1</td>
1085 <td></td>
1086 </tr>
1087 <tr>
1088 <td title='compbio.engine.client.CommandBuilderTester.testOptionsToCommand()'><b>testOptionsToCommand</b><br>Test class:Ant test</td>
1089 <td>compbio.engine.client.CommandBuilderTester@6bdc64a5</td><td>0</td>
1090 <td></td>
1091 </tr>
1092 <tr>
1093 <td title='compbio.metadata.RunnerConfigTester.testParameterToCommand()'><b>testParameterToCommand</b><br>Test class:Ant test</td>
1094 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1095 <td></td>
1096 </tr>
1097 <tr>
1098 <td title='compbio.runner.msa.ClustalWParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1099 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>2</td>
1100 <td></td>
1101 </tr>
1102 <tr>
1103 <td title='compbio.runner.msa.MafftParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1104 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>2</td>
1105 <td></td>
1106 </tr>
1107 <tr>
1108 <td title='compbio.runner.msa.MuscleParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1109 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>4</td>
1110 <td></td>
1111 </tr>
1112 <tr>
1113 <td title='compbio.runner.msa.ProbconsParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1114 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>1</td>
1115 <td></td>
1116 </tr>
1117 <tr>
1118 <td title='compbio.runner.msa.TcoffeeParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1119 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>12</td>
1120 <td></td>
1121 </tr>
1122 <tr>
1123 <td title='compbio.engine.cluster.drmaa.UtilTester.testParser()'><b>testParser</b><br>Test class:Ant test</td>
1124 <td>compbio.engine.cluster.drmaa.UtilTester@22e90943</td><td>0</td>
1125 <td></td>
1126 </tr>
1127 <tr>
1128 <td title='compbio.runner.msa.ClustalWTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1129 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
1130 <td></td>
1131 </tr>
1132 <tr>
1133 <td title='compbio.runner.msa.MafftTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1134 <td>compbio.runner.msa.MafftTester@259a8416</td><td>1</td>
1135 <td></td>
1136 </tr>
1137 <tr>
1138 <td title='compbio.runner.msa.MuscleTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1139 <td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
1140 <td></td>
1141 </tr>
1142 <tr>
1143 <td title='compbio.runner.msa.ProbconsTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1144 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
1145 <td></td>
1146 </tr>
1147 <tr>
1148 <td title='compbio.runner.msa.TcoffeeTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1149 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>1</td>
1150 <td></td>
1151 </tr>
1152 <tr>
1153 <td title='compbio.runner.msa.ClustalWParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1154 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>0</td>
1155 <td></td>
1156 </tr>
1157 <tr>
1158 <td title='compbio.runner.msa.MafftParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1159 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>2</td>
1160 <td></td>
1161 </tr>
1162 <tr>
1163 <td title='compbio.runner.msa.MuscleParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1164 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
1165 <td></td>
1166 </tr>
1167 <tr>
1168 <td title='compbio.runner.msa.TcoffeeParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1169 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>1</td>
1170 <td></td>
1171 </tr>
1172 <tr>
1173 <td title='compbio.data.sequence.FastaSequenceGeneratorTester.testProteinSequenceGeneration()'><b>testProteinSequenceGeneration</b><br>Test class:Ant test</td>
1174 <td>compbio.data.sequence.FastaSequenceGeneratorTester@163b4b1e</td><td>0</td>
1175 <td></td>
1176 </tr>
1177 <tr>
1178 <td title='compbio.engine.FilePullerTester.testPull()'><b>testPull</b><br>Test class:Ant test</td>
1179 <td>compbio.engine.FilePullerTester@5fa80aea</td><td>0</td>
1180 <td></td>
1181 </tr>
1182 <tr>
1183 <td title='compbio.engine.cluster.dundee._QueueTester.testQueue()'><b>testQueue</b><br>Test class:Ant test</td>
1184 <td>compbio.engine.cluster.dundee._QueueTester@715f1f9c</td><td>0</td>
1185 <td></td>
1186 </tr>
1187 <tr>
1188 <td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFile()'><b>testReadClustalFile</b><br>Test class:Ant test</td>
1189 <td>compbio.data.sequence.ClustalAlignmentUtilTester@38c52200</td><td>0</td>
1190 <td></td>
1191 </tr>
1192 <tr>
1193 <td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileLongNames()'><b>testReadClustalFileLongNames</b><br>Test class:Ant test</td>
1194 <td>compbio.data.sequence.ClustalAlignmentUtilTester@38c52200</td><td>0</td>
1195 <td></td>
1196 </tr>
1197 <tr>
1198 <td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileShortNames()'><b>testReadClustalFileShortNames</b><br>Test class:Ant test</td>
1199 <td>compbio.data.sequence.ClustalAlignmentUtilTester@38c52200</td><td>0</td>
1200 <td></td>
1201 </tr>
1202 <tr>
1203 <td title='compbio.data.sequence.SequenceUtilTester.testReadWriteFasta()'><b>testReadWriteFasta</b><br>Test class:Ant test</td>
1204 <td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
1205 <td></td>
1206 </tr>
1207 <tr>
1208 <td title='compbio.runner.msa.ClustalWTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
1209 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
1210 <td></td>
1211 </tr>
1212 <tr>
1213 <td title='compbio.runner.msa.MuscleTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
1214 <td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
1215 <td></td>
1216 </tr>
1217 <tr>
1218 <td title='compbio.runner.msa.ClustalWTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
1219 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>15</td>
1220 <td></td>
1221 </tr>
1222 <tr>
1223 <td title='compbio.runner.msa.MuscleTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
1224 <td>compbio.runner.msa.MuscleTester@37b994de</td><td>8</td>
1225 <td></td>
1226 </tr>
1227 <tr>
1228 <td title='compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()'><b>testRunOnClusterAsyncCheckStatusLongPoolingTime</b><br>Test class:Ant test</td>
1229 <td>compbio.runner.msa.MafftTester@259a8416</td><td>21</td>
1230 <td></td>
1231 </tr>
1232 <tr>
1233 <td title='compbio.runner.msa.ClustalWTester.testRunWithMatrix()'><b>testRunWithMatrix</b><br>Test class:Ant test</td>
1234 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
1235 <td></td>
1236 </tr>
1237 <tr>
1238 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testSchemaFromCodeGeneration()'><b>testSchemaFromCodeGeneration</b><br>Test class:Ant test</td>
1239 <td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
1240 <td></td>
1241 </tr>
1242 <tr>
1243 <td title='compbio.runner.msa.MafftTester.testSetInputTester()'><b>testSetInputTester</b><br>Test class:Ant test</td>
1244 <td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
1245 <td></td>
1246 </tr>
1247 <tr>
1248 <td title='compbio.runner.msa.ProbconsTester.testSetInputTester()'><b>testSetInputTester</b><br>Test class:Ant test</td>
1249 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
1250 <td></td>
1251 </tr>
1252 <tr>
1253 <td title='compbio.engine.client.CommandBuilderTester.testSpaceDelimiterExecutable()'><b>testSpaceDelimiterExecutable</b><br>Test class:Ant test</td>
1254 <td>compbio.engine.client.CommandBuilderTester@6bdc64a5</td><td>0</td>
1255 <td></td>
1256 </tr>
1257 <tr>
1258 <td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()'><b>testSubmit</b><br>Test class:Ant test</td>
1259 <td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18</td><td>18</td>
1260 <td></td>
1261 </tr>
1262 <tr>
1263 <td title='compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()'><b>testSubmit</b><br>Test class:Ant test</td>
1264 <td>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@4301ac93</td><td>17</td>
1265 <td></td>
1266 </tr>
1267 <tr>
1268 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1269 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
1270 <td></td>
1271 </tr>
1272 <tr>
1273 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1274 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
1275 <td></td>
1276 </tr>
1277 <tr>
1278 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1279 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
1280 <td></td>
1281 </tr>
1282 <tr>
1283 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1284 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
1285 <td></td>
1286 </tr>
1287 <tr>
1288 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1289 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
1290 <td></td>
1291 </tr>
1292 <tr>
1293 <td title='compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()'><b>testTaskList</b><br>Test class:Ant test</td>
1294 <td>compbio.engine.cluster.drmaa.ClusterSessionTester@7966340c</td><td>8</td>
1295 <td></td>
1296 </tr>
1297 <tr>
1298 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testUnMarshalling()'><b>testUnMarshalling</b><br>Test class:Ant test</td>
1299 <td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
1300 <td></td>
1301 </tr>
1302 <tr>
1303 <td title='compbio.metadata.OptionMarshallerTester.testUnMarshalling()'><b>testUnMarshalling</b><br>Test class:Ant test</td>
1304 <td>compbio.metadata.OptionMarshallerTester@372c9557</td><td>0</td>
1305 <td></td>
1306 </tr>
1307 <tr>
1308 <td title='compbio.metadata.RunnerConfigTester.testValidate()'><b>testValidate</b><br>Test class:Ant test</td>
1309 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1310 <td></td>
1311 </tr>
1312 <tr>
1313 <td title='compbio.metadata.RunnerConfigTester.testValidateBoundaryConstrainCheck()'><b>testValidateBoundaryConstrainCheck</b><br>Test class:Ant test</td>
1314 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1315 <td></td>
1316 </tr>
1317 <tr>
1318 <td title='compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck()'><b>testValidateLowerBoundaryConstrainCheck</b><br>Test class:Ant test</td>
1319 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1320 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1321 Min: -10.12
1322 Max: 0
1323
1324  For parameter: Option name: Matrix1
1325 Description: Protein weight matrix
1326 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1327 Is required: true
1328 Option Names:
1329 --AAMATRIX
1330 Type: Float
1331 Min: -10.12
1332 Max: 0
1333
1334
1335         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1336         at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
1337 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1790017034", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1338 <div class='stack-trace' id='stack-trace1790017034'><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1339 Min: -10.12
1340 Max: 0
1341
1342  For parameter: Option name: Matrix1
1343 Description: Protein weight matrix
1344 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1345 Is required: true
1346 Option Names:
1347 --AAMATRIX
1348 Type: Float
1349 Min: -10.12
1350 Max: 0
1351
1352
1353         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1354         at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
1355         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1356         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1357         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1358         at java.lang.reflect.Method.invoke(Method.java:597)
1359         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1360         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1361         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1362         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1363         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1364         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1365         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1366         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1367         at org.testng.TestRunner.run(TestRunner.java:486)
1368         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1369         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1370         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1371         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1372         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1373         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1374         at org.testng.TestNG.run(TestNG.java:784)
1375         at org.testng.TestNG.privateMain(TestNG.java:949)
1376         at org.testng.TestNG.main(TestNG.java:922)
1377 </pre></div></td>
1378 </tr>
1379 <tr>
1380 <td title='compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck()'><b>testValidateUpperBoundaryConstrainCheck</b><br>Test class:Ant test</td>
1381 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1382 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1383 Min: -10.12
1384 Max: 0
1385
1386  For parameter: Option name: Matrix1
1387 Description: Protein weight matrix
1388 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1389 Is required: true
1390 Option Names:
1391 --AAMATRIX
1392 Type: Float
1393 Min: -10.12
1394 Max: 0
1395
1396
1397         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1398         at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
1399 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace603950563", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1400 <div class='stack-trace' id='stack-trace603950563'><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1401 Min: -10.12
1402 Max: 0
1403
1404  For parameter: Option name: Matrix1
1405 Description: Protein weight matrix
1406 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1407 Is required: true
1408 Option Names:
1409 --AAMATRIX
1410 Type: Float
1411 Min: -10.12
1412 Max: 0
1413
1414
1415         at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1416         at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
1417         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1418         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1419         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1420         at java.lang.reflect.Method.invoke(Method.java:597)
1421         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1422         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1423         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1424         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1425         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1426         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1427         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1428         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1429         at org.testng.TestRunner.run(TestRunner.java:486)
1430         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1431         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1432         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1433         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1434         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1435         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1436         at org.testng.TestNG.run(TestNG.java:784)
1437         at org.testng.TestNG.privateMain(TestNG.java:949)
1438         at org.testng.TestNG.main(TestNG.java:922)
1439 </pre></div></td>
1440 </tr>
1441 <tr>
1442 <td title='compbio.metadata.RunnerConfigTester.testValidateValueConstrain()'><b>testValidateValueConstrain</b><br>Test class:Ant test</td>
1443 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1444 <td><div><pre>javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
1445
1446         at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
1447         at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
1448 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1313551855", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1449 <div class='stack-trace' id='stack-trace1313551855'><pre>javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
1450
1451         at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
1452         at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
1453         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1454         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1455         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1456         at java.lang.reflect.Method.invoke(Method.java:597)
1457         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1458         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1459         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1460         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1461         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1462         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1463         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1464         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1465         at org.testng.TestRunner.run(TestRunner.java:486)
1466         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1467         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1468         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1469         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1470         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1471         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1472         at org.testng.TestNG.run(TestNG.java:784)
1473         at org.testng.TestNG.privateMain(TestNG.java:949)
1474         at org.testng.TestNG.main(TestNG.java:922)
1475 </pre></div></td>
1476 </tr>
1477 <tr>
1478 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testValidation()'><b>testValidation</b><br>Test class:Ant test</td>
1479 <td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
1480 <td></td>
1481 </tr>
1482 <tr>
1483 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling()'><b>testValidationOnMarshalling</b><br>Test class:Ant test</td>
1484 <td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
1485 <td><div><pre>javax.xml.bind.MarshalException
1486  - with linked exception:
1487 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
1488         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
1489         at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
1490         at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
1491         at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
1492         at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
1493 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.
1494         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
1495         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
1496         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
1497         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
1498         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
1499         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
1500         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
1501         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
1502         at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
1503         at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
1504         at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
1505         at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
1506         at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
1507         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
1508         at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
1509         at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
1510         at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
1511         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
1512         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
1513         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
1514         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
1515         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
1516         ... 26 more
1517 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace831577209", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1518 <div class='stack-trace' id='stack-trace831577209'><pre>javax.xml.bind.MarshalException
1519  - with linked exception:
1520 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
1521         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
1522         at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
1523         at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
1524         at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
1525         at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
1526         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1527         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1528         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1529         at java.lang.reflect.Method.invoke(Method.java:597)
1530         at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1531         at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1532         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1533         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1534         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1535         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1536         at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1537         at org.testng.TestRunner.privateRun(TestRunner.java:592)
1538         at org.testng.TestRunner.run(TestRunner.java:486)
1539         at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1540         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1541         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1542         at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1543         at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1544         at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1545         at org.testng.TestNG.run(TestNG.java:784)
1546         at org.testng.TestNG.privateMain(TestNG.java:949)
1547         at org.testng.TestNG.main(TestNG.java:922)
1548 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.
1549         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
1550         at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
1551         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
1552         at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
1553         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
1554         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
1555         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
1556         at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
1557         at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
1558         at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
1559         at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
1560         at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
1561         at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
1562         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
1563         at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
1564         at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
1565         at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
1566         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
1567         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
1568         at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
1569         at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
1570         at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
1571         ... 26 more
1572 </pre></div></td>
1573 </tr>
1574 <tr>
1575 <td title='compbio.metadata.OptionCombinatorTester.testgetAllOptions()'><b>testgetAllOptions</b><br>Test class:Ant test</td>
1576 <td>compbio.metadata.OptionCombinatorTester@79b66b06</td><td>0</td>
1577 <td></td>
1578 </tr>
1579 <tr>
1580 <td title='compbio.metadata.OptionCombinatorTester.testgetAllParameters()'><b>testgetAllParameters</b><br>Test class:Ant test</td>
1581 <td>compbio.metadata.OptionCombinatorTester@79b66b06</td><td>0</td>
1582 <td></td>
1583 </tr>
1584 <tr>
1585 <td title='compbio.data.sequence.SequenceUtilTester.testisNonAmbNucleotideSequence()'><b>testisNonAmbNucleotideSequence</b><br>Test class:Ant test</td>
1586 <td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
1587 <td></td>
1588 </tr>
1589 <tr>
1590 <td title='compbio.data.sequence.SequenceUtilTester.testisProteinSequence()'><b>testisProteinSequence</b><br>Test class:Ant test</td>
1591 <td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
1592 <td></td>
1593 </tr>
1594 <tr>
1595 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration()'><b>validateClustalConfiguration</b><br>Test class:Ant test</td>
1596 <td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
1597 <td></td>
1598 </tr>
1599 <tr>
1600 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration()'><b>validateMafftConfiguration</b><br>Test class:Ant test</td>
1601 <td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
1602 <td></td>
1603 </tr>
1604 <tr>
1605 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration()'><b>validateMuscleConfiguration</b><br>Test class:Ant test</td>
1606 <td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
1607 <td></td>
1608 </tr>
1609 <tr>
1610 <td title='compbio.metadata.PresetTester.validatePresets()'><b>validatePresets</b><br>Test class:Ant test</td>
1611 <td>compbio.metadata.PresetTester@50009f0d</td><td>0</td>
1612 <td></td>
1613 </tr>
1614 <tr>
1615 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration()'><b>validateTcoffeeConfiguration</b><br>Test class:Ant test</td>
1616 <td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
1617 <td></td>
1618 </tr>
1619 </table><p>
1620 </body>
1621 </html>