3 <title>TestNG: Ant test</title>
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56 <h2 align='center'>Ant test</h2><table border='1' align="center">
58 <td>Tests passed/Failed/Skipped:</td><td>216/0/0</td>
60 <td>Started on:</td><td>Thu Jun 23 10:34:54 BST 2011</td>
62 <tr><td>Total time:</td><td>453 seconds (453928 ms)</td>
64 <td>Included groups:</td><td></td>
66 <td>Excluded groups:</td><td>webservices performance </td>
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>
78 <td title='compbio.data.sequence.SequenceUtilTester.loadJronnFile()'><b>loadJronnFile</b><br>Test class:Ant test</td>
79 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
83 <td title='compbio.metadata.PresetTester.marshallPreset()'><b>marshallPreset</b><br>Test class:Ant test</td>
84 <td>compbio.metadata.PresetTester@7a4fe91e</td><td>0</td>
88 <td title='compbio.runner.conservation.AAConTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
89 <td>compbio.runner.conservation.AAConTester@1959e6e8</td><td>1</td>
93 <td title='compbio.runner.disorder.DisemblTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
94 <td>compbio.runner.disorder.DisemblTester@5d469658</td><td>0</td>
98 <td title='compbio.runner.disorder.GlobPlotTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
99 <td>compbio.runner.disorder.GlobPlotTester@45389b3f</td><td>0</td>
103 <td title='compbio.runner.disorder.JronnTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
104 <td>compbio.runner.disorder.JronnTester@3d3b5a3a</td><td>18</td>
108 <td title='compbio.runner.msa.ClustalWTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
109 <td>compbio.runner.msa.ClustalWTester@3a0b53e</td><td>0</td>
113 <td title='compbio.runner.msa.MafftTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
114 <td>compbio.runner.msa.MafftTester@5f0f0625</td><td>0</td>
118 <td title='compbio.runner.msa.MuscleTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
119 <td>compbio.runner.msa.MuscleTester@63f8247d</td><td>0</td>
123 <td title='compbio.runner.msa.ProbconsTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
124 <td>compbio.runner.msa.ProbconsTester@32830122</td><td>0</td>
128 <td title='compbio.runner.msa.TcoffeeTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
129 <td>compbio.runner.msa.TcoffeeTester@54a6af6e</td><td>0</td>
133 <td title='compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()'><b>readStatisticsClusterExecution</b><br>Test class:Ant test</td>
134 <td>compbio.runner.msa.ClustalWTester@3a0b53e</td><td>1</td>
138 <td title='compbio.data.sequence.FastaReaderTester.test()'><b>test</b><br>Test class:Ant test</td>
139 <td>compbio.data.sequence.FastaReaderTester@2dc0435</td><td>0</td>
143 <td title='compbio.engine.PulledFileCacheTester.test()'><b>test</b><br>Test class:Ant test</td>
144 <td>compbio.engine.PulledFileCacheTester@472462b3</td><td>5</td>
148 <td title='compbio.runner.msa.ClustalWParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
149 <td>compbio.runner.msa.ClustalWParametersTester@74e2ad16</td><td>1</td>
153 <td title='compbio.runner.msa.MafftParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
154 <td>compbio.runner.msa.MafftParametersTester@35a8d460</td><td>3</td>
158 <td title='compbio.runner.msa.MuscleParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
159 <td>compbio.runner.msa.MuscleParametersTester@535c97e4</td><td>4</td>
163 <td title='compbio.runner.msa.ProbconsParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
164 <td>compbio.runner.msa.ProbconsParametersTester@3823bdd1</td><td>1</td>
168 <td title='compbio.runner.msa.TcoffeeParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
169 <td>compbio.runner.msa.TcoffeeParametersTester@36bf7916</td><td>4</td>
173 <td title='compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation()'><b>testAsyncCancelOperation</b><br>Test class:Ant test</td>
174 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>0</td>
178 <td title='compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation()'><b>testAsyncRetrievOperation</b><br>Test class:Ant test</td>
179 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>0</td>
183 <td title='compbio.engine.FilePullerTester.testCache()'><b>testCache</b><br>Test class:Ant test</td>
184 <td>compbio.engine.FilePullerTester@1e670479</td><td>6</td>
188 <td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()'><b>testCancel</b><br>Test class:Ant test</td>
189 <td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@57c8b24d</td><td>1</td>
190 <td><div><pre>compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/jaba2/local_jobsout/ClustalW#6405924652151282 with file name TO1381.clustal.cluster.out is not found!
191 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:73)
192 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:34)
193 at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:207)
194 at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
195 Caused by: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/jaba2/local_jobsout/ClustalW#6405924652151282 with file name TO1381.clustal.cluster.out is not found!
196 at compbio.runner.Util.readClustalFile(Util.java:93)
197 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:70)
199 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace566947760", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
200 <div class='stack-trace' id='stack-trace566947760'><pre>compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/jaba2/local_jobsout/ClustalW#6405924652151282 with file name TO1381.clustal.cluster.out is not found!
201 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:73)
202 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:34)
203 at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:207)
204 at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
205 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
206 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
207 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
208 at java.lang.reflect.Method.invoke(Method.java:597)
209 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
210 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
211 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
212 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
213 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
214 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
215 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
216 at org.testng.TestRunner.privateRun(TestRunner.java:592)
217 at org.testng.TestRunner.run(TestRunner.java:486)
218 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
219 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
220 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
221 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
222 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
223 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
224 at org.testng.TestNG.run(TestNG.java:784)
225 at org.testng.TestNG.privateMain(TestNG.java:949)
226 at org.testng.TestNG.main(TestNG.java:922)
227 Caused by: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/jaba2/local_jobsout/ClustalW#6405924652151282 with file name TO1381.clustal.cluster.out is not found!
228 at compbio.runner.Util.readClustalFile(Util.java:93)
229 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:70)
234 <td title='compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()'><b>testCancel</b><br>Test class:Ant test</td>
235 <td>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@39320a41</td><td>1</td>
239 <td title='compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally()'><b>testCancelCompletedTaskLocally</b><br>Test class:Ant test</td>
240 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>3</td>
244 <td title='compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally()'><b>testCancelCompletedTaskLocally</b><br>Test class:Ant test</td>
245 <td>compbio.engine.local.LocalRunnerTester@3fde891b</td><td>0</td>
246 <td><div><pre>java.util.concurrent.CancellationException
247 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
248 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
249 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
250 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
251 at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
252 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace101429742", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
253 <div class='stack-trace' id='stack-trace101429742'><pre>java.util.concurrent.CancellationException
254 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
255 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
256 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
257 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
258 at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
259 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
260 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
261 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
262 at java.lang.reflect.Method.invoke(Method.java:597)
263 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
264 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
265 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
266 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
267 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
268 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
269 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
270 at org.testng.TestRunner.privateRun(TestRunner.java:592)
271 at org.testng.TestRunner.run(TestRunner.java:486)
272 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
273 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
274 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
275 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
276 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
277 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
278 at org.testng.TestNG.run(TestNG.java:784)
279 at org.testng.TestNG.privateMain(TestNG.java:949)
280 at org.testng.TestNG.main(TestNG.java:922)
284 <td title='compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally()'><b>testCancelLocally</b><br>Test class:Ant test</td>
285 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>0</td>
286 <td><div><pre>java.util.concurrent.CancellationException
287 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
288 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
289 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
290 at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
291 at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
292 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1986875184", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
293 <div class='stack-trace' id='stack-trace1986875184'><pre>java.util.concurrent.CancellationException
294 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
295 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
296 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
297 at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
298 at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
299 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
300 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
301 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
302 at java.lang.reflect.Method.invoke(Method.java:597)
303 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
304 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
305 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
306 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
307 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
308 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
309 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
310 at org.testng.TestRunner.privateRun(TestRunner.java:592)
311 at org.testng.TestRunner.run(TestRunner.java:486)
312 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
313 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
314 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
315 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
316 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
317 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
318 at org.testng.TestNG.run(TestNG.java:784)
319 at org.testng.TestNG.privateMain(TestNG.java:949)
320 at org.testng.TestNG.main(TestNG.java:922)
324 <td title='compbio.engine.local.LocalRunnerTester.testCancelLocally()'><b>testCancelLocally</b><br>Test class:Ant test</td>
325 <td>compbio.engine.local.LocalRunnerTester@3fde891b</td><td>0</td>
326 <td><div><pre>java.util.concurrent.CancellationException
327 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
328 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
329 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
330 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
331 at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
332 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace58766585", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
333 <div class='stack-trace' id='stack-trace58766585'><pre>java.util.concurrent.CancellationException
334 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
335 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
336 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
337 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
338 at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
339 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
340 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
341 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
342 at java.lang.reflect.Method.invoke(Method.java:597)
343 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
344 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
345 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
346 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
347 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
348 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
349 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
350 at org.testng.TestRunner.privateRun(TestRunner.java:592)
351 at org.testng.TestRunner.run(TestRunner.java:486)
352 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
353 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
354 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
355 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
356 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
357 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
358 at org.testng.TestNG.run(TestNG.java:784)
359 at org.testng.TestNG.privateMain(TestNG.java:949)
360 at org.testng.TestNG.main(TestNG.java:922)
364 <td title='compbio.data.sequence.SequenceUtilTester.testCleanProteinSequence()'><b>testCleanProteinSequence</b><br>Test class:Ant test</td>
365 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
369 <td title='compbio.data.sequence.SequenceUtilTester.testCleanSequence()'><b>testCleanSequence</b><br>Test class:Ant test</td>
370 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
374 <td title='compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()'><b>testClusterEngineConf</b><br>Test class:Ant test</td>
375 <td>compbio.engine.conf.PropertyHelperManagerTester@4ee14d81</td><td>0</td>
379 <td title='compbio.runner.msa.MafftTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
380 <td>compbio.runner.msa.MafftTester@5f0f0625</td><td>1</td>
384 <td title='compbio.runner.msa.ProbconsTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
385 <td>compbio.runner.msa.ProbconsTester@32830122</td><td>2</td>
389 <td title='compbio.runner.msa.TcoffeeTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
390 <td>compbio.runner.msa.TcoffeeTester@54a6af6e</td><td>5</td>
394 <td title='compbio.stat.collector.ExecutionStatCollectorTester.testCollectStat()'><b>testCollectStat</b><br>Test class:Ant test</td>
395 <td>compbio.stat.collector.ExecutionStatCollectorTester@b478a2d</td><td>0</td>
399 <td title='compbio.engine.client.CommandBuilderTester.testCommandBuilding()'><b>testCommandBuilding</b><br>Test class:Ant test</td>
400 <td>compbio.engine.client.CommandBuilderTester@25cbfa42</td><td>0</td>
404 <td title='compbio.runner.msa.ClustalWParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
405 <td>compbio.runner.msa.ClustalWParametersTester@74e2ad16</td><td>0</td>
409 <td title='compbio.runner.msa.MafftParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
410 <td>compbio.runner.msa.MafftParametersTester@35a8d460</td><td>0</td>
414 <td title='compbio.runner.msa.MuscleParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
415 <td>compbio.runner.msa.MuscleParametersTester@535c97e4</td><td>0</td>
419 <td title='compbio.runner.msa.ProbconsParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
420 <td>compbio.runner.msa.ProbconsParametersTester@3823bdd1</td><td>0</td>
424 <td title='compbio.runner.msa.TcoffeeParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
425 <td>compbio.runner.msa.TcoffeeParametersTester@36bf7916</td><td>0</td>
429 <td title='compbio.runner.conservation.AAConTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
430 <td>compbio.runner.conservation.AAConTester@1959e6e8</td><td>0</td>
434 <td title='compbio.runner.disorder.DisemblTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
435 <td>compbio.runner.disorder.DisemblTester@5d469658</td><td>0</td>
439 <td title='compbio.runner.disorder.GlobPlotTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
440 <td>compbio.runner.disorder.GlobPlotTester@45389b3f</td><td>0</td>
444 <td title='compbio.runner.disorder.IUPredTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
445 <td>compbio.runner.disorder.IUPredTester@758689a</td><td>0</td>
449 <td title='compbio.runner.disorder.JronnTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
450 <td>compbio.runner.disorder.JronnTester@3d3b5a3a</td><td>0</td>
454 <td title='compbio.runner.msa.ClustalWTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
455 <td>compbio.runner.msa.ClustalWTester@3a0b53e</td><td>0</td>
459 <td title='compbio.runner.msa.MafftTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
460 <td>compbio.runner.msa.MafftTester@5f0f0625</td><td>0</td>
464 <td title='compbio.runner.msa.MuscleTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
465 <td>compbio.runner.msa.MuscleTester@63f8247d</td><td>0</td>
469 <td title='compbio.runner.msa.ProbconsTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
470 <td>compbio.runner.msa.ProbconsTester@32830122</td><td>0</td>
474 <td title='compbio.runner.msa.TcoffeeTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
475 <td>compbio.runner.msa.TcoffeeTester@54a6af6e</td><td>0</td>
479 <td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
480 <td>compbio.runner.msa.ClustalWParametersTester@74e2ad16</td><td>0</td>
484 <td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
485 <td>compbio.runner.msa.MafftParametersTester@35a8d460</td><td>1</td>
489 <td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
490 <td>compbio.runner.msa.MuscleParametersTester@535c97e4</td><td>1</td>
494 <td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
495 <td>compbio.runner.msa.ProbconsParametersTester@3823bdd1</td><td>37</td>
499 <td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
500 <td>compbio.runner.msa.TcoffeeParametersTester@36bf7916</td><td>4</td>
504 <td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
505 <td>compbio.runner.msa.ClustalWParametersTester@74e2ad16</td><td>0</td>
509 <td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
510 <td>compbio.runner.msa.MafftParametersTester@35a8d460</td><td>0</td>
514 <td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
515 <td>compbio.runner.msa.MuscleParametersTester@535c97e4</td><td>1</td>
519 <td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
520 <td>compbio.runner.msa.ProbconsParametersTester@3823bdd1</td><td>0</td>
524 <td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
525 <td>compbio.runner.msa.TcoffeeParametersTester@36bf7916</td><td>2</td>
529 <td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
530 <td>compbio.runner.msa.ClustalWParametersTester@74e2ad16</td><td>0</td>
534 <td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
535 <td>compbio.runner.msa.MafftParametersTester@35a8d460</td><td>3</td>
539 <td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
540 <td>compbio.runner.msa.MuscleParametersTester@535c97e4</td><td>2</td>
544 <td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
545 <td>compbio.runner.msa.ProbconsParametersTester@3823bdd1</td><td>70</td>
549 <td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
550 <td>compbio.runner.msa.TcoffeeParametersTester@36bf7916</td><td>8</td>
554 <td title='compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue()'><b>testCreateNumParameterWithoutValidValue</b><br>Test class:Ant test</td>
555 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
556 <td><div><pre>java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
557 Description: DNA weight matrix
561 Without possible values! Please define possible value first!
562 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
563 at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
564 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace42185103", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
565 <div class='stack-trace' id='stack-trace42185103'><pre>java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
566 Description: DNA weight matrix
570 Without possible values! Please define possible value first!
571 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
572 at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
573 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
574 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
575 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
576 at java.lang.reflect.Method.invoke(Method.java:597)
577 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
578 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
579 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
580 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
581 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
582 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
583 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
584 at org.testng.TestRunner.privateRun(TestRunner.java:592)
585 at org.testng.TestRunner.run(TestRunner.java:486)
586 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
587 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
588 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
589 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
590 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
591 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
592 at org.testng.TestNG.run(TestNG.java:784)
593 at org.testng.TestNG.privateMain(TestNG.java:949)
594 at org.testng.TestNG.main(TestNG.java:922)
598 <td title='compbio.metadata.RunnerConfigTester.testCreateParameter()'><b>testCreateParameter</b><br>Test class:Ant test</td>
599 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
600 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
601 Description: Protein weight matrix
602 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
613 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
614 at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
615 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1373581442", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
616 <div class='stack-trace' id='stack-trace1373581442'><pre>compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
617 Description: Protein weight matrix
618 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
629 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
630 at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
631 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
632 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
633 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
634 at java.lang.reflect.Method.invoke(Method.java:597)
635 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
636 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
637 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
638 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
639 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
640 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
641 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
642 at org.testng.TestRunner.privateRun(TestRunner.java:592)
643 at org.testng.TestRunner.run(TestRunner.java:486)
644 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
645 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
646 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
647 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
648 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
649 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
650 at org.testng.TestNG.run(TestNG.java:784)
651 at org.testng.TestNG.privateMain(TestNG.java:949)
652 at org.testng.TestNG.main(TestNG.java:922)
656 <td title='compbio.metadata.RunnerConfigTester.testCreateParameterWithValidValueConstrain()'><b>testCreateParameterWithValidValueConstrain</b><br>Test class:Ant test</td>
657 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
661 <td title='compbio.data.sequence.SequenceUtilTester.testDeepCleanSequence()'><b>testDeepCleanSequence</b><br>Test class:Ant test</td>
662 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
666 <td title='compbio.runner.msa.ClustalWParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
667 <td>compbio.runner.msa.ClustalWParametersTester@74e2ad16</td><td>0</td>
671 <td title='compbio.runner.msa.MafftParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
672 <td>compbio.runner.msa.MafftParametersTester@35a8d460</td><td>4</td>
676 <td title='compbio.runner.msa.MuscleParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
677 <td>compbio.runner.msa.MuscleParametersTester@535c97e4</td><td>0</td>
681 <td title='compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
682 <td>compbio.runner.msa.ProbconsParametersTester@3823bdd1</td><td>4</td>
686 <td title='compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
687 <td>compbio.runner.msa.TcoffeeParametersTester@36bf7916</td><td>3</td>
691 <td title='compbio.runner.msa.MafftTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
692 <td>compbio.runner.msa.MafftTester@5f0f0625</td><td>0</td>
696 <td title='compbio.runner.msa.ProbconsTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
697 <td>compbio.runner.msa.ProbconsTester@32830122</td><td>0</td>
701 <td title='compbio.runner.msa.TcoffeeTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
702 <td>compbio.runner.msa.TcoffeeTester@54a6af6e</td><td>0</td>
706 <td title='compbio.engine.FilePullerTester.testGet()'><b>testGet</b><br>Test class:Ant test</td>
707 <td>compbio.engine.FilePullerTester@1e670479</td><td>0</td>
711 <td title='compbio.engine.EngineConfiguratorTester.testGetAsyncEngine()'><b>testGetAsyncEngine</b><br>Test class:Ant test</td>
712 <td>compbio.engine.EngineConfiguratorTester@4513e9fd</td><td>0</td>
716 <td title='compbio.engine.client.PathValidatorTester.testGetClassPath()'><b>testGetClassPath</b><br>Test class:Ant test</td>
717 <td>compbio.engine.client.PathValidatorTester@729b1670</td><td>0</td>
721 <td title='compbio.engine.FilePullerTester.testGetDelay()'><b>testGetDelay</b><br>Test class:Ant test</td>
722 <td>compbio.engine.FilePullerTester@1e670479</td><td>0</td>
726 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
727 <td>compbio.engine.conf.DirectoryManagerTester@79fcf790</td><td>0</td>
731 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
732 <td>compbio.engine.conf.DirectoryManagerTester@79fcf790</td><td>0</td>
736 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
737 <td>compbio.engine.conf.DirectoryManagerTester@79fcf790</td><td>0</td>
741 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
742 <td>compbio.engine.conf.DirectoryManagerTester@79fcf790</td><td>0</td>
746 <td title='compbio.data.sequence.FastaSequenceTester.testGetFormattedFasta()'><b>testGetFormattedFasta</b><br>Test class:Ant test</td>
747 <td>compbio.data.sequence.FastaSequenceTester@5ec24193</td><td>0</td>
751 <td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()'><b>testGetJobStatus</b><br>Test class:Ant test</td>
752 <td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@57c8b24d</td><td>4</td>
756 <td title='compbio.stat.servlet.util.StatCollectionTester.testGetStats()'><b>testGetStats</b><br>Test class:Ant test</td>
757 <td>compbio.stat.servlet.util.StatCollectionTester@26c1186f</td><td>0</td>
761 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
762 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>19</td>
766 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
767 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>19</td>
771 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
772 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>19</td>
776 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
777 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>19</td>
781 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
782 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>19</td>
786 <td title='compbio.engine.EngineConfiguratorTester.testGetSyncEngine()'><b>testGetSyncEngine</b><br>Test class:Ant test</td>
787 <td>compbio.engine.EngineConfiguratorTester@4513e9fd</td><td>0</td>
791 <td title='compbio.runner._impl.OBTester.testGetTestArgsCommand()'><b>testGetTestArgsCommand</b><br>Test class:Ant test</td>
792 <td>compbio.runner._impl.OBTester@2658dd2d</td><td>0</td>
796 <td title='compbio.runner._impl.RPSBlastTester.testGetTestArgsCommand()'><b>testGetTestArgsCommand</b><br>Test class:Ant test</td>
797 <td>compbio.runner._impl.RPSBlastTester@1420c906</td><td>0</td>
801 <td title='compbio.runner._impl.MclTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
802 <td>compbio.runner._impl.MclTester@f35f44e</td><td>0</td>
806 <td title='compbio.runner._impl.NetNglycTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
807 <td>compbio.runner._impl.NetNglycTester@1f3a34af</td><td>0</td>
811 <td title='compbio.runner._impl.OBTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
812 <td>compbio.runner._impl.OBTester@2658dd2d</td><td>0</td>
816 <td title='compbio.runner._impl.RPSBlastTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
817 <td>compbio.runner._impl.RPSBlastTester@1420c906</td><td>0</td>
821 <td title='compbio.runner._impl.RonnTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
822 <td>compbio.runner._impl.RonnTester@746db33c</td><td>0</td>
826 <td title='compbio.runner._impl.Tmhmm2Tester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
827 <td>compbio.runner._impl.Tmhmm2Tester@4e1263db</td><td>0</td>
831 <td title='compbio.stat.collector.ExecutionStatCollectorTester.testHasCompleted()'><b>testHasCompleted</b><br>Test class:Ant test</td>
832 <td>compbio.stat.collector.ExecutionStatCollectorTester@b478a2d</td><td>0</td>
836 <td title='compbio.engine.client.PathValidatorTester.testIsAbsolutePath()'><b>testIsAbsolutePath</b><br>Test class:Ant test</td>
837 <td>compbio.engine.client.PathValidatorTester@729b1670</td><td>0</td>
841 <td title='compbio.runner.msa.LimitTester.testLimitExceeded()'><b>testLimitExceeded</b><br>Test class:Ant test</td>
842 <td>compbio.runner.msa.LimitTester@2bdafb4e</td><td>0</td>
846 <td title='compbio.engine.LoadBalancerTester.testLoadBalance()'><b>testLoadBalance</b><br>Test class:Ant test</td>
847 <td>compbio.engine.LoadBalancerTester@7d56b386</td><td>0</td>
851 <td title='compbio.runner.msa.LimitTester.testLoadLimits()'><b>testLoadLimits</b><br>Test class:Ant test</td>
852 <td>compbio.runner.msa.LimitTester@2bdafb4e</td><td>0</td>
856 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testMarshalling()'><b>testMarshalling</b><br>Test class:Ant test</td>
857 <td>compbio.engine.conf.RunnerConfigMarshallerTester@29a7789c</td><td>0</td>
861 <td title='compbio.metadata.OptionMarshallerTester.testMarshalling()'><b>testMarshalling</b><br>Test class:Ant test</td>
862 <td>compbio.metadata.OptionMarshallerTester@6087e704</td><td>0</td>
863 <td><div><pre>javax.xml.bind.MarshalException
864 - with linked exception:
865 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
866 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:323)
867 at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
868 at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
869 at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
870 at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
871 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.
872 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
873 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
874 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
875 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
876 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
877 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
878 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
879 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
880 at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
881 at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
882 at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:128)
883 at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:106)
884 at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:310)
885 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:699)
886 at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:69)
887 at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:172)
888 at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:159)
889 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:344)
890 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:597)
891 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:328)
892 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:498)
893 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:320)
895 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace180466017", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
896 <div class='stack-trace' id='stack-trace180466017'><pre>javax.xml.bind.MarshalException
897 - with linked exception:
898 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
899 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:323)
900 at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
901 at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
902 at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
903 at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
904 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
905 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
906 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
907 at java.lang.reflect.Method.invoke(Method.java:597)
908 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
909 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
910 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
911 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
912 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
913 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
914 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
915 at org.testng.TestRunner.privateRun(TestRunner.java:592)
916 at org.testng.TestRunner.run(TestRunner.java:486)
917 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
918 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
919 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
920 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
921 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
922 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
923 at org.testng.TestNG.run(TestNG.java:784)
924 at org.testng.TestNG.privateMain(TestNG.java:949)
925 at org.testng.TestNG.main(TestNG.java:922)
926 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.
927 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
928 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
929 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
930 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
931 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
932 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
933 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
934 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
935 at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
936 at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
937 at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:128)
938 at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:106)
939 at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:310)
940 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:699)
941 at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:69)
942 at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:172)
943 at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:159)
944 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:344)
945 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:597)
946 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:328)
947 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:498)
948 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:320)
953 <td title='compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally()'><b>testMultipleCancelLocally</b><br>Test class:Ant test</td>
954 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>0</td>
955 <td><div><pre>java.util.concurrent.CancellationException
956 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
957 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
958 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
959 at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
960 at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
961 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1121006800", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
962 <div class='stack-trace' id='stack-trace1121006800'><pre>java.util.concurrent.CancellationException
963 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
964 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
965 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
966 at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
967 at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
968 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
969 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
970 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
971 at java.lang.reflect.Method.invoke(Method.java:597)
972 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
973 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
974 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
975 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
976 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
977 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
978 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
979 at org.testng.TestRunner.privateRun(TestRunner.java:592)
980 at org.testng.TestRunner.run(TestRunner.java:486)
981 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
982 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
983 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
984 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
985 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
986 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
987 at org.testng.TestNG.run(TestNG.java:784)
988 at org.testng.TestNG.privateMain(TestNG.java:949)
989 at org.testng.TestNG.main(TestNG.java:922)
993 <td title='compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally()'><b>testMultipleCancelLocally</b><br>Test class:Ant test</td>
994 <td>compbio.engine.local.LocalRunnerTester@3fde891b</td><td>0</td>
995 <td><div><pre>java.util.concurrent.CancellationException
996 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
997 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
998 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
999 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
1000 at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
1001 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace752158675", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1002 <div class='stack-trace' id='stack-trace752158675'><pre>java.util.concurrent.CancellationException
1003 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
1004 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
1005 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
1006 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
1007 at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
1008 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1009 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1010 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1011 at java.lang.reflect.Method.invoke(Method.java:597)
1012 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1013 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1014 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1015 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1016 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1017 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1018 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1019 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1020 at org.testng.TestRunner.run(TestRunner.java:486)
1021 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1022 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1023 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1024 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1025 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1026 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1027 at org.testng.TestNG.run(TestNG.java:784)
1028 at org.testng.TestNG.privateMain(TestNG.java:949)
1029 at org.testng.TestNG.main(TestNG.java:922)
1033 <td title='compbio.runner.msa.TcoffeeTester.testNcore()'><b>testNcore</b><br>Test class:Ant test</td>
1034 <td>compbio.runner.msa.TcoffeeTester@54a6af6e</td><td>0</td>
1038 <td title='compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate()'><b>testOptionNoDefaultValidate</b><br>Test class:Ant test</td>
1039 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
1040 <td><div><pre>javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
1041 Description: Protein weight matrix
1042 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1049 at compbio.metadata.Option.validate(Option.java:317)
1050 at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
1051 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace858139636", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1052 <div class='stack-trace' id='stack-trace858139636'><pre>javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
1053 Description: Protein weight matrix
1054 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1061 at compbio.metadata.Option.validate(Option.java:317)
1062 at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
1063 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1064 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1065 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1066 at java.lang.reflect.Method.invoke(Method.java:597)
1067 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1068 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1069 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1070 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1071 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1072 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1073 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1074 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1075 at org.testng.TestRunner.run(TestRunner.java:486)
1076 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1077 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1078 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1079 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1080 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1081 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1082 at org.testng.TestNG.run(TestNG.java:784)
1083 at org.testng.TestNG.privateMain(TestNG.java:949)
1084 at org.testng.TestNG.main(TestNG.java:922)
1088 <td title='compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue()'><b>testOptionSetInvalidValue</b><br>Test class:Ant test</td>
1089 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
1090 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
1091 Description: Protein weight matrix
1092 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1099 at compbio.metadata.Option.setDefaultValue(Option.java:130)
1100 at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
1101 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace391683389", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1102 <div class='stack-trace' id='stack-trace391683389'><pre>compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
1103 Description: Protein weight matrix
1104 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1111 at compbio.metadata.Option.setDefaultValue(Option.java:130)
1112 at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
1113 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1114 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1115 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1116 at java.lang.reflect.Method.invoke(Method.java:597)
1117 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1118 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1119 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1120 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1121 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1122 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1123 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1124 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1125 at org.testng.TestRunner.run(TestRunner.java:486)
1126 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1127 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1128 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1129 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1130 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1131 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1132 at org.testng.TestNG.run(TestNG.java:784)
1133 at org.testng.TestNG.privateMain(TestNG.java:949)
1134 at org.testng.TestNG.main(TestNG.java:922)
1138 <td title='compbio.metadata.RunnerConfigTester.testOptionToCommand()'><b>testOptionToCommand</b><br>Test class:Ant test</td>
1139 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
1143 <td title='compbio.runner.msa.ClustalWParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1144 <td>compbio.runner.msa.ClustalWParametersTester@74e2ad16</td><td>0</td>
1148 <td title='compbio.runner.msa.MafftParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1149 <td>compbio.runner.msa.MafftParametersTester@35a8d460</td><td>0</td>
1153 <td title='compbio.runner.msa.MuscleParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1154 <td>compbio.runner.msa.MuscleParametersTester@535c97e4</td><td>1</td>
1158 <td title='compbio.runner.msa.ProbconsParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1159 <td>compbio.runner.msa.ProbconsParametersTester@3823bdd1</td><td>0</td>
1163 <td title='compbio.runner.msa.TcoffeeParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1164 <td>compbio.runner.msa.TcoffeeParametersTester@36bf7916</td><td>0</td>
1168 <td title='compbio.runner.msa.ClustalWTester.testOptionsLocally()'><b>testOptionsLocally</b><br>Test class:Ant test</td>
1169 <td>compbio.runner.msa.ClustalWTester@3a0b53e</td><td>0</td>
1173 <td title='compbio.engine.client.CommandBuilderTester.testOptionsToCommand()'><b>testOptionsToCommand</b><br>Test class:Ant test</td>
1174 <td>compbio.engine.client.CommandBuilderTester@25cbfa42</td><td>0</td>
1178 <td title='compbio.metadata.RunnerConfigTester.testParameterToCommand()'><b>testParameterToCommand</b><br>Test class:Ant test</td>
1179 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
1183 <td title='compbio.runner.msa.ClustalWParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1184 <td>compbio.runner.msa.ClustalWParametersTester@74e2ad16</td><td>1</td>
1188 <td title='compbio.runner.msa.MafftParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1189 <td>compbio.runner.msa.MafftParametersTester@35a8d460</td><td>1</td>
1193 <td title='compbio.runner.msa.MuscleParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1194 <td>compbio.runner.msa.MuscleParametersTester@535c97e4</td><td>1</td>
1198 <td title='compbio.runner.msa.ProbconsParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1199 <td>compbio.runner.msa.ProbconsParametersTester@3823bdd1</td><td>1</td>
1203 <td title='compbio.runner.msa.TcoffeeParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1204 <td>compbio.runner.msa.TcoffeeParametersTester@36bf7916</td><td>3</td>
1208 <td title='compbio.engine.cluster.drmaa.UtilTester.testParser()'><b>testParser</b><br>Test class:Ant test</td>
1209 <td>compbio.engine.cluster.drmaa.UtilTester@43f4ebd</td><td>0</td>
1213 <td title='compbio.runner.conservation.AAConTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1214 <td>compbio.runner.conservation.AAConTester@1959e6e8</td><td>0</td>
1218 <td title='compbio.runner.disorder.DisemblTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1219 <td>compbio.runner.disorder.DisemblTester@5d469658</td><td>1</td>
1223 <td title='compbio.runner.disorder.GlobPlotTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1224 <td>compbio.runner.disorder.GlobPlotTester@45389b3f</td><td>0</td>
1228 <td title='compbio.runner.disorder.IUPredTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1229 <td>compbio.runner.disorder.IUPredTester@758689a</td><td>0</td>
1233 <td title='compbio.runner.disorder.JronnTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1234 <td>compbio.runner.disorder.JronnTester@3d3b5a3a</td><td>18</td>
1238 <td title='compbio.runner.msa.ClustalWTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1239 <td>compbio.runner.msa.ClustalWTester@3a0b53e</td><td>0</td>
1243 <td title='compbio.runner.msa.MafftTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1244 <td>compbio.runner.msa.MafftTester@5f0f0625</td><td>0</td>
1248 <td title='compbio.runner.msa.MuscleTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1249 <td>compbio.runner.msa.MuscleTester@63f8247d</td><td>0</td>
1253 <td title='compbio.runner.msa.ProbconsTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1254 <td>compbio.runner.msa.ProbconsTester@32830122</td><td>0</td>
1258 <td title='compbio.runner.msa.TcoffeeTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1259 <td>compbio.runner.msa.TcoffeeTester@54a6af6e</td><td>0</td>
1263 <td title='compbio.metadata.PresetTester.testPresetWithMuptiOptions()'><b>testPresetWithMuptiOptions</b><br>Test class:Ant test</td>
1264 <td>compbio.metadata.PresetTester@7a4fe91e</td><td>0</td>
1268 <td title='compbio.runner.msa.ClustalWParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1269 <td>compbio.runner.msa.ClustalWParametersTester@74e2ad16</td><td>0</td>
1273 <td title='compbio.runner.msa.MafftParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1274 <td>compbio.runner.msa.MafftParametersTester@35a8d460</td><td>0</td>
1278 <td title='compbio.runner.msa.MuscleParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1279 <td>compbio.runner.msa.MuscleParametersTester@535c97e4</td><td>0</td>
1283 <td title='compbio.runner.msa.TcoffeeParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1284 <td>compbio.runner.msa.TcoffeeParametersTester@36bf7916</td><td>0</td>
1288 <td title='compbio.data.sequence.FastaSequenceGeneratorTester.testProteinSequenceGeneration()'><b>testProteinSequenceGeneration</b><br>Test class:Ant test</td>
1289 <td>compbio.data.sequence.FastaSequenceGeneratorTester@3a98350a</td><td>0</td>
1293 <td title='compbio.engine.FilePullerTester.testPull()'><b>testPull</b><br>Test class:Ant test</td>
1294 <td>compbio.engine.FilePullerTester@1e670479</td><td>0</td>
1298 <td title='compbio.engine.cluster.dundee._QueueTester.testQueue()'><b>testQueue</b><br>Test class:Ant test</td>
1299 <td>compbio.engine.cluster.dundee._QueueTester@584a5c78</td><td>0</td>
1303 <td title='compbio.data.sequence.SequenceUtilTester.testReadAAConResults()'><b>testReadAAConResults</b><br>Test class:Ant test</td>
1304 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
1308 <td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFile()'><b>testReadClustalFile</b><br>Test class:Ant test</td>
1309 <td>compbio.data.sequence.ClustalAlignmentUtilTester@44739f3f</td><td>0</td>
1313 <td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileLongNames()'><b>testReadClustalFileLongNames</b><br>Test class:Ant test</td>
1314 <td>compbio.data.sequence.ClustalAlignmentUtilTester@44739f3f</td><td>0</td>
1318 <td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileShortNames()'><b>testReadClustalFileShortNames</b><br>Test class:Ant test</td>
1319 <td>compbio.data.sequence.ClustalAlignmentUtilTester@44739f3f</td><td>0</td>
1323 <td title='compbio.data.sequence.SequenceUtilTester.testReadDisemblResults()'><b>testReadDisemblResults</b><br>Test class:Ant test</td>
1324 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
1328 <td title='compbio.data.sequence.SequenceUtilTester.testReadGlobPlotResults()'><b>testReadGlobPlotResults</b><br>Test class:Ant test</td>
1329 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
1333 <td title='compbio.data.sequence.SequenceUtilTester.testReadIUPredForGlobDomain()'><b>testReadIUPredForGlobDomain</b><br>Test class:Ant test</td>
1334 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
1338 <td title='compbio.data.sequence.SequenceUtilTester.testReadIUPredForShortAndLongDisorder()'><b>testReadIUPredForShortAndLongDisorder</b><br>Test class:Ant test</td>
1339 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
1343 <td title='compbio.runner.disorder.IUPredTester.testReadResults()'><b>testReadResults</b><br>Test class:Ant test</td>
1344 <td>compbio.runner.disorder.IUPredTester@758689a</td><td>0</td>
1348 <td title='compbio.data.sequence.SequenceUtilTester.testReadWriteFasta()'><b>testReadWriteFasta</b><br>Test class:Ant test</td>
1349 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
1353 <td title='compbio.runner.conservation.AAConTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
1354 <td>compbio.runner.conservation.AAConTester@1959e6e8</td><td>0</td>
1358 <td title='compbio.runner.disorder.DisemblTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
1359 <td>compbio.runner.disorder.DisemblTester@5d469658</td><td>0</td>
1363 <td title='compbio.runner.disorder.GlobPlotTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
1364 <td>compbio.runner.disorder.GlobPlotTester@45389b3f</td><td>0</td>
1368 <td title='compbio.runner.disorder.IUPredTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
1369 <td>compbio.runner.disorder.IUPredTester@758689a</td><td>0</td>
1373 <td title='compbio.runner.disorder.JronnTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
1374 <td>compbio.runner.disorder.JronnTester@3d3b5a3a</td><td>18</td>
1378 <td title='compbio.runner.msa.ClustalWTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
1379 <td>compbio.runner.msa.ClustalWTester@3a0b53e</td><td>0</td>
1383 <td title='compbio.runner.msa.MuscleTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
1384 <td>compbio.runner.msa.MuscleTester@63f8247d</td><td>0</td>
1388 <td title='compbio.runner.conservation.AAConTester.testRunLocallyOnTwoCpu()'><b>testRunLocallyOnTwoCpu</b><br>Test class:Ant test</td>
1389 <td>compbio.runner.conservation.AAConTester@1959e6e8</td><td>0</td>
1393 <td title='compbio.runner.disorder.JronnTester.testRunLocallyOnTwoCpu()'><b>testRunLocallyOnTwoCpu</b><br>Test class:Ant test</td>
1394 <td>compbio.runner.disorder.JronnTester@3d3b5a3a</td><td>7</td>
1398 <td title='compbio.runner.disorder.IUPredTester.testRunLocallyWithParams()'><b>testRunLocallyWithParams</b><br>Test class:Ant test</td>
1399 <td>compbio.runner.disorder.IUPredTester@758689a</td><td>0</td>
1403 <td title='compbio.runner.conservation.AAConTester.testRunLocallyWithPreset()'><b>testRunLocallyWithPreset</b><br>Test class:Ant test</td>
1404 <td>compbio.runner.conservation.AAConTester@1959e6e8</td><td>0</td>
1408 <td title='compbio.runner.conservation.AAConTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
1409 <td>compbio.runner.conservation.AAConTester@1959e6e8</td><td>3</td>
1413 <td title='compbio.runner.disorder.DisemblTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
1414 <td>compbio.runner.disorder.DisemblTester@5d469658</td><td>2</td>
1418 <td title='compbio.runner.disorder.GlobPlotTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
1419 <td>compbio.runner.disorder.GlobPlotTester@45389b3f</td><td>2</td>
1423 <td title='compbio.runner.disorder.IUPredTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
1424 <td>compbio.runner.disorder.IUPredTester@758689a</td><td>3</td>
1428 <td title='compbio.runner.disorder.JronnTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
1429 <td>compbio.runner.disorder.JronnTester@3d3b5a3a</td><td>13</td>
1433 <td title='compbio.runner.msa.ClustalWTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
1434 <td>compbio.runner.msa.ClustalWTester@3a0b53e</td><td>5</td>
1438 <td title='compbio.runner.msa.MuscleTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
1439 <td>compbio.runner.msa.MuscleTester@63f8247d</td><td>3</td>
1443 <td title='compbio.runner.conservation.AAConTester.testRunOnClusterAsync()'><b>testRunOnClusterAsync</b><br>Test class:Ant test</td>
1444 <td>compbio.runner.conservation.AAConTester@1959e6e8</td><td>5</td>
1448 <td title='compbio.runner.disorder.DisemblTester.testRunOnClusterAsync()'><b>testRunOnClusterAsync</b><br>Test class:Ant test</td>
1449 <td>compbio.runner.disorder.DisemblTester@5d469658</td><td>6</td>
1453 <td title='compbio.runner.disorder.GlobPlotTester.testRunOnClusterAsync()'><b>testRunOnClusterAsync</b><br>Test class:Ant test</td>
1454 <td>compbio.runner.disorder.GlobPlotTester@45389b3f</td><td>6</td>
1458 <td title='compbio.runner.disorder.IUPredTester.testRunOnClusterAsync()'><b>testRunOnClusterAsync</b><br>Test class:Ant test</td>
1459 <td>compbio.runner.disorder.IUPredTester@758689a</td><td>6</td>
1463 <td title='compbio.runner.disorder.JronnTester.testRunOnClusterAsync()'><b>testRunOnClusterAsync</b><br>Test class:Ant test</td>
1464 <td>compbio.runner.disorder.JronnTester@3d3b5a3a</td><td>11</td>
1468 <td title='compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()'><b>testRunOnClusterAsyncCheckStatusLongPoolingTime</b><br>Test class:Ant test</td>
1469 <td>compbio.runner.msa.MafftTester@5f0f0625</td><td>5</td>
1473 <td title='compbio.runner.msa.ClustalWTester.testRunWithMatrix()'><b>testRunWithMatrix</b><br>Test class:Ant test</td>
1474 <td>compbio.runner.msa.ClustalWTester@3a0b53e</td><td>0</td>
1478 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testSchemaFromCodeGeneration()'><b>testSchemaFromCodeGeneration</b><br>Test class:Ant test</td>
1479 <td>compbio.engine.conf.RunnerConfigMarshallerTester@29a7789c</td><td>0</td>
1483 <td title='compbio.runner.msa.MafftTester.testSetInputTester()'><b>testSetInputTester</b><br>Test class:Ant test</td>
1484 <td>compbio.runner.msa.MafftTester@5f0f0625</td><td>0</td>
1488 <td title='compbio.runner.msa.ProbconsTester.testSetInputTester()'><b>testSetInputTester</b><br>Test class:Ant test</td>
1489 <td>compbio.runner.msa.ProbconsTester@32830122</td><td>0</td>
1493 <td title='compbio.runner.disorder.IUPredTester.testSetParameter()'><b>testSetParameter</b><br>Test class:Ant test</td>
1494 <td>compbio.runner.disorder.IUPredTester@758689a</td><td>0</td>
1498 <td title='compbio.engine.client.CommandBuilderTester.testSpaceDelimiterExecutable()'><b>testSpaceDelimiterExecutable</b><br>Test class:Ant test</td>
1499 <td>compbio.engine.client.CommandBuilderTester@25cbfa42</td><td>0</td>
1503 <td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()'><b>testSubmit</b><br>Test class:Ant test</td>
1504 <td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@57c8b24d</td><td>3</td>
1508 <td title='compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()'><b>testSubmit</b><br>Test class:Ant test</td>
1509 <td>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@39320a41</td><td>3</td>
1513 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1514 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>0</td>
1518 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1519 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>0</td>
1523 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1524 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>0</td>
1528 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1529 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>0</td>
1533 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1534 <td>compbio.engine.local.AsyncLocalRunnerTester@31df5f21</td><td>0</td>
1538 <td title='compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()'><b>testTaskList</b><br>Test class:Ant test</td>
1539 <td>compbio.engine.cluster.drmaa.ClusterSessionTester@23de4dd8</td><td>3</td>
1543 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testUnMarshalling()'><b>testUnMarshalling</b><br>Test class:Ant test</td>
1544 <td>compbio.engine.conf.RunnerConfigMarshallerTester@29a7789c</td><td>0</td>
1548 <td title='compbio.metadata.OptionMarshallerTester.testUnMarshalling()'><b>testUnMarshalling</b><br>Test class:Ant test</td>
1549 <td>compbio.metadata.OptionMarshallerTester@6087e704</td><td>0</td>
1553 <td title='compbio.stat.collector.ExecutionStatCollectorTester.testUpdateStatTester()'><b>testUpdateStatTester</b><br>Test class:Ant test</td>
1554 <td>compbio.stat.collector.ExecutionStatCollectorTester@b478a2d</td><td>35</td>
1558 <td title='compbio.metadata.RunnerConfigTester.testValidate()'><b>testValidate</b><br>Test class:Ant test</td>
1559 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
1563 <td title='compbio.metadata.RunnerConfigTester.testValidateBoundaryConstrainCheck()'><b>testValidateBoundaryConstrainCheck</b><br>Test class:Ant test</td>
1564 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
1568 <td title='compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck()'><b>testValidateLowerBoundaryConstrainCheck</b><br>Test class:Ant test</td>
1569 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
1570 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1574 For parameter: Option name: Matrix1
1575 Description: Protein weight matrix
1576 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1585 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1586 at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
1587 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1382320624", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1588 <div class='stack-trace' id='stack-trace1382320624'><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1592 For parameter: Option name: Matrix1
1593 Description: Protein weight matrix
1594 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1603 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1604 at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
1605 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1606 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1607 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1608 at java.lang.reflect.Method.invoke(Method.java:597)
1609 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1610 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1611 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1612 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1613 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1614 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1615 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1616 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1617 at org.testng.TestRunner.run(TestRunner.java:486)
1618 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1619 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1620 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1621 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1622 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1623 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1624 at org.testng.TestNG.run(TestNG.java:784)
1625 at org.testng.TestNG.privateMain(TestNG.java:949)
1626 at org.testng.TestNG.main(TestNG.java:922)
1630 <td title='compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck()'><b>testValidateUpperBoundaryConstrainCheck</b><br>Test class:Ant test</td>
1631 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
1632 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1636 For parameter: Option name: Matrix1
1637 Description: Protein weight matrix
1638 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1647 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1648 at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
1649 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace853232781", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1650 <div class='stack-trace' id='stack-trace853232781'><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1654 For parameter: Option name: Matrix1
1655 Description: Protein weight matrix
1656 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1665 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1666 at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
1667 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1668 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1669 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1670 at java.lang.reflect.Method.invoke(Method.java:597)
1671 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1672 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1673 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1674 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1675 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1676 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1677 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1678 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1679 at org.testng.TestRunner.run(TestRunner.java:486)
1680 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1681 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1682 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1683 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1684 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1685 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1686 at org.testng.TestNG.run(TestNG.java:784)
1687 at org.testng.TestNG.privateMain(TestNG.java:949)
1688 at org.testng.TestNG.main(TestNG.java:922)
1692 <td title='compbio.metadata.RunnerConfigTester.testValidateValueConstrain()'><b>testValidateValueConstrain</b><br>Test class:Ant test</td>
1693 <td>compbio.metadata.RunnerConfigTester@1451ef4e</td><td>0</td>
1694 <td><div><pre>javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
1696 at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
1697 at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
1698 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace206051672", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1699 <div class='stack-trace' id='stack-trace206051672'><pre>javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
1701 at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
1702 at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
1703 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1704 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1705 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1706 at java.lang.reflect.Method.invoke(Method.java:597)
1707 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1708 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1709 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1710 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1711 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1712 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1713 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1714 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1715 at org.testng.TestRunner.run(TestRunner.java:486)
1716 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1717 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1718 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1719 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1720 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1721 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1722 at org.testng.TestNG.run(TestNG.java:784)
1723 at org.testng.TestNG.privateMain(TestNG.java:949)
1724 at org.testng.TestNG.main(TestNG.java:922)
1728 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testValidation()'><b>testValidation</b><br>Test class:Ant test</td>
1729 <td>compbio.engine.conf.RunnerConfigMarshallerTester@29a7789c</td><td>0</td>
1733 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling()'><b>testValidationOnMarshalling</b><br>Test class:Ant test</td>
1734 <td>compbio.engine.conf.RunnerConfigMarshallerTester@29a7789c</td><td>0</td>
1735 <td><div><pre>javax.xml.bind.MarshalException
1736 - with linked exception:
1737 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
1738 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:323)
1739 at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
1740 at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
1741 at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
1742 at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:259)
1743 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.
1744 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
1745 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
1746 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
1747 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
1748 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
1749 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
1750 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
1751 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
1752 at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
1753 at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
1754 at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:128)
1755 at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:106)
1756 at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:310)
1757 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:699)
1758 at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:69)
1759 at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:172)
1760 at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:159)
1761 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:344)
1762 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:597)
1763 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:328)
1764 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:498)
1765 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:320)
1767 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1252050054", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1768 <div class='stack-trace' id='stack-trace1252050054'><pre>javax.xml.bind.MarshalException
1769 - with linked exception:
1770 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
1771 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:323)
1772 at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:249)
1773 at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
1774 at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
1775 at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:259)
1776 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1777 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1778 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1779 at java.lang.reflect.Method.invoke(Method.java:597)
1780 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1781 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1782 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1783 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1784 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1785 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1786 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1787 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1788 at org.testng.TestRunner.run(TestRunner.java:486)
1789 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1790 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1791 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1792 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1793 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1794 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1795 at org.testng.TestNG.run(TestNG.java:784)
1796 at org.testng.TestNG.privateMain(TestNG.java:949)
1797 at org.testng.TestNG.main(TestNG.java:922)
1798 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.
1799 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
1800 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
1801 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
1802 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
1803 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
1804 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
1805 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
1806 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
1807 at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
1808 at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
1809 at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:128)
1810 at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:106)
1811 at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:310)
1812 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:699)
1813 at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:69)
1814 at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:172)
1815 at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:159)
1816 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:344)
1817 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:597)
1818 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:328)
1819 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:498)
1820 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:320)
1825 <td title='compbio.stat.collector.StatDBTester.testVerifyJobsCount()'><b>testVerifyJobsCount</b><br>Test class:Ant test</td>
1826 <td>compbio.stat.collector.StatDBTester@5c09624</td><td>0</td>
1830 <td title='compbio.metadata.OptionCombinatorTester.testgetAllOptions()'><b>testgetAllOptions</b><br>Test class:Ant test</td>
1831 <td>compbio.metadata.OptionCombinatorTester@2afb6c5f</td><td>0</td>
1835 <td title='compbio.metadata.OptionCombinatorTester.testgetAllParameters()'><b>testgetAllParameters</b><br>Test class:Ant test</td>
1836 <td>compbio.metadata.OptionCombinatorTester@2afb6c5f</td><td>0</td>
1840 <td title='compbio.data.sequence.SequenceUtilTester.testisNonAmbNucleotideSequence()'><b>testisNonAmbNucleotideSequence</b><br>Test class:Ant test</td>
1841 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
1845 <td title='compbio.data.sequence.SequenceUtilTester.testisProteinSequence()'><b>testisProteinSequence</b><br>Test class:Ant test</td>
1846 <td>compbio.data.sequence.SequenceUtilTester@235f4a7f</td><td>0</td>
1850 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration()'><b>validateClustalConfiguration</b><br>Test class:Ant test</td>
1851 <td>compbio.engine.conf.PropertyHelperManagerTester@4ee14d81</td><td>0</td>
1855 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration()'><b>validateMafftConfiguration</b><br>Test class:Ant test</td>
1856 <td>compbio.engine.conf.PropertyHelperManagerTester@4ee14d81</td><td>0</td>
1860 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration()'><b>validateMuscleConfiguration</b><br>Test class:Ant test</td>
1861 <td>compbio.engine.conf.PropertyHelperManagerTester@4ee14d81</td><td>0</td>
1865 <td title='compbio.metadata.PresetTester.validatePresets()'><b>validatePresets</b><br>Test class:Ant test</td>
1866 <td>compbio.metadata.PresetTester@7a4fe91e</td><td>0</td>
1870 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration()'><b>validateTcoffeeConfiguration</b><br>Test class:Ant test</td>
1871 <td>compbio.engine.conf.PropertyHelperManagerTester@4ee14d81</td><td>0</td>