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>165/0/0</td>
60 <td>Started on:</td><td>Wed Feb 17 15:34:08 GMT 2010</td>
62 <tr><td>Total time:</td><td>524 seconds (524407 ms)</td>
64 <td>Included groups:</td><td></td>
66 <td>Excluded groups:</td><td>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.metadata.PresetTester.marshallPreset()'><b>marshallPreset</b><br>Test class:Ant test</td>
79 <td>compbio.metadata.PresetTester@50009f0d</td><td>0</td>
83 <td title='compbio.runner.msa.ClustalWTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
84 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>1</td>
88 <td title='compbio.runner.msa.MafftTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
89 <td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
93 <td title='compbio.runner.msa.MuscleTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
94 <td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
98 <td title='compbio.runner.msa.ProbconsTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
99 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
103 <td title='compbio.runner.msa.TcoffeeTester.readStatistics()'><b>readStatistics</b><br>Test class:Ant test</td>
104 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
108 <td title='compbio.runner.msa.ClustalWTester.readStatisticsClusterExecution()'><b>readStatisticsClusterExecution</b><br>Test class:Ant test</td>
109 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>8</td>
113 <td title='compbio.engine.PulledFileCacheTester.test()'><b>test</b><br>Test class:Ant test</td>
114 <td>compbio.engine.PulledFileCacheTester@1164b9b6</td><td>5</td>
118 <td title='compbio.runner.msa.ClustalWParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
119 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>3</td>
123 <td title='compbio.runner.msa.MafftParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
124 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>6</td>
128 <td title='compbio.runner.msa.MuscleParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
129 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>7</td>
133 <td title='compbio.runner.msa.ProbconsParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
134 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>2</td>
138 <td title='compbio.runner.msa.TcoffeeParametersTester.testArguments()'><b>testArguments</b><br>Test class:Ant test</td>
139 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>8</td>
143 <td title='compbio.engine.local.AsyncLocalRunnerTester.testAsyncCancelOperation()'><b>testAsyncCancelOperation</b><br>Test class:Ant test</td>
144 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
148 <td title='compbio.engine.local.AsyncLocalRunnerTester.testAsyncRetrievOperation()'><b>testAsyncRetrievOperation</b><br>Test class:Ant test</td>
149 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
153 <td title='compbio.engine.FilePullerTester.testCache()'><b>testCache</b><br>Test class:Ant test</td>
154 <td>compbio.engine.FilePullerTester@5fa80aea</td><td>6</td>
158 <td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel()'><b>testCancel</b><br>Test class:Ant test</td>
159 <td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18</td><td>1</td>
160 <td><div><pre>compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
161 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
162 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
163 at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
164 at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
165 Caused by: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
166 at compbio.runner.Util.readClustalFile(Util.java:126)
167 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
169 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1915626539", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
170 <div class='stack-trace' id='stack-trace1915626539'><pre>compbio.metadata.ResultNotAvailableException: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
171 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:79)
172 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:37)
173 at compbio.engine.client.ConfExecutable.getResults(ConfExecutable.java:206)
174 at compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testCancel(DrmaaAsyncClusterEngineTester.java:109)
175 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
176 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
177 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
178 at java.lang.reflect.Method.invoke(Method.java:597)
179 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
180 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
181 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
182 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
183 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
184 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
185 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
186 at org.testng.TestRunner.privateRun(TestRunner.java:592)
187 at org.testng.TestRunner.run(TestRunner.java:486)
188 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
189 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
190 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
191 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
192 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
193 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
194 at org.testng.TestNG.run(TestNG.java:784)
195 at org.testng.TestNG.privateMain(TestNG.java:949)
196 at org.testng.TestNG.main(TestNG.java:922)
197 Caused by: java.io.FileNotFoundException: Result for the jobId /homes/pvtroshin/workspace/clustengine/jobsout/local/ClustalW#6731244848891847 with file name TO1381.clustal.cluster.out is not found!
198 at compbio.runner.Util.readClustalFile(Util.java:126)
199 at compbio.runner.msa.ClustalW.getResults(ClustalW.java:76)
204 <td title='compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testCancel()'><b>testCancel</b><br>Test class:Ant test</td>
205 <td>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@4301ac93</td><td>1</td>
209 <td title='compbio.engine.local.AsyncLocalRunnerTester.testCancelCompletedTaskLocally()'><b>testCancelCompletedTaskLocally</b><br>Test class:Ant test</td>
210 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>3</td>
214 <td title='compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally()'><b>testCancelCompletedTaskLocally</b><br>Test class:Ant test</td>
215 <td>compbio.engine.local.LocalRunnerTester@4b2922f6</td><td>0</td>
216 <td><div><pre>java.util.concurrent.CancellationException
217 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
218 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
219 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
220 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
221 at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
222 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1132612908", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
223 <div class='stack-trace' id='stack-trace1132612908'><pre>java.util.concurrent.CancellationException
224 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
225 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
226 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
227 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
228 at compbio.engine.local.LocalRunnerTester.testCancelCompletedTaskLocally(LocalRunnerTester.java:139)
229 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
230 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
231 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
232 at java.lang.reflect.Method.invoke(Method.java:597)
233 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
234 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
235 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
236 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
237 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
238 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
239 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
240 at org.testng.TestRunner.privateRun(TestRunner.java:592)
241 at org.testng.TestRunner.run(TestRunner.java:486)
242 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
243 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
244 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
245 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
246 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
247 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
248 at org.testng.TestNG.run(TestNG.java:784)
249 at org.testng.TestNG.privateMain(TestNG.java:949)
250 at org.testng.TestNG.main(TestNG.java:922)
254 <td title='compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally()'><b>testCancelLocally</b><br>Test class:Ant test</td>
255 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
256 <td><div><pre>java.util.concurrent.CancellationException
257 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
258 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
259 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
260 at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
261 at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
262 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1931494437", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
263 <div class='stack-trace' id='stack-trace1931494437'><pre>java.util.concurrent.CancellationException
264 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
265 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
266 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
267 at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
268 at compbio.engine.local.AsyncLocalRunnerTester.testCancelLocally(AsyncLocalRunnerTester.java:105)
269 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
270 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
271 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
272 at java.lang.reflect.Method.invoke(Method.java:597)
273 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
274 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
275 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
276 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
277 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
278 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
279 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
280 at org.testng.TestRunner.privateRun(TestRunner.java:592)
281 at org.testng.TestRunner.run(TestRunner.java:486)
282 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
283 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
284 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
285 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
286 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
287 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
288 at org.testng.TestNG.run(TestNG.java:784)
289 at org.testng.TestNG.privateMain(TestNG.java:949)
290 at org.testng.TestNG.main(TestNG.java:922)
294 <td title='compbio.engine.local.LocalRunnerTester.testCancelLocally()'><b>testCancelLocally</b><br>Test class:Ant test</td>
295 <td>compbio.engine.local.LocalRunnerTester@4b2922f6</td><td>0</td>
296 <td><div><pre>java.util.concurrent.CancellationException
297 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
298 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
299 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
300 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
301 at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
302 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1100010806", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
303 <div class='stack-trace' id='stack-trace1100010806'><pre>java.util.concurrent.CancellationException
304 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
305 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
306 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
307 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
308 at compbio.engine.local.LocalRunnerTester.testCancelLocally(LocalRunnerTester.java:66)
309 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
310 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
311 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
312 at java.lang.reflect.Method.invoke(Method.java:597)
313 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
314 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
315 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
316 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
317 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
318 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
319 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
320 at org.testng.TestRunner.privateRun(TestRunner.java:592)
321 at org.testng.TestRunner.run(TestRunner.java:486)
322 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
323 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
324 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
325 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
326 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
327 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
328 at org.testng.TestNG.run(TestNG.java:784)
329 at org.testng.TestNG.privateMain(TestNG.java:949)
330 at org.testng.TestNG.main(TestNG.java:922)
334 <td title='compbio.data.sequence.SequenceUtilTester.testCleanSequence()'><b>testCleanSequence</b><br>Test class:Ant test</td>
335 <td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
339 <td title='compbio.engine.conf.PropertyHelperManagerTester.testClusterEngineConf()'><b>testClusterEngineConf</b><br>Test class:Ant test</td>
340 <td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
344 <td title='compbio.runner.msa.MafftTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
345 <td>compbio.runner.msa.MafftTester@259a8416</td><td>11</td>
349 <td title='compbio.runner.msa.ProbconsTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
350 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>19</td>
354 <td title='compbio.runner.msa.TcoffeeTester.testClusterExecute()'><b>testClusterExecute</b><br>Test class:Ant test</td>
355 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>5</td>
359 <td title='compbio.engine.client.CommandBuilderTester.testCommandBuilding()'><b>testCommandBuilding</b><br>Test class:Ant test</td>
360 <td>compbio.engine.client.CommandBuilderTester@6bdc64a5</td><td>0</td>
364 <td title='compbio.runner.msa.ClustalWParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
365 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>0</td>
369 <td title='compbio.runner.msa.MafftParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
370 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>0</td>
374 <td title='compbio.runner.msa.MuscleParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
375 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
379 <td title='compbio.runner.msa.ProbconsParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
380 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>0</td>
384 <td title='compbio.runner.msa.TcoffeeParametersTester.testConfiguration()'><b>testConfiguration</b><br>Test class:Ant test</td>
385 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>0</td>
389 <td title='compbio.runner.msa.ClustalWTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
390 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
394 <td title='compbio.runner.msa.MafftTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
395 <td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
399 <td title='compbio.runner.msa.MuscleTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
400 <td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
404 <td title='compbio.runner.msa.ProbconsTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
405 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
409 <td title='compbio.runner.msa.TcoffeeTester.testConfigurationLoading()'><b>testConfigurationLoading</b><br>Test class:Ant test</td>
410 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
414 <td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
415 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>1</td>
419 <td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
420 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>3</td>
424 <td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
425 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>1</td>
429 <td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
430 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>38</td>
434 <td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMaxValues()'><b>testConstrainedParametersMaxValues</b><br>Test class:Ant test</td>
435 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>11</td>
439 <td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
440 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>1</td>
444 <td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
445 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>1</td>
449 <td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
450 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
454 <td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
455 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>0</td>
459 <td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersMinValues()'><b>testConstrainedParametersMinValues</b><br>Test class:Ant test</td>
460 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>5</td>
464 <td title='compbio.runner.msa.ClustalWParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
465 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>3</td>
469 <td title='compbio.runner.msa.MafftParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
470 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>7</td>
474 <td title='compbio.runner.msa.MuscleParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
475 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>7</td>
479 <td title='compbio.runner.msa.ProbconsParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
480 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>61</td>
484 <td title='compbio.runner.msa.TcoffeeParametersTester.testConstrainedParametersRandomValues()'><b>testConstrainedParametersRandomValues</b><br>Test class:Ant test</td>
485 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>21</td>
489 <td title='compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue()'><b>testCreateNumParameterWithoutValidValue</b><br>Test class:Ant test</td>
490 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
491 <td><div><pre>java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
492 Description: DNA weight matrix
496 Without possible values! Please define possible value first!
497 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
498 at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
499 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace713889609", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
500 <div class='stack-trace' id='stack-trace713889609'><pre>java.lang.IllegalStateException: Attempting to set default value for parameter: Option name: Matrix
501 Description: DNA weight matrix
505 Without possible values! Please define possible value first!
506 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:234)
507 at compbio.metadata.RunnerConfigTester.testCreateNumParameterWithoutValidValue(RunnerConfigTester.java:222)
508 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
509 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
510 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
511 at java.lang.reflect.Method.invoke(Method.java:597)
512 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
513 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
514 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
515 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
516 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
517 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
518 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
519 at org.testng.TestRunner.privateRun(TestRunner.java:592)
520 at org.testng.TestRunner.run(TestRunner.java:486)
521 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
522 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
523 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
524 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
525 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
526 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
527 at org.testng.TestNG.run(TestNG.java:784)
528 at org.testng.TestNG.privateMain(TestNG.java:949)
529 at org.testng.TestNG.main(TestNG.java:922)
533 <td title='compbio.metadata.RunnerConfigTester.testCreateParameter()'><b>testCreateParameter</b><br>Test class:Ant test</td>
534 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
535 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
536 Description: Protein weight matrix
537 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
548 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
549 at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
550 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace321958204", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
551 <div class='stack-trace' id='stack-trace321958204'><pre>compbio.metadata.WrongParameterException: Attempting to set illegal value 'pam22' for the parameter: Option name: Matrix1
552 Description: Protein weight matrix
553 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
564 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:240)
565 at compbio.metadata.RunnerConfigTester.testCreateParameter(RunnerConfigTester.java:93)
566 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
567 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
568 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
569 at java.lang.reflect.Method.invoke(Method.java:597)
570 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
571 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
572 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
573 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
574 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
575 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
576 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
577 at org.testng.TestRunner.privateRun(TestRunner.java:592)
578 at org.testng.TestRunner.run(TestRunner.java:486)
579 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
580 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
581 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
582 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
583 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
584 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
585 at org.testng.TestNG.run(TestNG.java:784)
586 at org.testng.TestNG.privateMain(TestNG.java:949)
587 at org.testng.TestNG.main(TestNG.java:922)
591 <td title='compbio.metadata.RunnerConfigTester.testCreateParameterWithValidValueConstrain()'><b>testCreateParameterWithValidValueConstrain</b><br>Test class:Ant test</td>
592 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
596 <td title='compbio.data.sequence.SequenceUtilTester.testDeepCleanSequence()'><b>testDeepCleanSequence</b><br>Test class:Ant test</td>
597 <td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
601 <td title='compbio.runner.msa.ClustalWParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
602 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>0</td>
606 <td title='compbio.runner.msa.MafftParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
607 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>20</td>
611 <td title='compbio.runner.msa.MuscleParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
612 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
616 <td title='compbio.runner.msa.ProbconsParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
617 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>14</td>
621 <td title='compbio.runner.msa.TcoffeeParametersTester.testDefaultParameters()'><b>testDefaultParameters</b><br>Test class:Ant test</td>
622 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>10</td>
626 <td title='compbio.runner.msa.MafftTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
627 <td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
631 <td title='compbio.runner.msa.ProbconsTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
632 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
636 <td title='compbio.runner.msa.TcoffeeTester.testExecute()'><b>testExecute</b><br>Test class:Ant test</td>
637 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
641 <td title='compbio.engine.FilePullerTester.testGet()'><b>testGet</b><br>Test class:Ant test</td>
642 <td>compbio.engine.FilePullerTester@5fa80aea</td><td>0</td>
646 <td title='compbio.engine.EngineConfiguratorTester.testGetAsyncEngine()'><b>testGetAsyncEngine</b><br>Test class:Ant test</td>
647 <td>compbio.engine.EngineConfiguratorTester@31f9338f</td><td>0</td>
651 <td title='compbio.engine.client.PathValidatorTester.testGetClassPath()'><b>testGetClassPath</b><br>Test class:Ant test</td>
652 <td>compbio.engine.client.PathValidatorTester@5253c3f5</td><td>0</td>
656 <td title='compbio.engine.FilePullerTester.testGetDelay()'><b>testGetDelay</b><br>Test class:Ant test</td>
657 <td>compbio.engine.FilePullerTester@5fa80aea</td><td>0</td>
661 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
662 <td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
666 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
667 <td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
671 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
672 <td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
676 <td title='compbio.engine.conf.DirectoryManagerTester.testGetDirectory()'><b>testGetDirectory</b></td>
677 <td>compbio.engine.conf.DirectoryManagerTester@1c1474ea</td><td>0</td>
681 <td title='compbio.data.sequence.FastaSequenceTester.testGetFormattedFasta()'><b>testGetFormattedFasta</b><br>Test class:Ant test</td>
682 <td>compbio.data.sequence.FastaSequenceTester@ec0a9f9</td><td>0</td>
686 <td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testGetJobStatus()'><b>testGetJobStatus</b><br>Test class:Ant test</td>
687 <td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18</td><td>20</td>
691 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
692 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>20</td>
696 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
697 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>20</td>
701 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
702 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>21</td>
706 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
707 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>40</td>
711 <td title='compbio.engine.local.AsyncLocalRunnerTester.testGetStatus()'><b>testGetStatus</b></td>
712 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>20</td>
716 <td title='compbio.engine.EngineConfiguratorTester.testGetSyncEngine()'><b>testGetSyncEngine</b><br>Test class:Ant test</td>
717 <td>compbio.engine.EngineConfiguratorTester@31f9338f</td><td>0</td>
721 <td title='compbio.runner._impl.OBTester.testGetTestArgsCommand()'><b>testGetTestArgsCommand</b><br>Test class:Ant test</td>
722 <td>compbio.runner._impl.OBTester@327124af</td><td>0</td>
726 <td title='compbio.runner._impl.RPSBlastTester.testGetTestArgsCommand()'><b>testGetTestArgsCommand</b><br>Test class:Ant test</td>
727 <td>compbio.runner._impl.RPSBlastTester@221f7708</td><td>0</td>
731 <td title='compbio.runner._impl.MclTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
732 <td>compbio.runner._impl.MclTester@4402a6ff</td><td>0</td>
736 <td title='compbio.runner._impl.NetNglycTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
737 <td>compbio.runner._impl.NetNglycTester@a21d23b</td><td>0</td>
741 <td title='compbio.runner._impl.OBTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
742 <td>compbio.runner._impl.OBTester@327124af</td><td>0</td>
746 <td title='compbio.runner._impl.RPSBlastTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
747 <td>compbio.runner._impl.RPSBlastTester@221f7708</td><td>0</td>
751 <td title='compbio.runner._impl.RonnTester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
752 <td>compbio.runner._impl.RonnTester@3fbfbfb8</td><td>0</td>
756 <td title='compbio.runner._impl.Tmhmm2Tester.testGetTestCommand()'><b>testGetTestCommand</b><br>Test class:Ant test</td>
757 <td>compbio.runner._impl.Tmhmm2Tester@45c3e9ba</td><td>0</td>
761 <td title='compbio.engine.client.PathValidatorTester.testIsAbsolutePath()'><b>testIsAbsolutePath</b><br>Test class:Ant test</td>
762 <td>compbio.engine.client.PathValidatorTester@5253c3f5</td><td>0</td>
766 <td title='compbio.runner.msa.LimitTester.testLoadLimits()'><b>testLoadLimits</b><br>Test class:Ant test</td>
767 <td>compbio.runner.msa.LimitTester@1b0c6cfc</td><td>0</td>
771 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testMarshalling()'><b>testMarshalling</b><br>Test class:Ant test</td>
772 <td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
776 <td title='compbio.metadata.OptionMarshallerTester.testMarshalling()'><b>testMarshalling</b><br>Test class:Ant test</td>
777 <td>compbio.metadata.OptionMarshallerTester@372c9557</td><td>0</td>
778 <td><div><pre>javax.xml.bind.MarshalException
779 - with linked exception:
780 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
781 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
782 at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
783 at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
784 at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
785 at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
786 Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
787 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
788 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
789 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
790 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
791 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
792 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
793 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
794 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
795 at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
796 at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
797 at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
798 at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
799 at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
800 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
801 at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
802 at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
803 at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
804 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
805 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
806 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
807 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
808 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
810 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1691463635", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
811 <div class='stack-trace' id='stack-trace1691463635'><pre>javax.xml.bind.MarshalException
812 - with linked exception:
813 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
814 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
815 at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
816 at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
817 at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
818 at compbio.metadata.OptionMarshallerTester.testMarshalling(OptionMarshallerTester.java:140)
819 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
820 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
821 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
822 at java.lang.reflect.Method.invoke(Method.java:597)
823 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
824 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
825 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
826 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
827 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
828 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
829 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
830 at org.testng.TestRunner.privateRun(TestRunner.java:592)
831 at org.testng.TestRunner.run(TestRunner.java:486)
832 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
833 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
834 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
835 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
836 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
837 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
838 at org.testng.TestNG.run(TestNG.java:784)
839 at org.testng.TestNG.privateMain(TestNG.java:949)
840 at org.testng.TestNG.main(TestNG.java:922)
841 Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
842 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
843 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
844 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
845 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
846 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
847 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
848 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
849 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
850 at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
851 at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
852 at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
853 at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
854 at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
855 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
856 at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
857 at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
858 at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
859 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
860 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
861 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
862 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
863 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
868 <td title='compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally()'><b>testMultipleCancelLocally</b><br>Test class:Ant test</td>
869 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
870 <td><div><pre>java.util.concurrent.CancellationException
871 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
872 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
873 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
874 at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
875 at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
876 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1281054121", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
877 <div class='stack-trace' id='stack-trace1281054121'><pre>java.util.concurrent.CancellationException
878 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
879 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
880 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
881 at compbio.engine.local.AsyncLocalRunner.getResults(AsyncLocalRunner.java:130)
882 at compbio.engine.local.AsyncLocalRunnerTester.testMultipleCancelLocally(AsyncLocalRunnerTester.java:239)
883 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
884 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
885 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
886 at java.lang.reflect.Method.invoke(Method.java:597)
887 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
888 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
889 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
890 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
891 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
892 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
893 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
894 at org.testng.TestRunner.privateRun(TestRunner.java:592)
895 at org.testng.TestRunner.run(TestRunner.java:486)
896 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
897 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
898 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
899 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
900 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
901 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
902 at org.testng.TestNG.run(TestNG.java:784)
903 at org.testng.TestNG.privateMain(TestNG.java:949)
904 at org.testng.TestNG.main(TestNG.java:922)
908 <td title='compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally()'><b>testMultipleCancelLocally</b><br>Test class:Ant test</td>
909 <td>compbio.engine.local.LocalRunnerTester@4b2922f6</td><td>0</td>
910 <td><div><pre>java.util.concurrent.CancellationException
911 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
912 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
913 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
914 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
915 at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
916 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace764924063", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
917 <div class='stack-trace' id='stack-trace764924063'><pre>java.util.concurrent.CancellationException
918 at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:220)
919 at java.util.concurrent.FutureTask.get(FutureTask.java:83)
920 at compbio.engine.local.LocalEngineUtil.getResults(LocalEngineUtil.java:108)
921 at compbio.engine.local.LocalRunner.waitForResult(LocalRunner.java:99)
922 at compbio.engine.local.LocalRunnerTester.testMultipleCancelLocally(LocalRunnerTester.java:114)
923 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
924 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
925 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
926 at java.lang.reflect.Method.invoke(Method.java:597)
927 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
928 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
929 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
930 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
931 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
932 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
933 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
934 at org.testng.TestRunner.privateRun(TestRunner.java:592)
935 at org.testng.TestRunner.run(TestRunner.java:486)
936 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
937 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
938 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
939 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
940 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
941 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
942 at org.testng.TestNG.run(TestNG.java:784)
943 at org.testng.TestNG.privateMain(TestNG.java:949)
944 at org.testng.TestNG.main(TestNG.java:922)
948 <td title='compbio.runner.msa.TcoffeeTester.testNcore()'><b>testNcore</b><br>Test class:Ant test</td>
949 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>0</td>
953 <td title='compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate()'><b>testOptionNoDefaultValidate</b><br>Test class:Ant test</td>
954 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
955 <td><div><pre>javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
956 Description: Protein weight matrix
957 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
964 at compbio.metadata.Option.validate(Option.java:317)
965 at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
966 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace283755922", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
967 <div class='stack-trace' id='stack-trace283755922'><pre>javax.xml.bind.ValidationException: Default value is required as multiple optionNames are defined for option: Option name: Matrix1
968 Description: Protein weight matrix
969 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
976 at compbio.metadata.Option.validate(Option.java:317)
977 at compbio.metadata.RunnerConfigTester.testOptionNoDefaultValidate(RunnerConfigTester.java:149)
978 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
979 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
980 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
981 at java.lang.reflect.Method.invoke(Method.java:597)
982 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
983 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
984 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
985 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
986 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
987 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
988 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
989 at org.testng.TestRunner.privateRun(TestRunner.java:592)
990 at org.testng.TestRunner.run(TestRunner.java:486)
991 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
992 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
993 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
994 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
995 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
996 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
997 at org.testng.TestNG.run(TestNG.java:784)
998 at org.testng.TestNG.privateMain(TestNG.java:949)
999 at org.testng.TestNG.main(TestNG.java:922)
1003 <td title='compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue()'><b>testOptionSetInvalidValue</b><br>Test class:Ant test</td>
1004 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1005 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
1006 Description: Protein weight matrix
1007 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1014 at compbio.metadata.Option.setDefaultValue(Option.java:130)
1015 at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
1016 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1260681385", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1017 <div class='stack-trace' id='stack-trace1260681385'><pre>compbio.metadata.WrongParameterException: Attempting to set illegal defaultValue 'AAA' which is not defined optionNames for option: Option name: Matrix1
1018 Description: Protein weight matrix
1019 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1026 at compbio.metadata.Option.setDefaultValue(Option.java:130)
1027 at compbio.metadata.RunnerConfigTester.testOptionSetInvalidValue(RunnerConfigTester.java:172)
1028 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1029 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1030 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1031 at java.lang.reflect.Method.invoke(Method.java:597)
1032 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1033 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1034 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1035 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1036 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1037 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1038 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1039 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1040 at org.testng.TestRunner.run(TestRunner.java:486)
1041 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1042 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1043 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1044 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1045 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1046 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1047 at org.testng.TestNG.run(TestNG.java:784)
1048 at org.testng.TestNG.privateMain(TestNG.java:949)
1049 at org.testng.TestNG.main(TestNG.java:922)
1053 <td title='compbio.metadata.RunnerConfigTester.testOptionToCommand()'><b>testOptionToCommand</b><br>Test class:Ant test</td>
1054 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1058 <td title='compbio.runner.msa.ClustalWParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1059 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>2</td>
1063 <td title='compbio.runner.msa.MafftParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1064 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>4</td>
1068 <td title='compbio.runner.msa.MuscleParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1069 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>2</td>
1073 <td title='compbio.runner.msa.ProbconsParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1074 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>0</td>
1078 <td title='compbio.runner.msa.TcoffeeParametersTester.testOptions()'><b>testOptions</b><br>Test class:Ant test</td>
1079 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>0</td>
1083 <td title='compbio.runner.msa.ClustalWTester.testOptionsLocally()'><b>testOptionsLocally</b><br>Test class:Ant test</td>
1084 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>1</td>
1088 <td title='compbio.engine.client.CommandBuilderTester.testOptionsToCommand()'><b>testOptionsToCommand</b><br>Test class:Ant test</td>
1089 <td>compbio.engine.client.CommandBuilderTester@6bdc64a5</td><td>0</td>
1093 <td title='compbio.metadata.RunnerConfigTester.testParameterToCommand()'><b>testParameterToCommand</b><br>Test class:Ant test</td>
1094 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1098 <td title='compbio.runner.msa.ClustalWParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1099 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>2</td>
1103 <td title='compbio.runner.msa.MafftParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1104 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>2</td>
1108 <td title='compbio.runner.msa.MuscleParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1109 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>4</td>
1113 <td title='compbio.runner.msa.ProbconsParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1114 <td>compbio.runner.msa.ProbconsParametersTester@78dc9766</td><td>1</td>
1118 <td title='compbio.runner.msa.TcoffeeParametersTester.testParameters()'><b>testParameters</b><br>Test class:Ant test</td>
1119 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>12</td>
1123 <td title='compbio.engine.cluster.drmaa.UtilTester.testParser()'><b>testParser</b><br>Test class:Ant test</td>
1124 <td>compbio.engine.cluster.drmaa.UtilTester@22e90943</td><td>0</td>
1128 <td title='compbio.runner.msa.ClustalWTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1129 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
1133 <td title='compbio.runner.msa.MafftTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1134 <td>compbio.runner.msa.MafftTester@259a8416</td><td>1</td>
1138 <td title='compbio.runner.msa.MuscleTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1139 <td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
1143 <td title='compbio.runner.msa.ProbconsTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1144 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
1148 <td title='compbio.runner.msa.TcoffeeTester.testPersistance()'><b>testPersistance</b><br>Test class:Ant test</td>
1149 <td>compbio.runner.msa.TcoffeeTester@7df1bd98</td><td>1</td>
1153 <td title='compbio.runner.msa.ClustalWParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1154 <td>compbio.runner.msa.ClustalWParametersTester@132803ba</td><td>0</td>
1158 <td title='compbio.runner.msa.MafftParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1159 <td>compbio.runner.msa.MafftParametersTester@4cc72243</td><td>2</td>
1163 <td title='compbio.runner.msa.MuscleParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1164 <td>compbio.runner.msa.MuscleParametersTester@4355d3a3</td><td>0</td>
1168 <td title='compbio.runner.msa.TcoffeeParametersTester.testPresets()'><b>testPresets</b><br>Test class:Ant test</td>
1169 <td>compbio.runner.msa.TcoffeeParametersTester@41217e67</td><td>1</td>
1173 <td title='compbio.data.sequence.FastaSequenceGeneratorTester.testProteinSequenceGeneration()'><b>testProteinSequenceGeneration</b><br>Test class:Ant test</td>
1174 <td>compbio.data.sequence.FastaSequenceGeneratorTester@163b4b1e</td><td>0</td>
1178 <td title='compbio.engine.FilePullerTester.testPull()'><b>testPull</b><br>Test class:Ant test</td>
1179 <td>compbio.engine.FilePullerTester@5fa80aea</td><td>0</td>
1183 <td title='compbio.engine.cluster.dundee._QueueTester.testQueue()'><b>testQueue</b><br>Test class:Ant test</td>
1184 <td>compbio.engine.cluster.dundee._QueueTester@715f1f9c</td><td>0</td>
1188 <td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFile()'><b>testReadClustalFile</b><br>Test class:Ant test</td>
1189 <td>compbio.data.sequence.ClustalAlignmentUtilTester@38c52200</td><td>0</td>
1193 <td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileLongNames()'><b>testReadClustalFileLongNames</b><br>Test class:Ant test</td>
1194 <td>compbio.data.sequence.ClustalAlignmentUtilTester@38c52200</td><td>0</td>
1198 <td title='compbio.data.sequence.ClustalAlignmentUtilTester.testReadClustalFileShortNames()'><b>testReadClustalFileShortNames</b><br>Test class:Ant test</td>
1199 <td>compbio.data.sequence.ClustalAlignmentUtilTester@38c52200</td><td>0</td>
1203 <td title='compbio.data.sequence.SequenceUtilTester.testReadWriteFasta()'><b>testReadWriteFasta</b><br>Test class:Ant test</td>
1204 <td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
1208 <td title='compbio.runner.msa.ClustalWTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
1209 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
1213 <td title='compbio.runner.msa.MuscleTester.testRunLocally()'><b>testRunLocally</b><br>Test class:Ant test</td>
1214 <td>compbio.runner.msa.MuscleTester@37b994de</td><td>0</td>
1218 <td title='compbio.runner.msa.ClustalWTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
1219 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>15</td>
1223 <td title='compbio.runner.msa.MuscleTester.testRunOnCluster()'><b>testRunOnCluster</b><br>Test class:Ant test</td>
1224 <td>compbio.runner.msa.MuscleTester@37b994de</td><td>8</td>
1228 <td title='compbio.runner.msa.MafftTester.testRunOnClusterAsyncCheckStatusLongPoolingTime()'><b>testRunOnClusterAsyncCheckStatusLongPoolingTime</b><br>Test class:Ant test</td>
1229 <td>compbio.runner.msa.MafftTester@259a8416</td><td>21</td>
1233 <td title='compbio.runner.msa.ClustalWTester.testRunWithMatrix()'><b>testRunWithMatrix</b><br>Test class:Ant test</td>
1234 <td>compbio.runner.msa.ClustalWTester@4125d61e</td><td>0</td>
1238 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testSchemaFromCodeGeneration()'><b>testSchemaFromCodeGeneration</b><br>Test class:Ant test</td>
1239 <td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
1243 <td title='compbio.runner.msa.MafftTester.testSetInputTester()'><b>testSetInputTester</b><br>Test class:Ant test</td>
1244 <td>compbio.runner.msa.MafftTester@259a8416</td><td>0</td>
1248 <td title='compbio.runner.msa.ProbconsTester.testSetInputTester()'><b>testSetInputTester</b><br>Test class:Ant test</td>
1249 <td>compbio.runner.msa.ProbconsTester@5a57e787</td><td>0</td>
1253 <td title='compbio.engine.client.CommandBuilderTester.testSpaceDelimiterExecutable()'><b>testSpaceDelimiterExecutable</b><br>Test class:Ant test</td>
1254 <td>compbio.engine.client.CommandBuilderTester@6bdc64a5</td><td>0</td>
1258 <td title='compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester.testSubmit()'><b>testSubmit</b><br>Test class:Ant test</td>
1259 <td>compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester@24e33e18</td><td>18</td>
1263 <td title='compbio.engine.cluster.drmaa.DrmaaClusterEngineTester.testSubmit()'><b>testSubmit</b><br>Test class:Ant test</td>
1264 <td>compbio.engine.cluster.drmaa.DrmaaClusterEngineTester@4301ac93</td><td>17</td>
1268 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1269 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
1273 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1274 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
1278 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1279 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
1283 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1284 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
1288 <td title='compbio.engine.local.AsyncLocalRunnerTester.testSubmitLocally()'><b>testSubmitLocally</b></td>
1289 <td>compbio.engine.local.AsyncLocalRunnerTester@7461f533</td><td>0</td>
1293 <td title='compbio.engine.cluster.drmaa.ClusterSessionTester.testTaskList()'><b>testTaskList</b><br>Test class:Ant test</td>
1294 <td>compbio.engine.cluster.drmaa.ClusterSessionTester@7966340c</td><td>8</td>
1298 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testUnMarshalling()'><b>testUnMarshalling</b><br>Test class:Ant test</td>
1299 <td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
1303 <td title='compbio.metadata.OptionMarshallerTester.testUnMarshalling()'><b>testUnMarshalling</b><br>Test class:Ant test</td>
1304 <td>compbio.metadata.OptionMarshallerTester@372c9557</td><td>0</td>
1308 <td title='compbio.metadata.RunnerConfigTester.testValidate()'><b>testValidate</b><br>Test class:Ant test</td>
1309 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1313 <td title='compbio.metadata.RunnerConfigTester.testValidateBoundaryConstrainCheck()'><b>testValidateBoundaryConstrainCheck</b><br>Test class:Ant test</td>
1314 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1318 <td title='compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck()'><b>testValidateLowerBoundaryConstrainCheck</b><br>Test class:Ant test</td>
1319 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1320 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1324 For parameter: Option name: Matrix1
1325 Description: Protein weight matrix
1326 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1335 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1336 at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
1337 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1790017034", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1338 <div class='stack-trace' id='stack-trace1790017034'><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1342 For parameter: Option name: Matrix1
1343 Description: Protein weight matrix
1344 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1353 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1354 at compbio.metadata.RunnerConfigTester.testValidateLowerBoundaryConstrainCheck(RunnerConfigTester.java:268)
1355 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1356 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1357 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1358 at java.lang.reflect.Method.invoke(Method.java:597)
1359 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1360 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1361 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1362 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1363 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1364 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1365 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1366 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1367 at org.testng.TestRunner.run(TestRunner.java:486)
1368 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1369 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1370 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1371 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1372 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1373 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1374 at org.testng.TestNG.run(TestNG.java:784)
1375 at org.testng.TestNG.privateMain(TestNG.java:949)
1376 at org.testng.TestNG.main(TestNG.java:922)
1380 <td title='compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck()'><b>testValidateUpperBoundaryConstrainCheck</b><br>Test class:Ant test</td>
1381 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1382 <td><div><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1386 For parameter: Option name: Matrix1
1387 Description: Protein weight matrix
1388 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1397 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1398 at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
1399 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace603950563", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1400 <div class='stack-trace' id='stack-trace603950563'><pre>compbio.metadata.WrongParameterException: Attempting to set default value outside boundaries defined by the constraint: Type: Float
1404 For parameter: Option name: Matrix1
1405 Description: Protein weight matrix
1406 URL: http://www.compbio.dundee.ac.uk/users/pvtroshin/ws/Index.html
1415 at compbio.metadata.Parameter.setDefaultValue(Parameter.java:248)
1416 at compbio.metadata.RunnerConfigTester.testValidateUpperBoundaryConstrainCheck(RunnerConfigTester.java:296)
1417 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1418 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1419 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1420 at java.lang.reflect.Method.invoke(Method.java:597)
1421 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1422 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1423 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1424 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1425 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1426 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1427 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1428 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1429 at org.testng.TestRunner.run(TestRunner.java:486)
1430 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1431 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1432 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1433 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1434 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1435 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1436 at org.testng.TestNG.run(TestNG.java:784)
1437 at org.testng.TestNG.privateMain(TestNG.java:949)
1438 at org.testng.TestNG.main(TestNG.java:922)
1442 <td title='compbio.metadata.RunnerConfigTester.testValidateValueConstrain()'><b>testValidateValueConstrain</b><br>Test class:Ant test</td>
1443 <td>compbio.metadata.RunnerConfigTester@58ca3783</td><td>0</td>
1444 <td><div><pre>javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
1446 at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
1447 at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
1448 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace1313551855", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1449 <div class='stack-trace' id='stack-trace1313551855'><pre>javax.xml.bind.ValidationException: Both boundaries (min and max) is undefined for ValueConstrain: Type: Float
1451 at compbio.metadata.ValueConstrain.validate(ValueConstrain.java:208)
1452 at compbio.metadata.RunnerConfigTester.testValidateValueConstrain(RunnerConfigTester.java:341)
1453 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1454 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1455 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1456 at java.lang.reflect.Method.invoke(Method.java:597)
1457 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1458 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1459 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1460 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1461 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1462 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1463 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1464 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1465 at org.testng.TestRunner.run(TestRunner.java:486)
1466 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1467 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1468 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1469 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1470 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1471 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1472 at org.testng.TestNG.run(TestNG.java:784)
1473 at org.testng.TestNG.privateMain(TestNG.java:949)
1474 at org.testng.TestNG.main(TestNG.java:922)
1478 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testValidation()'><b>testValidation</b><br>Test class:Ant test</td>
1479 <td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
1483 <td title='compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling()'><b>testValidationOnMarshalling</b><br>Test class:Ant test</td>
1484 <td>compbio.engine.conf.RunnerConfigMarshallerTester@710ca208</td><td>0</td>
1485 <td><div><pre>javax.xml.bind.MarshalException
1486 - with linked exception:
1487 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
1488 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
1489 at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
1490 at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
1491 at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
1492 at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
1493 Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
1494 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
1495 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
1496 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
1497 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
1498 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
1499 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
1500 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
1501 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
1502 at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
1503 at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
1504 at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
1505 at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
1506 at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
1507 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
1508 at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
1509 at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
1510 at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
1511 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
1512 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
1513 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
1514 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
1515 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
1517 ... Removed 22 stack frames</pre></div><a href='#' onClick='toggleBox("stack-trace831577209", this, "Click to show all stack frames", "Click to hide stack frames")'>Click to show all stack frames</a>
1518 <div class='stack-trace' id='stack-trace831577209'><pre>javax.xml.bind.MarshalException
1519 - with linked exception:
1520 [org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.]
1521 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:328)
1522 at com.sun.xml.bind.v2.runtime.MarshallerImpl.marshal(MarshallerImpl.java:254)
1523 at javax.xml.bind.helpers.AbstractMarshallerImpl.marshal(AbstractMarshallerImpl.java:75)
1524 at compbio.engine.conf.RunnerConfigMarshaller.writeAndValidate(RunnerConfigMarshaller.java:88)
1525 at compbio.engine.conf.RunnerConfigMarshallerTester.testValidationOnMarshalling(RunnerConfigMarshallerTester.java:258)
1526 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
1527 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
1528 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
1529 at java.lang.reflect.Method.invoke(Method.java:597)
1530 at org.testng.internal.MethodHelper.invokeMethod(MethodHelper.java:609)
1531 at org.testng.internal.Invoker.invokeMethod(Invoker.java:532)
1532 at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:686)
1533 at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1018)
1534 at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:128)
1535 at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112)
1536 at org.testng.TestRunner.runWorkers(TestRunner.java:759)
1537 at org.testng.TestRunner.privateRun(TestRunner.java:592)
1538 at org.testng.TestRunner.run(TestRunner.java:486)
1539 at org.testng.SuiteRunner.runTest(SuiteRunner.java:332)
1540 at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:327)
1541 at org.testng.SuiteRunner.privateRun(SuiteRunner.java:299)
1542 at org.testng.SuiteRunner.run(SuiteRunner.java:204)
1543 at org.testng.TestNG.createAndRunSuiteRunners(TestNG.java:912)
1544 at org.testng.TestNG.runSuitesLocally(TestNG.java:876)
1545 at org.testng.TestNG.run(TestNG.java:784)
1546 at org.testng.TestNG.privateMain(TestNG.java:949)
1547 at org.testng.TestNG.main(TestNG.java:922)
1548 Caused by: org.xml.sax.SAXParseException: cvc-complex-type.2.4.a: Invalid content was found starting with element 'options'. One of '{runnerClassName}' is expected.
1549 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
1550 at com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.error(ErrorHandlerWrapper.java:131)
1551 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:384)
1552 at com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:318)
1553 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator$XSIErrorReporter.reportError(XMLSchemaValidator.java:410)
1554 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.reportSchemaError(XMLSchemaValidator.java:3165)
1555 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.handleStartElement(XMLSchemaValidator.java:1777)
1556 at com.sun.org.apache.xerces.internal.impl.xs.XMLSchemaValidator.startElement(XMLSchemaValidator.java:685)
1557 at com.sun.org.apache.xerces.internal.jaxp.validation.ValidatorHandlerImpl.startElement(ValidatorHandlerImpl.java:549)
1558 at org.xml.sax.helpers.XMLFilterImpl.startElement(XMLFilterImpl.java:527)
1559 at com.sun.xml.bind.v2.runtime.output.SAXOutput.endStartTag(SAXOutput.java:124)
1560 at com.sun.xml.bind.v2.runtime.output.ForkXmlOutput.endStartTag(ForkXmlOutput.java:102)
1561 at com.sun.xml.bind.v2.runtime.XMLSerializer.endAttributes(XMLSerializer.java:305)
1562 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsXsiType(XMLSerializer.java:697)
1563 at com.sun.xml.bind.v2.runtime.property.ArrayElementNodeProperty.serializeItem(ArrayElementNodeProperty.java:65)
1564 at com.sun.xml.bind.v2.runtime.property.ArrayElementProperty.serializeListBody(ArrayElementProperty.java:168)
1565 at com.sun.xml.bind.v2.runtime.property.ArrayERProperty.serializeBody(ArrayERProperty.java:152)
1566 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeBody(ClassBeanInfoImpl.java:332)
1567 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsSoleContent(XMLSerializer.java:592)
1568 at com.sun.xml.bind.v2.runtime.ClassBeanInfoImpl.serializeRoot(ClassBeanInfoImpl.java:320)
1569 at com.sun.xml.bind.v2.runtime.XMLSerializer.childAsRoot(XMLSerializer.java:493)
1570 at com.sun.xml.bind.v2.runtime.MarshallerImpl.write(MarshallerImpl.java:325)
1575 <td title='compbio.metadata.OptionCombinatorTester.testgetAllOptions()'><b>testgetAllOptions</b><br>Test class:Ant test</td>
1576 <td>compbio.metadata.OptionCombinatorTester@79b66b06</td><td>0</td>
1580 <td title='compbio.metadata.OptionCombinatorTester.testgetAllParameters()'><b>testgetAllParameters</b><br>Test class:Ant test</td>
1581 <td>compbio.metadata.OptionCombinatorTester@79b66b06</td><td>0</td>
1585 <td title='compbio.data.sequence.SequenceUtilTester.testisNonAmbNucleotideSequence()'><b>testisNonAmbNucleotideSequence</b><br>Test class:Ant test</td>
1586 <td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
1590 <td title='compbio.data.sequence.SequenceUtilTester.testisProteinSequence()'><b>testisProteinSequence</b><br>Test class:Ant test</td>
1591 <td>compbio.data.sequence.SequenceUtilTester@ad72200</td><td>0</td>
1595 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateClustalConfiguration()'><b>validateClustalConfiguration</b><br>Test class:Ant test</td>
1596 <td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
1600 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateMafftConfiguration()'><b>validateMafftConfiguration</b><br>Test class:Ant test</td>
1601 <td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
1605 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateMuscleConfiguration()'><b>validateMuscleConfiguration</b><br>Test class:Ant test</td>
1606 <td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>
1610 <td title='compbio.metadata.PresetTester.validatePresets()'><b>validatePresets</b><br>Test class:Ant test</td>
1611 <td>compbio.metadata.PresetTester@50009f0d</td><td>0</td>
1615 <td title='compbio.engine.conf.PropertyHelperManagerTester.validateTcoffeeConfiguration()'><b>validateTcoffeeConfiguration</b><br>Test class:Ant test</td>
1616 <td>compbio.engine.conf.PropertyHelperManagerTester@307bd0d</td><td>0</td>