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