Class name	Method name	Groups
compbio.engine.client.CommandBuilderTester
@Test
	testOptionsToCommand
	testSpaceDelimiterExecutable
	testCommandBuilding
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.RunnerConfigTester
@Test
	testValidateUpperBoundaryConstrainCheck
	testOptionSetInvalidValue
	testValidateBoundaryConstrainCheck
	testValidateValueConstrain
	testCreateParameterWithValidValueConstrain
	testValidateLowerBoundaryConstrainCheck
	testOptionNoDefaultValidate
	testCreateParameter
	testOptionToCommand
	testParameterToCommand
	testCreateNumParameterWithoutValidValue
	testValidate
@BeforeClass
@BeforeMethod
	setup
@AfterMethod
@AfterClass
compbio.runner._impl.NetNglycTester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.MafftParametersTester
@Test
	testConstrainedParametersMaxValues	runner non_windows
	testConstrainedParametersRandomValues	runner non_windows
	testConstrainedParametersMinValues	runner non_windows
	testArguments	runner non_windows
	testOptions	runner non_windows
	testDefaultParameters	runner non_windows
	testParameters	runner non_windows
	testPresets	runner non_windows
	testConfiguration
@BeforeClass
@BeforeMethod
	setup	runner non_windows
@AfterMethod
@AfterClass
compbio.engine.EngineConfiguratorTester
@Test
	testGetAsyncEngine
	testGetSyncEngine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.RonnTester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.ProbconsTester
@Test
	testExecute	runner non_windows
	testPersistance	runner non_windows
	testClusterExecute	cluster runner non_windows
	testSetInputTester	runner non_windows
	testConfigurationLoading	runner
	readStatistics	runner non_windows
@BeforeClass
@BeforeMethod
	init	cluster runner non_windows
@AfterMethod
@AfterClass
compbio.engine.conf.PropertyHelperManagerTester
@Test
	testClusterEngineConf	cluster
	validateClustalConfiguration
	validateTcoffeeConfiguration
	validateMuscleConfiguration
	validateMafftConfiguration
@BeforeClass
	testLoadResources
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.FilePullerTester
@Test
	testGet
	testCache	engine
	testGetDelay	engine
	testPull	engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.OptionCombinatorTester
@Test
	testgetAllParameters
	testgetAllOptions
@BeforeClass
@BeforeMethod
	setup
@AfterMethod
@AfterClass
compbio.runner.msa.MuscleTester
@Test
	testRunOnCluster	cluster runner
	testRunOnClusterAsync	cluster runner
	testPersistance	runner
	testConfigurationLoading	runner
	readStatistics	runner
	testRunLocally	runner
@BeforeClass
@BeforeMethod
	init
@AfterMethod
@AfterClass
compbio.runner.msa.TcoffeeTester
@Test
	testExecute	runner non_windows
	testPersistance	cluster runner non_windows
	testNcore	runner non_windows
	testClusterExecute	cluster runner non_windows
	testConfigurationLoading	runner
	readStatistics	runner non_windows
@BeforeClass
@BeforeMethod
	init	cluster runner non_windows
@AfterMethod
@AfterClass
compbio.runner.msa.LimitTester
@Test
	testLoadLimits
@BeforeClass
@BeforeMethod
	setup	runner
@AfterMethod
@AfterClass
compbio.runner._impl.OBTester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
	testGetTestArgsCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.local.AsyncLocalRunnerTester
@Test
	testCancelLocally	engine
	testMultipleCancelLocally	engine
	testAsyncCancelOperation	engine
	testAsyncRetrievOperation	engine
	testSubmitLocally	engine
	testCancelCompletedTaskLocally	engine
	testGetStatus	engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.local.LocalRunnerTester
@Test
	testCancelLocally	engine
	testMultipleCancelLocally	engine
	testCancelCompletedTaskLocally	engine
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.Tmhmm2Tester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.MafftTester
@Test
	testExecute	runner non_windows
	testRunOnClusterAsyncCheckStatusShortPoolingTime	cluster runner non_windows
	testPersistance	runner non_windows
	testClusterExecute	cluster runner non_windows
	testSetInputTester	runner non_windows
	testConfigurationLoading	runner
	readStatistics	runner non_windows
	testRunOnClusterAsyncCheckStatusLongPoolingTime	cluster runner non_windows
@BeforeClass
@BeforeMethod
	init	cluster runner non_windows
@AfterMethod
@AfterClass
compbio.data.sequence.ClustalAlignmentUtilTester
@Test
	testReadClustalFile
	testReadClustalFileLongNames
	testReadClustalFileShortNames
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.MuscleParametersTester
@Test
	testConstrainedParametersMaxValues	runner
	testConstrainedParametersRandomValues	runner
	testConstrainedParametersMinValues	runner
	testArguments	runner
	testOptions	runner
	testDefaultParameters	runner
	testParameters	runner
	testPresets	runner
	testConfiguration
@BeforeClass
@BeforeMethod
	setup	runner
@AfterMethod
@AfterClass
compbio.data.sequence.FastaSequenceGeneratorTester
@Test
	testProteinSequenceGeneration
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.ClusterSessionTester
@Test
	testTaskList	engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.data.sequence.FastaSequenceTester
@Test
	testGetFormattedFasta
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.client.PathValidatorTester
@Test
	testIsAbsolutePath
	testGetClassPath
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.data.sequence.SequenceUtilTester
@Test
	testDeepCleanSequence
	testReadWriteFasta
	testisNonAmbNucleotideSequence
	testisProteinSequence
	testCleanSequence
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.TcoffeeParametersTester
@Test
	testConstrainedParametersMaxValues	runner non_windows
	testConstrainedParametersRandomValues	runner non_windows
	testConstrainedParametersMinValues	runner non_windows
	testArguments	runner non_windows
	testOptions	runner non_windows
	testDefaultParameters	runner non_windows
	testParameters	runner non_windows
	testPresets	runner non_windows
	testConfiguration
@BeforeClass
@BeforeMethod
	setup	runner non_windows
@AfterMethod
@AfterClass
compbio.runner.msa.ClustalWTester
@Test
	testRunOnCluster	cluster runner
	testPersistance	runner
	testAddParameters
	testOptionsLocally	runner
	readStatisticsClusterExecution	cluster runner
	testConfigurationLoading	runner
	testRunWithMatrix	runner
	readStatistics	runner
	testRunLocally	runner
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.UtilTester
@Test
	testParser
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.conf.DirectoryManagerTester
@Test
	testGetDirectory
	testNanoTime
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.DrmaaClusterEngineTester
@Test
	testSubmit	engine cluster
	testCancel	engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester
@Test
	testSubmit	engine cluster
	testCancel	engine cluster
	testGetJobStatus	engine cluster
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.PresetTester
@Test
	marshallPreset
	validatePresets
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.metadata.OptionMarshallerTester
@Test
	testUnMarshalling
	testMarshalling
@BeforeClass
@BeforeMethod
	setup
@AfterMethod
@AfterClass
compbio.runner.msa.ClustalWParametersTester
@Test
	testConstrainedParametersMaxValues	runner
	testConstrainedParametersRandomValues	runner
	testConstrainedParametersMinValues	runner
	testArguments	runner
	testOptions	runner
	testDefaultParameters	runner
	testParameters	runner
	testPresets	runner
	testConfiguration
@BeforeClass
@BeforeMethod
	setup	runner
@AfterMethod
@AfterClass
compbio.runner._impl.RPSBlastTester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
	testGetTestArgsCommand
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.PulledFileCacheTester
@Test
	test
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner._impl.MclTester
@Test
	testGetTestCommand
	testBuildCommand	cluster runner
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.engine.cluster.dundee._QueueTester
@Test
	testQueue
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
compbio.runner.msa.ProbconsParametersTester
@Test
	testConstrainedParametersMaxValues	runner non_windows
	testConstrainedParametersRandomValues	runner non_windows
	testConstrainedParametersMinValues	runner non_windows
	testArguments	runner non_windows
	testOptions	runner non_windows
	testDefaultParameters	runner non_windows
	testParameters	runner non_windows
	testConfiguration
@BeforeClass
@BeforeMethod
	setup	runner non_windows
@AfterMethod
@AfterClass
compbio.engine.conf.RunnerConfigMarshallerTester
@Test
	testValidationOnMarshalling
	testUnMarshalling
	testValidation
	testSchemaFromCodeGeneration
	testMarshalling
@BeforeClass
@BeforeMethod
	setup
@AfterMethod
@AfterClass