X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ftests%2FAnt%20suite%2Fclasses.html;h=2ff180842671cd38dab7f87a94f9404c4596c83f;hb=f1bdd8da517901fe1d7957d388ea579ad1fbaa3b;hp=34aa37e7d8861c255691e23ce92fbcaa2761da9e;hpb=cb02e8a08893701386c270a8bf9d0f08b9cbc4db;p=jabaws.git diff --git a/website/tests/Ant suite/classes.html b/website/tests/Ant suite/classes.html index 34aa37e..2ff1808 100644 --- a/website/tests/Ant suite/classes.html +++ b/website/tests/Ant suite/classes.html @@ -34,58 +34,19 @@ @AfterClass -compbio.metadata.RunnerConfigTester +compbio.runner._impl.NetNglycTester    @Test   -testValidateUpperBoundaryConstrainCheck -  - -  -testOptionSetInvalidValue -  - -  -testValidateBoundaryConstrainCheck -  - -  -testValidateValueConstrain -  - -  -testCreateParameterWithValidValueConstrain -  - -  -testValidateLowerBoundaryConstrainCheck -  - -  -testOptionNoDefaultValidate -  - -  -testCreateParameter -  - -  -testOptionToCommand -  - -  -testParameterToCommand -  - -  -testCreateNumParameterWithoutValidValue -  +testBuildCommand +cluster runner +   -testValidate +testGetTestCommand   @BeforeClass @@ -94,30 +55,25 @@ @BeforeMethod -  -setup -  - @AfterMethod @AfterClass -compbio.runner._impl.NetNglycTester +compbio.engine.EngineConfiguratorTester    @Test   -testGetTestCommand +testGetAsyncEngine     -testBuildCommand -cluster runner - +testGetSyncEngine +  @BeforeClass @@ -131,56 +87,42 @@ @AfterClass -compbio.runner.msa.MafftParametersTester +compbio.runner.disorder.GlobPlotTester    @Test   -testConstrainedParametersMaxValues -runner non_windows - - -  -testConstrainedParametersRandomValues -runner non_windows - - -  -testConstrainedParametersMinValues -runner non_windows +testRunOnCluster +cluster runner   -testArguments -runner non_windows +testPersistance +runner   -testOptions -runner non_windows +testRunOnClusterAsync +cluster runner   -testDefaultParameters -runner non_windows +testConfigurationLoading +runner   -testParameters -runner non_windows +readStatistics +runner   -testPresets -runner non_windows +testRunLocally +runner -  -testConfiguration -  - @BeforeClass @@ -188,9 +130,8 @@   -setup -runner non_windows - +init +  @AfterMethod @@ -198,18 +139,26 @@ @AfterClass -compbio.engine.EngineConfiguratorTester +compbio.stat.collector.ExecutionStatCollectorTester    @Test   -testGetAsyncEngine +testHasCompleted     -testGetSyncEngine +testHasTimedOut +  + +  +testCollectStat +  + +  +testUpdateStatTester   @BeforeClass @@ -224,19 +173,45 @@ @AfterClass -compbio.runner._impl.RonnTester +compbio.engine.local.AsyncLocalRunnerTester    @Test   -testGetTestCommand -  +testCancelLocally +engine +   -testBuildCommand -cluster runner +testMultipleCancelLocally +engine + + +  +testAsyncCancelOperation +engine + + +  +testAsyncRetrievOperation +engine + + +  +testSubmitLocally +engine + + +  +testCancelCompletedTaskLocally +engine + + +  +testGetStatus +engine @BeforeClass @@ -251,7 +226,7 @@ @AfterClass -compbio.runner.msa.ProbconsTester +compbio.runner.msa.MafftTester    @Test @@ -263,6 +238,11 @@   +testRunOnClusterAsyncCheckStatusShortPoolingTime +cluster runner non_windows + + +  testPersistance runner non_windows @@ -287,6 +267,11 @@ runner non_windows +  +testRunOnClusterAsyncCheckStatusLongPoolingTime +cluster runner non_windows + + @BeforeClass @@ -304,40 +289,27 @@ @AfterClass -compbio.engine.conf.PropertyHelperManagerTester +compbio.data.sequence.ClustalAlignmentUtilTester    @Test   -testClusterEngineConf -cluster - - -  -validateClustalConfiguration -  - -  -validateTcoffeeConfiguration +testReadClustalFile     -validateMuscleConfiguration +testReadClustalFileLongNames     -validateMafftConfiguration +testReadClustalFileShortNames   @BeforeClass -  -testLoadResources -  - @BeforeMethod @@ -347,29 +319,50 @@ @AfterClass -compbio.engine.FilePullerTester +compbio.runner.disorder.IUPredTester    @Test   -testGet -  +testRunOnCluster +cluster runner +   -testCache -engine +testReadResults +runner   -testGetDelay -engine +testPersistance +runner   -testPull -engine +testRunOnClusterAsync +cluster runner + + +  +testSetParameter +runner + + +  +testConfigurationLoading +runner + + +  +testRunLocally +runner + + +  +testRunLocallyWithParams +runner @BeforeClass @@ -378,24 +371,28 @@ @BeforeMethod +  +init +  + @AfterMethod @AfterClass -compbio.metadata.OptionCombinatorTester +compbio.engine.client.PathValidatorTester    @Test   -testgetAllParameters +testIsAbsolutePath     -testgetAllOptions +testGetClassPath   @BeforeClass @@ -404,61 +401,98 @@ @BeforeMethod -  -setup -  - @AfterMethod @AfterClass -compbio.runner.msa.MuscleTester +compbio.stat.collector.StatDBTester    @Test   -testRunOnCluster -cluster runner - +testReadOneMonthData +    -testRunOnClusterAsync -cluster runner - +testVerifyJobsCount +    -testPersistance -runner - +testReadYearData +    -testConfigurationLoading -runner - +testGetEarliestRecord +  -  -readStatistics -runner +@BeforeClass   -testRunLocally -runner +init +  + +@BeforeMethod + + +@AfterMethod + + +@AfterClass + + +compbio.stat.servlet.util.StatCollectionTester +   + +@Test +  +testGetStats +  + @BeforeClass @BeforeMethod +@AfterMethod + + +@AfterClass + + +compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester +   + +@Test + +   -init -  +testSubmit +engine cluster + + +  +testCancel +engine cluster + + +  +testGetJobStatus +engine cluster + + +@BeforeClass + + +@BeforeMethod + @AfterMethod @@ -466,30 +500,63 @@ @AfterClass -compbio.runner.msa.TcoffeeTester +compbio.engine.cluster.drmaa.DrmaaClusterEngineTester    @Test   -testExecute -runner non_windows +testSubmit +engine cluster + + +  +testCancel +engine cluster + + +@BeforeClass + + +@BeforeMethod + + +@AfterMethod + + +@AfterClass + + +compbio.runner.conservation.AAConTester +   + +@Test + + +  +testRunOnCluster +runner + + +  +testRunLocallyWithPreset +runner   testPersistance -cluster runner non_windows +runner   -testNcore -runner non_windows +testRunOnClusterAsync +cluster runner   -testClusterExecute -cluster runner non_windows +testRunLocallyOnTwoCpu +runner   @@ -499,7 +566,12 @@   readStatistics -runner non_windows +runner + + +  +testRunLocally +runner @BeforeClass @@ -510,7 +582,37 @@   init -cluster runner non_windows +  + +@AfterMethod + + +@AfterClass + + +compbio.runner._impl.RPSBlastTester +   + +@Test + + +  +testBuildCommand +cluster runner + + +  +testGetTestCommand +  + +  +testGetTestArgsCommand +  + +@BeforeClass + + +@BeforeMethod @AfterMethod @@ -519,14 +621,14 @@ @AfterClass -compbio.runner.msa.LimitTester +compbio.engine.PulledFileCacheTester    @Test   -testLoadLimits +test   @BeforeClass @@ -535,34 +637,121 @@ @BeforeMethod +@AfterMethod + + +@AfterClass + + +compbio.runner.disorder.DisemblTester +   + +@Test + +   -setup +testRunOnCluster +cluster runner + + +  +testPersistance runner +  +testRunOnClusterAsync +cluster runner + + +  +testConfigurationLoading +runner + + +  +readStatistics +runner + + +  +testRunLocally +runner + + +@BeforeClass + + +@BeforeMethod + + +  +init +  + @AfterMethod @AfterClass -compbio.runner._impl.OBTester +compbio.runner._impl.MclTester    @Test   +testBuildCommand +cluster runner + + +  testGetTestCommand   +@BeforeClass + + +@BeforeMethod + + +@AfterMethod + + +@AfterClass + + +compbio.engine.cluster.dundee._QueueTester +   + +@Test + +   -testBuildCommand -cluster runner +testQueue +  + +@BeforeClass + + +@BeforeMethod + + +@AfterMethod + + +@AfterClass + + +compbio.engine.LoadBalancerTester +   + +@Test   -testGetTestArgsCommand +testLoadBalance   @BeforeClass @@ -577,78 +766,177 @@ @AfterClass -compbio.engine.local.AsyncLocalRunnerTester +compbio.runner.msa.ProbconsParametersTester    @Test   -testCancelLocally -engine +testConstrainedParametersMaxValues +runner non_windows   -testMultipleCancelLocally -engine +testConstrainedParametersRandomValues +runner non_windows   -testAsyncCancelOperation -engine +testConstrainedParametersMinValues +runner non_windows   -testAsyncRetrievOperation -engine +testArguments +runner non_windows   -testSubmitLocally -engine +testOptions +runner non_windows   -testCancelCompletedTaskLocally -engine +testDefaultParameters +runner non_windows   -testGetStatus -engine +testParameters +runner non_windows +  +testConfiguration +  + @BeforeClass @BeforeMethod +  +setup +runner non_windows + + @AfterMethod @AfterClass -compbio.engine.local.LocalRunnerTester +compbio.metadata.RunnerConfigTester    @Test   -testCancelLocally -engine +testValidateUpperBoundaryConstrainCheck +  + +  +testOptionSetInvalidValue +  + +  +testValidateBoundaryConstrainCheck +  + +  +testValidateValueConstrain +  + +  +testCreateParameterWithValidValueConstrain +  + +  +testValidateLowerBoundaryConstrainCheck +  + +  +testOptionNoDefaultValidate +  + +  +testCreateParameter +  + +  +testOptionToCommand +  + +  +testParameterToCommand +  + +  +testCreateNumParameterWithoutValidValue +  + +  +testValidate +  + +@BeforeClass + + +@BeforeMethod   -testMultipleCancelLocally -engine +setup +  + +@AfterMethod + + +@AfterClass + + +compbio.runner.disorder.JronnTester +   + +@Test   -testCancelCompletedTaskLocally -engine +testRunOnCluster +cluster runner + + +  +testPersistance +runner + + +  +testRunOnClusterAsync +cluster runner + + +  +testRunLocallyOnTwoCpu +runner + + +  +testConfigurationLoading +runner + + +  +readStatistics +runner + + +  +testRunLocally +runner @BeforeClass @@ -657,27 +945,98 @@ @BeforeMethod +  +init +  + @AfterMethod @AfterClass -compbio.runner._impl.Tmhmm2Tester +compbio.runner.msa.MafftParametersTester    @Test   -testGetTestCommand +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._impl.RonnTester +   + +@Test + +   testBuildCommand cluster runner +  +testGetTestCommand +  + @BeforeClass @@ -690,7 +1049,7 @@ @AfterClass -compbio.runner.msa.MafftTester +compbio.runner.msa.ProbconsTester    @Test @@ -702,11 +1061,6 @@   -testRunOnClusterAsyncCheckStatusShortPoolingTime -cluster runner non_windows - - -  testPersistance runner non_windows @@ -731,11 +1085,6 @@ runner non_windows -  -testRunOnClusterAsyncCheckStatusLongPoolingTime -cluster runner non_windows - - @BeforeClass @@ -753,27 +1102,40 @@ @AfterClass -compbio.data.sequence.ClustalAlignmentUtilTester +compbio.engine.conf.PropertyHelperManagerTester    @Test   -testReadClustalFile +testClusterEngineConf +cluster + + +  +validateClustalConfiguration     -testReadClustalFileLongNames +validateTcoffeeConfiguration     -testReadClustalFileShortNames +validateMuscleConfiguration +  + +  +validateMafftConfiguration   @BeforeClass +  +testLoadResources +  + @BeforeMethod @@ -783,55 +1145,60 @@ @AfterClass -compbio.runner.msa.MuscleParametersTester +compbio.metadata.OptionCombinatorTester    @Test   -testConstrainedParametersMaxValues -runner - +testgetAllParameters +    -testConstrainedParametersRandomValues -runner +testgetAllOptions +  + +@BeforeClass -  -testConstrainedParametersMinValues -runner +@BeforeMethod   -testArguments -runner +setup +  + +@AfterMethod -  -testOptions -runner +@AfterClass -  -testDefaultParameters -runner +compbio.engine.FilePullerTester +   + +@Test   -testParameters -runner +testGet +  + +  +testCache +engine   -testPresets -runner +testGetDelay +engine   -testConfiguration -  +testPull +engine + @BeforeClass @@ -839,48 +1206,46 @@ @BeforeMethod -  -setup -runner - - @AfterMethod @AfterClass -compbio.data.sequence.FastaSequenceGeneratorTester +compbio.runner.msa.MuscleTester    @Test   -testProteinSequenceGeneration -  - -@BeforeClass +testRunOnCluster +cluster runner -@BeforeMethod +  +testPersistance +runner -@AfterMethod +  +testRunOnClusterAsync +cluster runner -@AfterClass +  +testConfigurationLoading +runner -compbio.engine.cluster.drmaa.ClusterSessionTester -   - -@Test +  +readStatistics +runner   -testTaskList -engine cluster +testRunLocally +runner @BeforeClass @@ -889,21 +1254,51 @@ @BeforeMethod +  +init +  + @AfterMethod @AfterClass -compbio.data.sequence.FastaSequenceTester +compbio.runner.msa.TcoffeeTester    @Test   -testGetFormattedFasta -  +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 @@ -911,24 +1306,34 @@ @BeforeMethod +  +init +cluster runner non_windows + + @AfterMethod @AfterClass -compbio.engine.client.PathValidatorTester +compbio.runner._impl.OBTester    @Test   -testIsAbsolutePath +testBuildCommand +cluster runner + + +  +testGetTestCommand     -testGetClassPath +testGetTestArgsCommand   @BeforeClass @@ -943,30 +1348,18 @@ @AfterClass -compbio.data.sequence.SequenceUtilTester +compbio.runner.msa.LimitTester    @Test   -testDeepCleanSequence -  - -  -testReadWriteFasta -  - -  -testisNonAmbNucleotideSequence -  - -  -testisProteinSequence +testLimitExceeded     -testCleanSequence +testLoadLimits   @BeforeClass @@ -975,60 +1368,63 @@ @BeforeMethod +  +setup +runner + + @AfterMethod @AfterClass -compbio.runner.msa.TcoffeeParametersTester +compbio.engine.local.LocalRunnerTester    @Test   -testConstrainedParametersMaxValues -runner non_windows +testCancelLocally +engine   -testConstrainedParametersRandomValues -runner non_windows +testMultipleCancelLocally +engine   -testConstrainedParametersMinValues -runner non_windows +testCancelCompletedTaskLocally +engine -  -testArguments -runner non_windows +@BeforeClass -  -testOptions -runner non_windows +@BeforeMethod -  -testDefaultParameters -runner non_windows +@AfterMethod -  -testParameters -runner non_windows +@AfterClass + + +compbio.runner._impl.Tmhmm2Tester +   + +@Test   -testPresets -runner non_windows +testBuildCommand +cluster runner   -testConfiguration +testGetTestCommand   @BeforeClass @@ -1037,87 +1433,87 @@ @BeforeMethod -  -setup -runner non_windows - - @AfterMethod @AfterClass -compbio.runner.msa.ClustalWTester +compbio.runner.msa.MuscleParametersTester    - -@Test - - -  -testRunOnCluster -cluster runner + +@Test   -testPersistance +testConstrainedParametersMaxValues runner   -testAddParameters -  +testConstrainedParametersRandomValues +runner +   -testOptionsLocally +testConstrainedParametersMinValues runner   -readStatisticsClusterExecution -cluster runner +testArguments +runner   -testConfigurationLoading +testOptions runner   -testRunWithMatrix +testDefaultParameters runner   -readStatistics +testParameters runner   -testRunLocally +testPresets runner +  +testConfiguration +  + @BeforeClass @BeforeMethod +  +setup +runner + + @AfterMethod @AfterClass -compbio.engine.cluster.drmaa.UtilTester +compbio.data.sequence.FastaSequenceGeneratorTester    @Test   -testParser +testProteinSequenceGeneration   @BeforeClass @@ -1132,19 +1528,16 @@ @AfterClass -compbio.engine.conf.DirectoryManagerTester +compbio.engine.cluster.drmaa.ClusterSessionTester    @Test   -testGetDirectory -  - -  -testNanoTime -  +testTaskList +engine cluster + @BeforeClass @@ -1158,21 +1551,15 @@ @AfterClass -compbio.engine.cluster.drmaa.DrmaaClusterEngineTester +compbio.data.sequence.FastaReaderTester    @Test   -testSubmit -engine cluster - - -  -testCancel -engine cluster - +test +  @BeforeClass @@ -1186,26 +1573,15 @@ @AfterClass -compbio.engine.cluster.drmaa.DrmaaAsyncClusterEngineTester +compbio.data.sequence.FastaSequenceTester    @Test   -testSubmit -engine cluster - - -  -testCancel -engine cluster - - -  -testGetJobStatus -engine cluster - +testGetFormattedFasta +  @BeforeClass @@ -1219,44 +1595,58 @@ @AfterClass -compbio.metadata.PresetTester +compbio.data.sequence.SequenceUtilTester    @Test   -marshallPreset +testReadIUPredForGlobDomain     -validatePresets +testDeepCleanSequence   -@BeforeClass - +  +testReadIUPredForShortAndLongDisorder +  -@BeforeMethod - +  +testCleanProteinSequence +  -@AfterMethod - +  +testReadWriteFasta +  -@AfterClass - +  +testReadAAConResults +  -compbio.metadata.OptionMarshallerTester -   +  +testReadGlobPlotResults +  -@Test - +  +testReadDisemblResults +    -testUnMarshalling +loadJronnFile     -testMarshalling +testisNonAmbNucleotideSequence +  + +  +testisProteinSequence +  + +  +testCleanSequence   @BeforeClass @@ -1265,17 +1655,13 @@ @BeforeMethod -  -setup -  - @AfterMethod @AfterClass -compbio.runner.msa.ClustalWParametersTester +compbio.runner.msa.TcoffeeParametersTester    @Test @@ -1283,42 +1669,42 @@   testConstrainedParametersMaxValues -runner +runner non_windows   testConstrainedParametersRandomValues -runner +runner non_windows   testConstrainedParametersMinValues -runner +runner non_windows   testArguments -runner +runner non_windows   testOptions -runner +runner non_windows   testDefaultParameters -runner +runner non_windows   testParameters -runner +runner non_windows   testPresets -runner +runner non_windows   @@ -1333,7 +1719,7 @@   setup -runner +runner non_windows @AfterMethod @@ -1342,25 +1728,78 @@ @AfterClass -compbio.runner._impl.RPSBlastTester +compbio.engine.cluster.drmaa.UtilTester    @Test   -testGetTestCommand +testParser   +@BeforeClass + + +@BeforeMethod + + +@AfterMethod + + +@AfterClass + + +compbio.runner.msa.ClustalWTester +   + +@Test + +   -testBuildCommand +testRunOnCluster cluster runner   -testGetTestArgsCommand +testAddParameters   +  +testPersistance +runner + + +  +testOptionsLocally +runner + + +  +readStatisticsClusterExecution +cluster runner + + +  +testRunWithMatrix +runner + + +  +testConfigurationLoading +runner + + +  +readStatistics +runner + + +  +testRunLocally +runner + + @BeforeClass @@ -1373,14 +1812,18 @@ @AfterClass -compbio.engine.PulledFileCacheTester +compbio.engine.conf.DirectoryManagerTester    @Test   -test +testGetDirectory +  + +  +testNanoTime   @BeforeClass @@ -1395,20 +1838,23 @@ @AfterClass -compbio.runner._impl.MclTester +compbio.metadata.PresetTester    @Test   -testGetTestCommand +testPresetWithMuptiOptions     -testBuildCommand -cluster runner - +marshallPreset +  + +  +validatePresets +  @BeforeClass @@ -1422,14 +1868,18 @@ @AfterClass -compbio.engine.cluster.dundee._QueueTester +compbio.metadata.OptionMarshallerTester    @Test   -testQueue +testUnMarshalling +  + +  +testMarshalling   @BeforeClass @@ -1438,13 +1888,17 @@ @BeforeMethod +  +setup +  + @AfterMethod @AfterClass -compbio.runner.msa.ProbconsParametersTester +compbio.runner.msa.ClustalWParametersTester    @Test @@ -1452,37 +1906,42 @@   testConstrainedParametersMaxValues -runner non_windows +runner   testConstrainedParametersRandomValues -runner non_windows +runner   testConstrainedParametersMinValues -runner non_windows +runner   testArguments -runner non_windows +runner   testOptions -runner non_windows +runner   testDefaultParameters -runner non_windows +runner   testParameters -runner non_windows +runner + + +  +testPresets +runner   @@ -1497,7 +1956,7 @@   setup -runner non_windows +runner @AfterMethod