Class | Line # | Actions | |||
---|---|---|---|---|---|
SequenceFeatures | 45 | 99 | 47 | 1.0100% |
Class SequenceFeatures |
Line # 45 |
99 |
47 |
1.0100% |
---|---|---|---|---|
SequenceFeatures() SequenceFeatures() | 5656 | 1.01 | 1.01 | 1.0 1.0100% |
SequenceFeatures(List<SequenceFeature>) SequenceFeatures(List<SequenceFeature>) | 7070 | 4.04 | 2.02 | 1.0 1.0100% |
add(SequenceFeature) : boolean add(SequenceFeature) : boolean | 8585 | 7.07 | 3.03 | 1.0 1.0100% |
findFeatures(int,int,String) : List<SequenceFeature> findFeatures(int,int,String) : List<SequenceFeature> | 106106 | 4.04 | 1.01 | 1.0 1.0100% |
getAllFeatures(String) : List<SequenceFeature> getAllFeatures(String) : List<SequenceFeature> | 123123 | 4.04 | 1.01 | 1.0 1.0100% |
getFeaturesByOntology(String) : List<SequenceFeature> getFeaturesByOntology(String) : List<SequenceFeature> | 138138 | 6.06 | 4.04 | 1.0 1.0100% |
getFeatureCount(boolean,String) : int getFeatureCount(boolean,String) : int | 162162 | 4.04 | 1.01 | 1.0 1.0100% |
getTotalFeatureLength(String) : int getTotalFeatureLength(String) : int | 177177 | 4.04 | 1.01 | 1.0 1.0100% |
getPositionalFeatures(String) : List<SequenceFeature> getPositionalFeatures(String) : List<SequenceFeature> | 192192 | 4.04 | 1.01 | 1.0 1.0100% |
varargToTypes(String) : Iterable<FeatureStore> varargToTypes(String) : Iterable<FeatureStore> | 213213 | 7.07 | 5.05 | 1.0 1.0100% |
getContactFeatures(String) : List<SequenceFeature> getContactFeatures(String) : List<SequenceFeature> | 237237 | 4.04 | 1.01 | 1.0 1.0100% |
getNonPositionalFeatures(String) : List<SequenceFeature> getNonPositionalFeatures(String) : List<SequenceFeature> | 252252 | 4.04 | 1.01 | 1.0 1.0100% |
delete(SequenceFeature) : boolean delete(SequenceFeature) : boolean | 267267 | 4.04 | 2.02 | 1.0 1.0100% |
hasFeatures() : boolean hasFeatures() : boolean | 283283 | 4.04 | 2.02 | 1.0 1.0100% |
getFeatureGroups(boolean,String) : Set<String> getFeatureGroups(boolean,String) : Set<String> | 299299 | 4.04 | 1.01 | 1.0 1.0100% |
getFeatureTypesForGroups(boolean,String) : Set<String> getFeatureTypesForGroups(boolean,String) : Set<String> | 316316 | 8.08 | 2.02 | 1.0 1.0100% |
getFeatureTypes(String) : Set<String> getFeatureTypes(String) : Set<String> | 345345 | 6.06 | 3.03 | 1.0 1.0100% |
isOntologyTerm(String,String) : boolean isOntologyTerm(String,String) : boolean | 370370 | 7.07 | 5.05 | 1.0 1.0100% |
getMinimumScore(String,boolean) : float getMinimumScore(String,boolean) : float | 390390 | 1.01 | 2.02 | 1.0 1.0100% |
getMaximumScore(String,boolean) : float getMaximumScore(String,boolean) : float | 401401 | 1.01 | 2.02 | 1.0 1.0100% |
sortFeatures(List<? extends IntervalI>,boolean) : void sortFeatures(List<? extends IntervalI>,boolean) : void | 416416 | 1.01 | 2.02 | 1.0 1.0100% |
getFeaturesForGroup(boolean,String,String) : List<SequenceFeature> getFeaturesForGroup(boolean,String,String) : List<SequenceFeature> | 435435 | 5.05 | 2.02 | 1.0 1.0100% |
shiftFeatures(int,int) : boolean shiftFeatures(int,int) : boolean | 453453 | 4.04 | 1.01 | 1.0 1.0100% |
deleteAll() : void deleteAll() : void | 467467 | 1.01 | 1.01 | 1.0 1.0100% |
0.46496814
|
jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere | 1PASS | ||
0.46496814
|
jalview.project.Jalview2xmlTests.viewRefPdbAnnotationjalview.project.Jalview2xmlTests.viewRefPdbAnnotation | 1PASS | ||
0.46496814
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews | 1PASS | ||
0.46496814
|
jalview.project.Jalview2xmlTests.testCopyViewSettingsjalview.project.Jalview2xmlTests.testCopyViewSettings | 1PASS | ||
0.46496814
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings | 1PASS | ||
0.42038217
|
jalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesByOntologyjalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesByOntology | 1PASS | ||
0.41401273
|
jalview.analysis.AlignmentUtilsTests.testFindCdsPositionsjalview.analysis.AlignmentUtilsTests.testFindCdsPositions | 1PASS | ||
0.40764332
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_HiddenColumnsjalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_HiddenColumns | 1PASS | ||
0.40764332
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModeljalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel | 1PASS | ||
0.40764332
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_hiddenFirstColumnjalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_hiddenFirstColumn | 1PASS | ||
0.40127388
|
jalview.ext.ensembl.EnsemblCdsTest.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblCdsTest.testGetIdentifyingFeatures | 1PASS | ||
0.40127388
|
jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures | 1PASS | ||
0.40127388
|
jalview.ext.ensembl.EnsemblGeneTest.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblGeneTest.testGetIdentifyingFeatures | 1PASS | ||
0.40127388
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances_withParamsjalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances_withParams | 1PASS | ||
0.40127388
|
jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice | 1PASS | ||
0.40127388
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistancesjalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances | 1PASS | ||
0.40127388
|
jalview.ext.ensembl.EnsemblCdsTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblCdsTest.testGetGenomicRangesFromFeatures | 1PASS | ||
0.40127388
|
jalview.ext.ensembl.EnsemblGenomeTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblGenomeTest.testGetGenomicRangesFromFeatures | 1PASS | ||
0.40127388
|
jalview.ext.ensembl.EnsemblGeneTest.testGetTranscriptFeaturesjalview.ext.ensembl.EnsemblGeneTest.testGetTranscriptFeatures | 1PASS | ||
0.40127388
|
jalview.analysis.AlignmentUtilsTests.testMapCdsToProteinjalview.analysis.AlignmentUtilsTests.testMapCdsToProtein | 1PASS | ||
0.40127388
|
jalview.ext.ensembl.EnsemblCdnaTest.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblCdnaTest.testGetIdentifyingFeatures | 1PASS | ||
0.40127388
|
jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_reverseStrandjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_reverseStrand | 1PASS | ||
0.40127388
|
jalview.ext.ensembl.EnsemblGenomeTest.testGetIdentifyingFeaturesjalview.ext.ensembl.EnsemblGenomeTest.testGetIdentifyingFeatures | 1PASS | ||
0.39490446
|
jalview.analysis.AlignmentUtilsTests.testFindCdsPositions_fivePrimeIncompletejalview.analysis.AlignmentUtilsTests.testFindCdsPositions_fivePrimeIncomplete | 1PASS | ||
0.39490446
|
jalview.analysis.AlignmentUtilsTests.testTransferFeatures_withSelectjalview.analysis.AlignmentUtilsTests.testTransferFeatures_withSelect | 1PASS | ||
0.38853502
|
jalview.analysis.AlignmentUtilsTests.testFindCdsForProtein_noUTRjalview.analysis.AlignmentUtilsTests.testFindCdsForProtein_noUTR | 1PASS | ||
0.38853502
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResiduejalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResidue | 1PASS | ||
0.37579617
|
jalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrandjalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand | 1PASS | ||
0.37579617
|
jalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_mixedStrandjalview.ext.ensembl.EnsemblCdnaTest.testGetGenomicRangesFromFeatures_mixedStrand | 1PASS | ||
0.37579617
|
jalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeaturesjalview.ext.ensembl.EnsemblGeneTest.testGetGenomicRangesFromFeatures | 1PASS | ||
0.3566879
|
jalview.commands.EditCommandTest.testCut_withFeatures_exhaustivejalview.commands.EditCommandTest.testCut_withFeatures_exhaustive | 1PASS | ||
0.34394905
|
jalview.io.FeaturesFileTest.testPrintGffFormatjalview.io.FeaturesFileTest.testPrintGffFormat | 1PASS | ||
0.34394905
|
jalview.commands.EditCommandTest.testCut_withFeaturesjalview.commands.EditCommandTest.testCut_withFeatures | 1PASS | ||
0.34394905
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFilterFeaturesForDisplayjalview.renderer.seqfeatures.FeatureRendererTest.testFilterFeaturesForDisplay | 1PASS | ||
0.3375796
|
jalview.gui.FeatureSettingsTest.testSaveLoadjalview.gui.FeatureSettingsTest.testSaveLoad | 1PASS | ||
0.3312102
|
jalview.io.FeaturesFileTest.testPrintJalviewFormat_withFiltersjalview.io.FeaturesFileTest.testPrintJalviewFormat_withFilters | 1PASS | ||
0.3312102
|
jalview.io.GenBankFileTest.testParsejalview.io.GenBankFileTest.testParse | 1PASS | ||
0.3312102
|
jalview.io.EmblFlatFileTest.testParsejalview.io.EmblFlatFileTest.testParse | 1PASS | ||
0.32484075
|
jalview.ext.jmol.JmolParserTest.testAlignmentLoaderjalview.ext.jmol.JmolParserTest.testAlignmentLoader | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.32484075
|
jalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMol | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.32484075
|
jalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotationjalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotation | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.32484075
|
jalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.32484075
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntryjalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntry | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.32484075
|
jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMadejalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.32484075
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.31847134
|
jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withGapjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withGap | 1PASS | ||
0.31847134
|
jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInBothSeqsjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInBothSeqs | 1PASS | ||
0.31847134
|
jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInEitherOneSeqjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInEitherOneSeq | 1PASS | ||
0.3121019
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumnjalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumn | 1PASS | ||
0.3057325
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_transparencySingleFeaturejalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_transparencySingleFeature | 1PASS | ||
0.3057325
|
jalview.gui.AlignFrameTest.testHideFeatureColumnsjalview.gui.AlignFrameTest.testHideFeatureColumns | 1PASS | ||
0.3057325
|
jalview.controller.AlignViewControllerTest.testFindColumnsWithFeaturejalview.controller.AlignViewControllerTest.testFindColumnsWithFeature | 1PASS | ||
0.3057325
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_transparencyTwoFeaturesjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_transparencyTwoFeatures | 1PASS | ||
0.29936305
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_graduatedFeatureColourjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_graduatedFeatureColour | 1PASS | ||
0.29936305
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_nestedFeaturesjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_nestedFeatures | 1PASS | ||
0.2866242
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_graduatedWithThresholdjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_graduatedWithThreshold | 1PASS | ||
0.28025478
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_multipleFeaturesAtPositionNoTransparencyjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_multipleFeaturesAtPositionNoTransparency | 1PASS | ||
0.28025478
|
jalview.datamodel.features.SequenceFeaturesTest.testGetAllFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetAllFeatures | 1PASS | ||
0.27388534
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_featureGroupNotDisplayedjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_featureGroupNotDisplayed | 1PASS | ||
0.27388534
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_contactFeaturejalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_contactFeature | 1PASS | ||
0.26751593
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_singleFeatureAtPositionjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_singleFeatureAtPosition | 1PASS | ||
0.26751593
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_singleFeatureNotAtPositionjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_singleFeatureNotAtPosition | 1PASS | ||
0.26751593
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_featureTypeNotDisplayedjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_featureTypeNotDisplayed | 1PASS | ||
0.26751593
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureAtEndjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureAtEnd | 1PASS | ||
0.25477707
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocusjalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocus | 1PASS | ||
0.2356688
|
jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureCountjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureCount | 1PASS | ||
0.2356688
|
jalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNonejalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNone | 1PASS | ||
0.22929937
|
jalview.commands.EditCommandTest.testUndo_cutjalview.commands.EditCommandTest.testUndo_cut | 1PASS | ||
0.22929937
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeaturesjalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeatures | 1PASS | ||
0.22929937
|
jalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMol | 1PASS | ||
0.22292994
|
jalview.renderer.seqfeatures.FeatureRendererTest.testIsVisiblejalview.renderer.seqfeatures.FeatureRendererTest.testIsVisible | 1PASS | ||
0.21656051
|
jalview.datamodel.SequenceTest.testGetSequenceFeaturesjalview.datamodel.SequenceTest.testGetSequenceFeatures | 1PASS | ||
0.21656051
|
jalview.datamodel.features.SequenceFeaturesTest.testGetTotalFeatureLengthjalview.datamodel.features.SequenceFeaturesTest.testGetTotalFeatureLength | 1PASS | ||
0.21019109
|
jalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsqjalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsq | 1PASS | ||
0.21019109
|
jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypesjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypes | 1PASS | ||
0.21019109
|
jalview.datamodel.features.SequenceFeaturesTest.testConstructorjalview.datamodel.features.SequenceFeaturesTest.testConstructor | 1PASS | ||
0.21019109
|
jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureGroupsjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureGroups | 1PASS | ||
0.21019109
|
jalview.io.vcf.VCFLoaderTest.testDoLoadjalview.io.vcf.VCFLoaderTest.testDoLoad | 1PASS | ||
0.21019109
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_gapPositionjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_gapPosition | 1PASS | ||
0.21019109
|
jalview.io.FeaturesFileTest.testParsejalview.io.FeaturesFileTest.testParse | 1PASS | ||
0.21019109
|
jalview.io.vcf.VCFLoaderTest.testLoadVCFContigjalview.io.vcf.VCFLoaderTest.testLoadVCFContig | 1PASS | ||
0.21019109
|
jalview.io.vcf.VCFLoaderTest.testDoLoad_reverseStrandjalview.io.vcf.VCFLoaderTest.testDoLoad_reverseStrand | 1PASS | ||
0.20382166
|
jalview.datamodel.features.SequenceFeaturesTest.testShiftFeaturesjalview.datamodel.features.SequenceFeaturesTest.testShiftFeatures | 1PASS | ||
0.19745223
|
jalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesForGroupjalview.datamodel.features.SequenceFeaturesTest.testGetFeaturesForGroup | 1PASS | ||
0.19745223
|
jalview.io.FeaturesFileTest.testPrintJalviewFormatjalview.io.FeaturesFileTest.testPrintJalviewFormat | 1PASS | ||
0.19745223
|
jalview.io.gff.GffTests.testResolveExonerateGffjalview.io.gff.GffTests.testResolveExonerateGff | 1PASS | ||
0.19745223
|
jalview.commands.EditCommandTest.testCutjalview.commands.EditCommandTest.testCut | 1PASS | ||
0.1910828
|
jalview.gui.AssociatePDBFileTest.testAssociatePDBFilejalview.gui.AssociatePDBFileTest.testAssociatePDBFile | 1PASS | ||
0.1910828
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.1910828
|
jalview.gui.AnnotationLabelsTest2.testIdWidthNoChangesjalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges | 1PASS | ||
0.1910828
|
mc_view.PDBfileTest.testParse_withJmolAddAlignmentAnnotationsmc_view.PDBfileTest.testParse_withJmolAddAlignmentAnnotations | 1PASS | ||
0.1910828
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.1910828
|
jalview.gui.AnnotationLabelsTest2.testIdWidthNoChangesjalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges | 1PASS | ||
0.1910828
|
jalview.datamodel.SequenceTest.testAddSequenceFeaturesjalview.datamodel.SequenceTest.testAddSequenceFeatures | 1PASS | ||
0.1910828
|
jalview.datamodel.features.SequenceFeaturesTest.testGetMinimumScore_getMaximumScorejalview.datamodel.features.SequenceFeaturesTest.testGetMinimumScore_getMaximumScore | 1PASS | ||
0.1910828
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.1910828
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.1910828
|
jalview.structure.StructureSelectionManagerTest.testSetMapping_seqFeaturesjalview.structure.StructureSelectionManagerTest.testSetMapping_seqFeatures | 1PASS | ||
0.1910828
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_noFeaturesShownjalview.renderer.seqfeatures.FeatureColourFinderTest.testFindFeatureColour_noFeaturesShown | 1PASS | ||
0.1910828
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.1910828
|
jalview.renderer.seqfeatures.FeatureColourFinderTest.testNoFeaturesDisplayedjalview.renderer.seqfeatures.FeatureColourFinderTest.testNoFeaturesDisplayed | 1PASS | ||
0.1910828
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.1910828
|
jalview.ext.jmol.JmolParserTest.testLocalPDBIdjalview.ext.jmol.JmolParserTest.testLocalPDBId | 1PASS | ||
0.1910828
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.1910828
|
mc_view.PDBfileTest.testParse_withJmol_noAnnotationsmc_view.PDBfileTest.testParse_withJmol_noAnnotations | 1PASS | ||
0.1910828
|
jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges | 1PASS | ||
0.1910828
|
jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypes_byOntologyjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypes_byOntology | 1PASS | ||
0.1910828
|
mc_view.PDBChainTest.testMakeResidueList_noAnnotationmc_view.PDBChainTest.testMakeResidueList_noAnnotation | 1PASS | ||
0.1910828
|
jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges | 1PASS | ||
0.18471338
|
jalview.io.FeaturesFileTest.simpleGff3FileLoaderjalview.io.FeaturesFileTest.simpleGff3FileLoader | 1PASS | ||
0.18471338
|
jalview.io.FeaturesFileTest.testParse_pureGff3jalview.io.FeaturesFileTest.testParse_pureGff3 | 1PASS | ||
0.18471338
|
jalview.analysis.AlignmentUtilsTests.testTransferFeaturesjalview.analysis.AlignmentUtilsTests.testTransferFeatures | 1PASS | ||
0.18471338
|
jalview.datamodel.SequenceTest.testCopyConstructor_withDatasetjalview.datamodel.SequenceTest.testCopyConstructor_withDataset | 1PASS | ||
0.18471338
|
jalview.io.FeaturesFileTest.readGff3Filejalview.io.FeaturesFileTest.readGff3File | 1PASS | ||
0.18471338
|
jalview.datamodel.SequenceTest.testCopyConstructor_noDatasetjalview.datamodel.SequenceTest.testCopyConstructor_noDataset | 1PASS | ||
0.18471338
|
jalview.datamodel.SequenceTest.testDeleteChars_withDbRefsAndFeaturesjalview.datamodel.SequenceTest.testDeleteChars_withDbRefsAndFeatures | 1PASS | ||
0.18471338
|
jalview.io.JSONFileTest.testGrpParsed_colourNonejalview.io.JSONFileTest.testGrpParsed_colourNone | 1PASS | ||
0.18471338
|
jalview.analysis.AlignmentUtilsTests.testTransferFeatures_withOmitjalview.analysis.AlignmentUtilsTests.testTransferFeatures_withOmit | 1PASS | ||
0.18471338
|
jalview.analysis.SeqsetUtilsTest.testSeqFeatureAdditionjalview.analysis.SeqsetUtilsTest.testSeqFeatureAddition | 1PASS | ||
0.18471338
|
jalview.datamodel.SequenceDummyTest.testBecomejalview.datamodel.SequenceDummyTest.testBecome | 1PASS | ||
0.18471338
|
jalview.io.FeaturesFileTest.testParse_jalviewFeaturesOnlyjalview.io.FeaturesFileTest.testParse_jalviewFeaturesOnly | 1PASS | ||
0.18471338
|
jalview.datamodel.SequenceTest.testDeriveSequence_existingDatasetjalview.datamodel.SequenceTest.testDeriveSequence_existingDataset | 1PASS | ||
0.18471338
|
jalview.io.FeaturesFileTest.simpleGff3RelaxedIdMatchingjalview.io.FeaturesFileTest.simpleGff3RelaxedIdMatching | 1PASS | ||
0.18471338
|
jalview.io.FeaturesFileTest.simpleGff3FileClassjalview.io.FeaturesFileTest.simpleGff3FileClass | 1PASS | ||
0.18471338
|
jalview.commands.EditCommandTest.testCut_withFeatures5primejalview.commands.EditCommandTest.testCut_withFeatures5prime | 1PASS | ||
0.18471338
|
jalview.io.FeaturesFileTest.testParse_mixedJalviewGffjalview.io.FeaturesFileTest.testParse_mixedJalviewGff | 1PASS | ||
0.18471338
|
jalview.analysis.AlignmentUtilsTests.testMakeCdsAlignmentjalview.analysis.AlignmentUtilsTests.testMakeCdsAlignment | 1PASS | ||
0.18471338
|
jalview.io.gff.InterProScanHelperTest.testProcessProteinMatchjalview.io.gff.InterProScanHelperTest.testProcessProteinMatch | 1PASS | ||
0.17834395
|
jalview.analysis.AlignmentSorterTest.testSortByFeature_scorejalview.analysis.AlignmentSorterTest.testSortByFeature_score | 1PASS | ||
0.17834395
|
jalview.datamodel.features.SequenceFeaturesTest.testGetNonPositionalFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetNonPositionalFeatures | 1PASS | ||
0.17834395
|
jalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypesForGroupsjalview.datamodel.features.SequenceFeaturesTest.testGetFeatureTypesForGroups | 1PASS | ||
0.17834395
|
jalview.datamodel.features.SequenceFeaturesTest.testGetPositionalFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetPositionalFeatures | 1PASS | ||
0.17834395
|
jalview.datamodel.features.SequenceFeaturesTest.testGetContactFeaturesjalview.datamodel.features.SequenceFeaturesTest.testGetContactFeatures | 1PASS | ||
0.1656051
|
jalview.datamodel.features.SequenceFeaturesTest.testDeletejalview.datamodel.features.SequenceFeaturesTest.testDelete | 1PASS | ||
0.1656051
|
jalview.io.FeaturesFileTest.testPrintGffFormat_withFiltersjalview.io.FeaturesFileTest.testPrintGffFormat_withFilters | 1PASS | ||
0.1656051
|
jalview.datamodel.features.SequenceFeaturesTest.testFindFeaturesjalview.datamodel.features.SequenceFeaturesTest.testFindFeatures | 1PASS | ||
0.15923567
|
jalview.ws.dbsources.UniprotTest.testGetUniprotSequencejalview.ws.dbsources.UniprotTest.testGetUniprotSequence | 1PASS | ||
0.15286624
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindFeatureAt_PointFeaturejalview.analysis.scoremodels.FeatureDistanceModelTest.testFindFeatureAt_PointFeature | 1PASS | ||
0.15286624
|
jalview.commands.TrimRegionCommandTest.testTrimRight_withUndoAndRedojalview.commands.TrimRegionCommandTest.testTrimRight_withUndoAndRedo | 1PASS | ||
0.15286624
|
jalview.io.gff.ExonerateHelperTest.testAddExonerateGffToAlignmentjalview.io.gff.ExonerateHelperTest.testAddExonerateGffToAlignment | 1PASS | ||
0.15286624
|
jalview.datamodel.AlignedCodonFrameTest.testRealiseWithjalview.datamodel.AlignedCodonFrameTest.testRealiseWith | 1PASS | ||
0.15286624
|
jalview.commands.TrimRegionCommandTest.testTrimLeft_withUndoAndRedojalview.commands.TrimRegionCommandTest.testTrimLeft_withUndoAndRedo | 1PASS | ||
0.14012739
|
jalview.io.AnnotatedPDBFileInputTest.checkPDBSequenceFeaturesjalview.io.AnnotatedPDBFileInputTest.checkPDBSequenceFeatures | 1PASS | ||
0.14012739
|
jalview.io.JSONFileTest.testSeqParsedjalview.io.JSONFileTest.testSeqParsed | 1PASS | ||
0.14012739
|
jalview.datamodel.features.SequenceFeaturesTest.testHasFeaturesjalview.datamodel.features.SequenceFeaturesTest.testHasFeatures | 1PASS | ||
0.14012739
|
jalview.datamodel.features.SequenceFeaturesTest.testVarargsToTypesjalview.datamodel.features.SequenceFeaturesTest.testVarargsToTypes | 1PASS | ||
0.13375796
|
jalview.analysis.FinderTest.testFind_featuresOnlyjalview.analysis.FinderTest.testFind_featuresOnly | 1PASS | ||
0.12738854
|
jalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReportjalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport | 1PASS | ||
0.12738854
|
jalview.datamodel.SequenceTest.testFindFeaturesjalview.datamodel.SequenceTest.testFindFeatures | 1PASS | ||
0.12101911
|
jalview.commands.EditCommandTest.testReplacejalview.commands.EditCommandTest.testReplace | 1PASS | ||
0.12101911
|
jalview.project.Jalview2xmlTests.testPAEsaveRestorejalview.project.Jalview2xmlTests.testPAEsaveRestore | 1PASS | ||
0.12101911
|
jalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroup | 1PASS | ||
0.12101911
|
jalview.io.PhylipFileTests.testInterleavedIOjalview.io.PhylipFileTests.testInterleavedIO | 1PASS | ||
0.12101911
|
jalview.gui.QuitHandlerTest.testSavedProjectChangesjalview.gui.QuitHandlerTest.testSavedProjectChanges | 1PASS | ||
0.12101911
|
jalview.gui.QuitHandlerTest.testWaitForSaveQuitjalview.gui.QuitHandlerTest.testWaitForSaveQuit | 1PASS | ||
0.12101911
|
jalview.commands.EditCommandTest.testUndo_multipleInsertGapsjalview.commands.EditCommandTest.testUndo_multipleInsertGaps | 1PASS | ||
0.12101911
|
jalview.datamodel.SequenceTest.testDeleteChars_withGapsjalview.datamodel.SequenceTest.testDeleteChars_withGaps | 1PASS | ||
0.12101911
|
jalview.project.Jalview2xmlTests.testColourByAnnotScoresjalview.project.Jalview2xmlTests.testColourByAnnotScores | 1PASS | ||
0.12101911
|
jalview.datamodel.SequenceGroupTest.testAddSequencejalview.datamodel.SequenceGroupTest.testAddSequence | 1PASS | ||
0.12101911
|
jalview.commands.EditCommandTest.testUndo_multipleCommandsjalview.commands.EditCommandTest.testUndo_multipleCommands | 1PASS | ||
0.12101911
|
jalview.io.PhylipFileTests.testSequentialIOjalview.io.PhylipFileTests.testSequentialIO | 1PASS | ||
0.12101911
|
jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation | 1PASS | ||
0.12101911
|
jalview.datamodel.SeqCigarTest.testSomethingjalview.datamodel.SeqCigarTest.testSomething | 1PASS | ||
0.12101911
|
jalview.gui.AlignmentPanelTest.testSetOverviewTitlejalview.gui.AlignmentPanelTest.testSetOverviewTitle | 1PASS | ||
0.12101911
|
jalview.commands.EditCommandTest.testAppendEdit_deleteGapjalview.commands.EditCommandTest.testAppendEdit_deleteGap | 1PASS | ||
0.12101911
|
jalview.gui.AlignViewportTest.testDeregisterMapping_onCloseViewjalview.gui.AlignViewportTest.testDeregisterMapping_onCloseView | 1PASS | ||
0.12101911
|
jalview.analysis.DnaTest.testTranslateCdna_simplejalview.analysis.DnaTest.testTranslateCdna_simple | 1PASS | ||
0.12101911
|
jalview.io.StockholmFileTest.curlyWUSSsecondaryStructureForRNASequencejalview.io.StockholmFileTest.curlyWUSSsecondaryStructureForRNASequence | 1PASS | ||
0.12101911
|
jalview.io.JalviewExportPropertiesTests.testImportExportPeriodGapsjalview.io.JalviewExportPropertiesTests.testImportExportPeriodGaps | 1PASS | ||
0.12101911
|
jalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeightjalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeight | 1PASS | ||
0.12101911
|
jalview.io.StockholmFileTest.fullWUSSsecondaryStructureForRNASequencejalview.io.StockholmFileTest.fullWUSSsecondaryStructureForRNASequence | 1PASS | ||
0.12101911
|
jalview.io.StockholmFileTest.pfamFileIOjalview.io.StockholmFileTest.pfamFileIO | 1PASS | ||
0.12101911
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverOverview | 1PASS | ||
0.12101911
|
jalview.io.StockholmFileTest.secondaryStructureForRNASequencejalview.io.StockholmFileTest.secondaryStructureForRNASequence | 1PASS | ||
0.12101911
|
jalview.project.Jalview2xmlTests.testTCoffeeScoresjalview.project.Jalview2xmlTests.testTCoffeeScores | 1PASS | ||
0.12101911
|
jalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverviewjalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverview | 1PASS | ||
0.12101911
|
jalview.datamodel.AlignmentTest.testPropagateInsertionsjalview.datamodel.AlignmentTest.testPropagateInsertions | 1PASS | ||
0.12101911
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverview | 1PASS | ||
0.12101911
|
jalview.analysis.DnaTest.testTranslateCdna_hiddenColumnsjalview.analysis.DnaTest.testTranslateCdna_hiddenColumns | 1PASS | ||
0.12101911
|
jalview.commands.EditCommandTest.testReplace_withGapsjalview.commands.EditCommandTest.testReplace_withGaps | 1PASS | ||
0.12101911
|
jalview.datamodel.SequenceTest.testTransferAnnotationjalview.datamodel.SequenceTest.testTransferAnnotation | 1PASS | ||
0.12101911
|
jalview.datamodel.CigarArrayTest.testConstructorjalview.datamodel.CigarArrayTest.testConstructor | 1PASS | ||
0.12101911
|
jalview.datamodel.AlignmentViewTest.testGetVisibleContigsjalview.datamodel.AlignmentViewTest.testGetVisibleContigs | 1PASS | ||
0.12101911
|
jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip | 1PASS | ||
0.12101911
|
jalview.analysis.DnaTest.testTranslateCdna_sequenceOrderIndependentjalview.analysis.DnaTest.testTranslateCdna_sequenceOrderIndependent | 1PASS | ||
0.12101911
|
jalview.gui.AlignFrameTest.testNewView_colourThresholdsjalview.gui.AlignFrameTest.testNewView_colourThresholds | 1PASS | ||
0.12101911
|
jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery | 1PASS | ||
0.12101911
|
jalview.datamodel.SequenceGroupTest.testAddOrRemovejalview.datamodel.SequenceGroupTest.testAddOrRemove | 1PASS | ||
0.12101911
|
jalview.analysis.DnaTest.testTranslateCdna_withUntranslatableCodonsAndHiddenColumnsjalview.analysis.DnaTest.testTranslateCdna_withUntranslatableCodonsAndHiddenColumns | 1PASS | ||
0.12101911
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqsjalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqs | 1PASS | ||
0.12101911
|
jalview.datamodel.AlignmentTest.testPropagateInsertionsOverlapjalview.datamodel.AlignmentTest.testPropagateInsertionsOverlap | 1PASS | ||
0.12101911
|
jalview.analysis.DnaTest.testTranslateCdna_withUntranslatableCodonsjalview.analysis.DnaTest.testTranslateCdna_withUntranslatableCodons | 1PASS | ||
0.12101911
|
jalview.io.AnnotationFileIOTest.exampleAnnotationFileIOjalview.io.AnnotationFileIOTest.exampleAnnotationFileIO | 1PASS | ||
0.12101911
|
jalview.gui.AlignFrameTest.testNewView_dsRefPreservedjalview.gui.AlignFrameTest.testNewView_dsRefPreserved | 1PASS | ||
0.12101911
|
jalview.io.StockholmFileTest.rfamFileIOjalview.io.StockholmFileTest.rfamFileIO | 1PASS | ||
0.12101911
|
jalview.analysis.TestAlignSeq.testGetMappingForS1_withLowerCasejalview.analysis.TestAlignSeq.testGetMappingForS1_withLowerCase | 1PASS | ||
0.12101911
|
jalview.commands.EditCommandTest.testUndo_insertGapjalview.commands.EditCommandTest.testUndo_insertGap | 1PASS | ||
0.12101911
|
jalview.datamodel.AlignmentViewTest.testGetVisibleAlignmentGapCharjalview.datamodel.AlignmentViewTest.testGetVisibleAlignmentGapChar | 1PASS | ||
0.12101911
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholdsjalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholds | 1PASS | ||
0.12101911
|
jalview.io.RNAMLfileTest.testRnamlToStockholmIOjalview.io.RNAMLfileTest.testRnamlToStockholmIO | 1PASS | ||
0.12101911
|
jalview.datamodel.SeqCigarTest.testFindPositionjalview.datamodel.SeqCigarTest.testFindPosition | 1PASS | ||
0.12101911
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColoursjalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColours | 1PASS | ||
0.12101911
|
jalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroup | 1PASS | ||
0.12101911
|
jalview.commands.EditCommandTest.testUndo_deleteGapjalview.commands.EditCommandTest.testUndo_deleteGap | 1PASS | ||
0.11464968
|
jalview.datamodel.features.SequenceFeaturesTest.testDeleteAlljalview.datamodel.features.SequenceFeaturesTest.testDeleteAll | 1PASS | ||
0.089171976
|
jalview.datamodel.features.SequenceFeaturesTest.testIsOntologyTermjalview.datamodel.features.SequenceFeaturesTest.testIsOntologyTerm | 1PASS | ||
0.08280255
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08280255
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.08280255
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.08280255
|
jalview.analysis.AlignmentUtilsTests.testMapProteinAlignmentToCdna_withStartAndStopCodonsjalview.analysis.AlignmentUtilsTests.testMapProteinAlignmentToCdna_withStartAndStopCodons | 1PASS | ||
0.08280255
|
jalview.analysis.AlignmentUtilsTests.testMapProteinAlignmentToCdna_withXrefsjalview.analysis.AlignmentUtilsTests.testMapProteinAlignmentToCdna_withXrefs | 1PASS | ||
0.08280255
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08280255
|
jalview.analysis.AlignmentUtilsTests.testMapProteinAlignmentToCdna_noXrefsjalview.analysis.AlignmentUtilsTests.testMapProteinAlignmentToCdna_noXrefs | 1PASS | ||
0.08280255
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.070063695
|
jalview.structures.models.AAStructureBindingModelTest.testImportPDBPreservesChainMappingsjalview.structures.models.AAStructureBindingModelTest.testImportPDBPreservesChainMappings | 1PASS | ||
0.070063695
|
jalview.ext.jmol.JmolParserTest.testParse_alternativeResiduesjalview.ext.jmol.JmolParserTest.testParse_alternativeResidues | 1PASS | ||
0.070063695
|
mc_view.PDBChainTest.testMakeResidueList_withTempFactormc_view.PDBChainTest.testMakeResidueList_withTempFactor | 1PASS | ||
0.070063695
|
mc_view.PDBChainTest.testMakeExactMappingmc_view.PDBChainTest.testMakeExactMapping | 1PASS | ||
0.070063695
|
jalview.io.EmblFlatFileTest.testParseToRNAjalview.io.EmblFlatFileTest.testParseToRNA | 1PASS | ||
0.070063695
|
jalview.ws.dbsources.UniprotTest.testimportOfProblemEntriesjalview.ws.dbsources.UniprotTest.testimportOfProblemEntries | 1PASS | ||
0.070063695
|
mc_view.PDBChainTest.testMakeCaBondListmc_view.PDBChainTest.testMakeCaBondList | 1PASS | ||
0.070063695
|
mc_view.PDBChainTest.testMakeCaBondList_nucleotidemc_view.PDBChainTest.testMakeCaBondList_nucleotide | 1PASS | ||
0.070063695
|
jalview.ext.jmol.JmolParserTest.testParse_missingResiduesjalview.ext.jmol.JmolParserTest.testParse_missingResidues | 1PASS | ||
0.070063695
|
mc_view.PDBfileTest.testParsemc_view.PDBfileTest.testParse | 1PASS | ||
0.070063695
|
jalview.ws.dbsources.EmblXmlSourceTest.testGetSequencejalview.ws.dbsources.EmblXmlSourceTest.testGetSequence | 1PASS | ||
0.070063695
|
jalview.ext.jmol.JmolParserTest.testFileParserjalview.ext.jmol.JmolParserTest.testFileParser | 1PASS | ||
0.070063695
|
mc_view.PDBfileTest.testParse_withAnnotations_noSSmc_view.PDBfileTest.testParse_withAnnotations_noSS | 1PASS | ||
0.06369427
|
jalview.analysis.AlignmentUtilsTests.testMakeCdsAlignment_alternativeTranscriptsjalview.analysis.AlignmentUtilsTests.testMakeCdsAlignment_alternativeTranscripts | 1PASS | ||
0.06369427
|
jalview.gui.ColourMenuHelperTest.testAddMenuItems_nucleotidejalview.gui.ColourMenuHelperTest.testAddMenuItems_nucleotide | 1PASS | ||
0.06369427
|
jalview.gui.PopupMenuTest.testHideInsertionsjalview.gui.PopupMenuTest.testHideInsertions | 1PASS | ||
0.06369427
|
jalview.datamodel.SequenceTest.testCreateDatasetSequencejalview.datamodel.SequenceTest.testCreateDatasetSequence | 1PASS | ||
0.06369427
|
jalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport_withEllipsisjalview.io.SequenceAnnotationReportTest.testCreateSequenceAnnotationReport_withEllipsis | 1PASS | ||
0.06369427
|
jalview.io.EmblFlatFileTest.testParse_noUniprotXrefjalview.io.EmblFlatFileTest.testParse_noUniprotXref | 1PASS | ||
0.06369427
|
jalview.analysis.CrossRefTest.testFindXrefSequences_fromDbRefMapjalview.analysis.CrossRefTest.testFindXrefSequences_fromDbRefMap | 1PASS | ||
0.06369427
|
jalview.gui.AlignFrameTest.testChangeColour_background_groupsAndThresholdsjalview.gui.AlignFrameTest.testChangeColour_background_groupsAndThresholds | 1PASS | ||
0.06369427
|
jalview.analysis.AlignmentUtilsTests.testMakeCdsAlignment_multipleProteinsjalview.analysis.AlignmentUtilsTests.testMakeCdsAlignment_multipleProteins | 1PASS | ||
0.06369427
|
jalview.analysis.AlignmentUtilsTests.testMakeCdsAlignment_filterProductsjalview.analysis.AlignmentUtilsTests.testMakeCdsAlignment_filterProducts | 1PASS | ||
0.044585988
|
jalview.util.MapListTest.testToStringjalview.util.MapListTest.testToString | 1PASS | ||
0.044585988
|
jalview.util.MapListTest.testLocateInTo_noIntronsjalview.util.MapListTest.testLocateInTo_noIntrons | 1PASS | ||
0.025477707
|
jalview.datamodel.features.SequenceFeaturesTest.testSortFeaturesjalview.datamodel.features.SequenceFeaturesTest.testSortFeatures | 1PASS | ||
0.01910828
|
jalview.datamodel.features.FeatureStoreTest.testShiftFeaturesjalview.datamodel.features.FeatureStoreTest.testShiftFeatures | 1PASS | ||
0.012738854
|
jalview.commands.EditCommandTest.testPriorState_removeGapsMultipleSeqsjalview.commands.EditCommandTest.testPriorState_removeGapsMultipleSeqs | 1PASS | ||
0.012738854
|
jalview.analysis.FinderTest.testFind_inDescriptionjalview.analysis.FinderTest.testFind_inDescription | 1PASS | ||
0.012738854
|
jalview.gui.SeqPanelTest.testFindColumn_unwrappedjalview.gui.SeqPanelTest.testFindColumn_unwrapped | 1PASS | ||
0.012738854
|
jalview.analysis.AAFrequencyTest.testCalculate_noProfilejalview.analysis.AAFrequencyTest.testCalculate_noProfile | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_withMapping_withUnmappedProteinjalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_withMapping_withUnmappedProtein | 1PASS | ||
0.012738854
|
jalview.io.ClustalFileTest.testParse_withNumberingjalview.io.ClustalFileTest.testParse_withNumbering | 1PASS | ||
0.012738854
|
jalview.gui.QuitHandlerTest.testForceQuitjalview.gui.QuitHandlerTest.testForceQuit | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testCreateDatasetAlignmentWithMappedToSeqsjalview.datamodel.AlignmentTest.testCreateDatasetAlignmentWithMappedToSeqs | 1PASS | ||
0.012738854
|
jalview.analysis.AAFrequencyTest.testCompleteConsensus_ignoreGaps_noLogojalview.analysis.AAFrequencyTest.testCompleteConsensus_ignoreGaps_noLogo | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testSetDatasetSequence_cascadingjalview.datamodel.SequenceTest.testSetDatasetSequence_cascading | 1PASS | ||
0.012738854
|
jalview.gui.StructureViewerTest.testGetSequencesForPdbsjalview.gui.StructureViewerTest.testGetSequencesForPdbs | 1PASS | ||
0.012738854
|
jalview.gui.AnnotationLabelsTest.testGetStatusMessagejalview.gui.AnnotationLabelsTest.testGetStatusMessage | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testSetDataset_selfReferencejalview.datamodel.AlignmentTest.testSetDataset_selfReference | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testGetStartGetEndjalview.datamodel.SequenceTest.testGetStartGetEnd | 1PASS | ||
0.012738854
|
jalview.gui.AnnotationChooserTest.testBuildActionButtonsPaneljalview.gui.AnnotationChooserTest.testBuildActionButtonsPanel | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testMatchContainsjalview.datamodel.SearchResultsTest.testMatchContains | 1PASS | ||
0.012738854
|
jalview.schemes.ClustalxColourSchemeTest.testFindColourjalview.schemes.ClustalxColourSchemeTest.testFindColour | 1PASS | ||
0.012738854
|
jalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjectsjalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjects | 1PASS | ||
0.012738854
|
jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip | 1PASS | ||
0.012738854
|
jalview.analysis.CrossRefTest.testFindXrefSourcesForSequence_proteinToDnajalview.analysis.CrossRefTest.testFindXrefSourcesForSequence_proteinToDna | 1PASS | ||
0.012738854
|
jalview.analysis.ConservationTest.testVerdictjalview.analysis.ConservationTest.testVerdict | 1PASS | ||
0.012738854
|
jalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_forwardToReversejalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_forwardToReverse | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testMarkMappedRegionjalview.datamodel.AlignedCodonFrameTest.testMarkMappedRegion | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testExpandContext_annotationjalview.analysis.AlignmentUtilsTests.testExpandContext_annotation | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_withTrailingPeptidejalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_withTrailingPeptide | 1PASS | ||
0.012738854
|
jalview.io.SequenceAnnotationReportTest.testAppendFeature_virtualFeaturejalview.io.SequenceAnnotationReportTest.testAppendFeature_virtualFeature | 1PASS | ||
0.012738854
|
jalview.commands.EditCommandTest.testPriorState_singleInsertjalview.commands.EditCommandTest.testPriorState_singleInsert | 1PASS | ||
0.012738854
|
jalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_reverseToForwardjalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_reverseToForward | 1PASS | ||
0.012738854
|
jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentAnnotationTests.testAdjustForAlignmentjalview.datamodel.AlignmentAnnotationTests.testAdjustForAlignment | 1PASS | ||
0.012738854
|
jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip | 1PASS | ||
0.012738854
|
jalview.util.DBRefUtilsTest.testParseToDbRefjalview.util.DBRefUtilsTest.testParseToDbRef | 1PASS | ||
0.012738854
|
jalview.datamodel.HiddenSequencesTest.testIsHiddenjalview.datamodel.HiddenSequencesTest.testIsHidden | 1PASS | ||
0.012738854
|
jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_nonejalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_none | 1PASS | ||
0.012738854
|
jalview.datamodel.HiddenColumnsTest.testGetVisibleStartAndEndIndexjalview.datamodel.HiddenColumnsTest.testGetVisibleStartAndEndIndex | 1PASS | ||
0.012738854
|
jalview.commands.EditCommandTest.testAddEdit_groupInsertGapsjalview.commands.EditCommandTest.testAddEdit_groupInsertGaps | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testCheckValidRangejalview.datamodel.SequenceTest.testCheckValidRange | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceGroupTest.testConstructor_listjalview.datamodel.SequenceGroupTest.testConstructor_list | 1PASS | ||
0.012738854
|
jalview.ext.jmol.JmolCommandsTest.testGetColourBySequenceCommands_hiddenColumnsjalview.ext.jmol.JmolCommandsTest.testGetColourBySequenceCommands_hiddenColumns | 1PASS | ||
0.012738854
|
jalview.datamodel.PAEContactMatrixTest.testMappableContactMatrixjalview.datamodel.PAEContactMatrixTest.testMappableContactMatrix | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testFindPosition_withCursorjalview.datamodel.SequenceTest.testFindPosition_withCursor | 1PASS | ||
0.012738854
|
jalview.gui.DesktopTests.testInternalCopyPastejalview.gui.DesktopTests.testInternalCopyPaste | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testGetVisibleWidthjalview.datamodel.AlignmentTest.testGetVisibleWidth | 1PASS | ||
0.012738854
|
jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip | 1PASS | ||
0.012738854
|
jalview.renderer.ContactGeometryTest.testCoverageofRangejalview.renderer.ContactGeometryTest.testCoverageofRange | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testFindPositionsjalview.datamodel.SequenceTest.testFindPositions | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testMapSequenceGroup_regionjalview.util.MappingUtilsTest.testMapSequenceGroup_region | 1PASS | ||
0.012738854
|
jalview.gui.AlignViewportTest.testSetSelectionGroupjalview.gui.AlignViewportTest.testSetSelectionGroup | 1PASS | ||
0.012738854
|
jalview.commands.EditCommandTest.testPriorState_removeAllGapsjalview.commands.EditCommandTest.testPriorState_removeAllGaps | 1PASS | ||
0.012738854
|
jalview.io.PhylipFileTests.testSequentialDataExtractionjalview.io.PhylipFileTests.testSequentialDataExtraction | 1PASS | ||
0.012738854
|
jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip | 1PASS | ||
0.012738854
|
jalview.io.BackupFilesTest.backupsEnabledSingleFileBackupTestjalview.io.BackupFilesTest.backupsEnabledSingleFileBackupTest | 1PASS | ||
0.012738854
|
jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_userdefjalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_userdef | 1PASS | ||
0.012738854
|
jalview.analysis.AnnotationSorterTest.testSort_timingUnsortedjalview.analysis.AnnotationSorterTest.testSort_timingUnsorted | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testCopyPasteStyleDerivesequence_withcontactMatrixAnnjalview.datamodel.SequenceTest.testCopyPasteStyleDerivesequence_withcontactMatrixAnn | 1PASS | ||
0.012738854
|
jalview.datamodel.DBRefEntryTest.testIsPrimaryCandidatejalview.datamodel.DBRefEntryTest.testIsPrimaryCandidate | 1PASS | ||
0.012738854
|
jalview.io.BackupFilesTest.noBackupsEnabledTestjalview.io.BackupFilesTest.noBackupsEnabledTest | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testEquals_orderDiffersjalview.datamodel.SearchResultsTest.testEquals_orderDiffers | 1PASS | ||
0.012738854
|
jalview.io.PhylipFileTests.testInterleavedDataExtractionjalview.io.PhylipFileTests.testInterleavedDataExtraction | 1PASS | ||
0.012738854
|
jalview.gui.AnnotationLabelsTest.testGetTooltipjalview.gui.AnnotationLabelsTest.testGetTooltip | 1PASS | ||
0.012738854
|
jalview.analysis.CrossRefTest.testFindXrefSequences_indirectDbrefToProteinjalview.analysis.CrossRefTest.testFindXrefSequences_indirectDbrefToProtein | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testIsProteinjalview.datamodel.SequenceTest.testIsProtein | 1PASS | ||
0.012738854
|
jalview.io.PfamFormatInputTest.testPfamFormatNoLimitsjalview.io.PfamFormatInputTest.testPfamFormatNoLimits | 1PASS | ||
0.012738854
|
jalview.datamodel.MatchTest.testEqualsjalview.datamodel.MatchTest.testEquals | 1PASS | ||
0.012738854
|
jalview.schemes.ColourSchemesTest.testRegisterColourSchemejalview.schemes.ColourSchemesTest.testRegisterColourScheme | 1PASS | ||
0.012738854
|
jalview.schemes.ColourSchemePropertyTest.testGetColourNamejalview.schemes.ColourSchemePropertyTest.testGetColourName | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testGetSubsequencejalview.datamodel.SequenceTest.testGetSubsequence | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testBuildSearchResults_withIntronjalview.util.MappingUtilsTest.testBuildSearchResults_withIntron | 1PASS | ||
0.012738854
|
jalview.gui.ScalePanelTest.testBuildPopupMenujalview.gui.ScalePanelTest.testBuildPopupMenu | 1PASS | ||
0.012738854
|
jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testDeleteHiddenSequencejalview.datamodel.AlignmentTest.testDeleteHiddenSequence | 1PASS | ||
0.012738854
|
jalview.datamodel.MappingTest.testCopyConstructorjalview.datamodel.MappingTest.testCopyConstructor | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testAddResultjalview.datamodel.SearchResultsTest.testAddResult | 1PASS | ||
0.012738854
|
jalview.renderer.ResidueColourFinderTest.testGetResidueColour_zappojalview.renderer.ResidueColourFinderTest.testGetResidueColour_zappo | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testAddDBRefjalview.datamodel.SequenceTest.testAddDBRef | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testGapMapjalview.datamodel.SequenceTest.testGapMap | 1PASS | ||
0.012738854
|
jalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_forward_targetgffjalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_forward_targetgff | 1PASS | ||
0.012738854
|
jalview.structures.models.AAStructureBindingModelTest.testBuildColoursMapjalview.structures.models.AAStructureBindingModelTest.testBuildColoursMap | 1PASS | ||
0.012738854
|
jalview.gui.structurechooser.StructureChooserQuerySourceTest.testUpSeqsjalview.gui.structurechooser.StructureChooserQuerySourceTest.testUpSeqs | 1PASS | ||
0.012738854
|
jalview.util.ComparisonTest.testIsNucleotideSequencejalview.util.ComparisonTest.testIsNucleotideSequence | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testCreateDatasetAlignmentjalview.datamodel.AlignmentTest.testCreateDatasetAlignment | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testFindPosition_withCursorAndEditsjalview.datamodel.SequenceTest.testFindPosition_withCursorAndEdits | 1PASS | ||
0.012738854
|
jalview.structure.StructureSelectionManagerTest.testRegisterMappingsjalview.structure.StructureSelectionManagerTest.testRegisterMappings | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testDeleteSequenceBySeqjalview.datamodel.AlignmentTest.testDeleteSequenceBySeq | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testFindMappingsForSequencejalview.util.MappingUtilsTest.testFindMappingsForSequence | 1PASS | ||
0.012738854
|
jalview.datamodel.HiddenColumnsTest.testHideInsertionsForjalview.datamodel.HiddenColumnsTest.testHideInsertionsFor | 1PASS | ||
0.012738854
|
jalview.gui.ScalePanelTest.testSelectColumns_withHiddenjalview.gui.ScalePanelTest.testSelectColumns_withHidden | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testGetSequencesjalview.datamodel.SearchResultsTest.testGetSequences | 1PASS | ||
0.012738854
|
jalview.project.Jalview2xmlTests.testMergeDatasetsforViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforViews | 1PASS | ||
0.012738854
|
jalview.schemes.ResidueColourSchemeTest.testIsApplicableTo_dynamicColourSchemejalview.schemes.ResidueColourSchemeTest.testIsApplicableTo_dynamicColourScheme | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testFindCdsForProteinjalview.analysis.AlignmentUtilsTests.testFindCdsForProtein | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testTransferGeneLocijalview.analysis.AlignmentUtilsTests.testTransferGeneLoci | 1PASS | ||
0.012738854
|
jalview.analysis.CrossRefTest.testSearchDatasetjalview.analysis.CrossRefTest.testSearchDataset | 1PASS | ||
0.012738854
|
jalview.gui.QuitHandlerTest.testSavedAlignmentChangesjalview.gui.QuitHandlerTest.testSavedAlignmentChanges | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testGetPrimaryDBRefs_nucleotidejalview.datamodel.SequenceTest.testGetPrimaryDBRefs_nucleotide | 1PASS | ||
0.012738854
|
jalview.analysis.DnaTest.testReverseSequencejalview.analysis.DnaTest.testReverseSequence | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testHashcodejalview.datamodel.SearchResultsTest.testHashcode | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonIteratorTest.testNextjalview.datamodel.AlignedCodonIteratorTest.testNext | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testGetSequencesByNamejalview.analysis.AlignmentUtilsTests.testGetSequencesByName | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAlignProteinAsDna_incompleteStartCodonjalview.analysis.AlignmentUtilsTests.testAlignProteinAsDna_incompleteStartCodon | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testMapColumnSelection_proteinToDnajalview.util.MappingUtilsTest.testMapColumnSelection_proteinToDna | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentAnnotationTests.testLiftOverjalview.datamodel.AlignmentAnnotationTests.testLiftOver | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testAlignAs_cdnaAsProtein_singleSequencejalview.datamodel.AlignmentTest.testAlignAs_cdnaAsProtein_singleSequence | 1PASS | ||
0.012738854
|
jalview.gui.PaintRefresherTest.testGetAssociatedPanelsjalview.gui.PaintRefresherTest.testGetAssociatedPanels | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_keepIntronGapsOnlyjalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_keepIntronGapsOnly | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testPadGapsjalview.datamodel.AlignmentTest.testPadGaps | 1PASS | ||
0.012738854
|
jalview.renderer.ScaleRendererTest.testCalculateMarksjalview.renderer.ScaleRendererTest.testCalculateMarks | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testInsertGapsAndGapmapsjalview.datamodel.SequenceTest.testInsertGapsAndGapmaps | 1PASS | ||
0.012738854
|
jalview.datamodel.HiddenColumnsTest.testHideColumnsjalview.datamodel.HiddenColumnsTest.testHideColumns | 1PASS | ||
0.012738854
|
jalview.viewmodel.ViewportRangesTest.testPageUpDownWrappedjalview.viewmodel.ViewportRangesTest.testPageUpDownWrapped | 1PASS | ||
0.012738854
|
jalview.gui.SeqPanelTest.testGetEditStatusMessage_lockedEditingjalview.gui.SeqPanelTest.testGetEditStatusMessage_lockedEditing | 1PASS | ||
0.012738854
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_noAnnotationsjalview.gui.SeqPanelTest.testFindMousePosition_wrapped_noAnnotations | 1PASS | ||
0.012738854
|
jalview.commands.EditCommandTest.testLeftRight_Justify_and_preserves_gapsjalview.commands.EditCommandTest.testLeftRight_Justify_and_preserves_gaps | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testFindAlignedSequencejalview.datamodel.AlignedCodonFrameTest.testFindAlignedSequence | 1PASS | ||
0.012738854
|
jalview.datamodel.ColumnSelectionTest.testHideColumns_withSelectionjalview.datamodel.ColumnSelectionTest.testHideColumns_withSelection | 1PASS | ||
0.012738854
|
jalview.io.RNAMLfileTest.testRnamlSeqImportjalview.io.RNAMLfileTest.testRnamlSeqImport | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.012738854
|
jalview.analysis.AlignSeqTest.testIndexEncode_peptidejalview.analysis.AlignSeqTest.testIndexEncode_peptide | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testReplacejalview.datamodel.SequenceTest.testReplace | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testInvolvesSequencejalview.datamodel.SearchResultsTest.testInvolvesSequence | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testCouldReplaceSequencejalview.datamodel.AlignedCodonFrameTest.testCouldReplaceSequence | 1PASS | ||
0.012738854
|
jalview.schemes.ResidueColourSchemeTest.testIsApplicableTojalview.schemes.ResidueColourSchemeTest.testIsApplicableTo | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAddMappedPositions_withStopCodonjalview.analysis.AlignmentUtilsTests.testAddMappedPositions_withStopCodon | 1PASS | ||
0.012738854
|
jalview.analysis.CrossRefTest.testSameSequencejalview.analysis.CrossRefTest.testSameSequence | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.012738854
|
jalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxyjalview.ext.htsjdk.TestHtsContigDb.testGetSequenceProxy | 1PASS | ||
0.012738854
|
jalview.io.BackupFilesTest.backupsEnabledRollMaxTestjalview.io.BackupFilesTest.backupsEnabledRollMaxTest | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAddReferenceAnnotationsjalview.analysis.AlignmentUtilsTests.testAddReferenceAnnotations | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.012738854
|
jalview.gui.AlignViewportTest.testSetGlobalColourSchemejalview.gui.AlignViewportTest.testSetGlobalColourScheme | 1PASS | ||
0.012738854
|
jalview.controller.AlignViewControllerTest.testSelectColumnsWithHighlightjalview.controller.AlignViewControllerTest.testSelectColumnsWithHighlight | 1PASS | ||
0.012738854
|
jalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_forward_querygffjalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_forward_querygff | 1PASS | ||
0.012738854
|
jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip | 1PASS | ||
0.012738854
|
jalview.viewmodel.ViewportRangesTest.testScrollUp_wrappedjalview.viewmodel.ViewportRangesTest.testScrollUp_wrapped | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testFindIndex_withCursorjalview.datamodel.SequenceTest.testFindIndex_withCursor | 1PASS | ||
0.012738854
|
jalview.datamodel.MappingTest.testToStringjalview.datamodel.MappingTest.testToString | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testFindOrCreateForNullCalcIdjalview.datamodel.AlignmentTest.testFindOrCreateForNullCalcId | 1PASS | ||
0.012738854
|
jalview.analysis.CrossRefTest.testFindXrefSequences_noDbrefsjalview.analysis.CrossRefTest.testFindXrefSequences_noDbrefs | 1PASS | ||
0.012738854
|
jalview.viewmodel.ViewportRangesTest.testGetWrappedMaxScrolljalview.viewmodel.ViewportRangesTest.testGetWrappedMaxScroll | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testMarkColumnsjalview.datamodel.SearchResultsTest.testMarkColumns | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testGetMappedRegionjalview.datamodel.AlignedCodonFrameTest.testGetMappedRegion | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testInsertCharAtjalview.datamodel.SequenceTest.testInsertCharAt | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testMapSequenceGroup_sharedDatasetjalview.util.MappingUtilsTest.testMapSequenceGroup_sharedDataset | 1PASS | ||
0.012738854
|
jalview.util.UrlLinkTest.testCreateLinksFromSequencejalview.util.UrlLinkTest.testCreateLinksFromSequence | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testHaveCrossRefjalview.analysis.AlignmentUtilsTests.testHaveCrossRef | 1PASS | ||
0.012738854
|
jalview.util.ComparisonTest.testIsNucleotide_sequencesjalview.util.ComparisonTest.testIsNucleotide_sequences | 1PASS | ||
0.012738854
|
jalview.io.StockholmFileTest.stockholmFileRnaSSSpaceCharsjalview.io.StockholmFileTest.stockholmFileRnaSSSpaceChars | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testGapBitsetjalview.datamodel.SequenceTest.testGapBitset | 1PASS | ||
0.012738854
|
jalview.util.DBRefUtilsTest.testParseToDbRef_PDBjalview.util.DBRefUtilsTest.testParseToDbRef_PDB | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testMapCdnaToProtein_forSubsequencejalview.analysis.AlignmentUtilsTests.testMapCdnaToProtein_forSubsequence | 1PASS | ||
0.012738854
|
jalview.viewmodel.OverviewDimensionsHideHiddenTest.testConstructorjalview.viewmodel.OverviewDimensionsHideHiddenTest.testConstructor | 1PASS | ||
0.012738854
|
jalview.project.Jalview2xmlTests.testMergeDatasetsforManyViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforManyViews | 1PASS | ||
0.012738854
|
jalview.analysis.ConservationTest.testCalculate_noThresholdjalview.analysis.ConservationTest.testCalculate_noThreshold | 1PASS | ||
0.012738854
|
jalview.viewmodel.ViewportRangesTest.testSetViewportLocationjalview.viewmodel.ViewportRangesTest.testSetViewportLocation | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons_forSubSequencesjalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons_forSubSequences | 1PASS | ||
0.012738854
|
jalview.renderer.seqfeatures.FeatureRendererTest.testGetColourjalview.renderer.seqfeatures.FeatureRendererTest.testGetColour | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testHasCrossRefjalview.analysis.AlignmentUtilsTests.testHasCrossRef | 1PASS | ||
0.012738854
|
jalview.viewmodel.ViewportRangesTest.testGetWrappedScrollPositionjalview.viewmodel.ViewportRangesTest.testGetWrappedScrollPosition | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testMapSequenceGroup_columnsjalview.util.MappingUtilsTest.testMapSequenceGroup_columns | 1PASS | ||
0.012738854
|
mc_view.PDBfileTest.testIsRnamc_view.PDBfileTest.testIsRna | 1PASS | ||
0.012738854
|
jalview.datamodel.HiddenSequencesTest.testAdjustHeightSequenceAddedjalview.datamodel.HiddenSequencesTest.testAdjustHeightSequenceAdded | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAlignAsSameSequencesMultipleSubSeqjalview.analysis.AlignmentUtilsTests.testAlignAsSameSequencesMultipleSubSeq | 1PASS | ||
0.012738854
|
jalview.gui.SeqPanelTest.testGetEditStatusMessagejalview.gui.SeqPanelTest.testGetEditStatusMessage | 1PASS | ||
0.012738854
|
jalview.io.PfamFormatInputTest.testPfamFormatValidLimitsjalview.io.PfamFormatInputTest.testPfamFormatValidLimits | 1PASS | ||
0.012738854
|
jalview.commands.EditCommandTest.testPriorState_singleInsertWithOffsetjalview.commands.EditCommandTest.testPriorState_singleInsertWithOffset | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testMapProteinAlignmentToCdna_prioritiseXrefsjalview.analysis.AlignmentUtilsTests.testMapProteinAlignmentToCdna_prioritiseXrefs | 1PASS | ||
0.012738854
|
jalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_forwardToForwardjalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_forwardToForward | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testAlignAs_cdnaAsProteinjalview.datamodel.AlignmentTest.testAlignAs_cdnaAsProtein | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testGetCoveringMappingjalview.datamodel.AlignedCodonFrameTest.testGetCoveringMapping | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.012738854
|
jalview.io.NewickFileTests.testTreeIOjalview.io.NewickFileTests.testTreeIO | 1PASS | ||
0.012738854
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_annotationsjalview.gui.SeqPanelTest.testFindMousePosition_wrapped_annotations | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAddMappedPositionsjalview.analysis.AlignmentUtilsTests.testAddMappedPositions | 1PASS | ||
0.012738854
|
jalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimportjalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimport | 1PASS | ||
0.012738854
|
jalview.commands.EditCommandTest.testAddEdit_multipleDeleteGapjalview.commands.EditCommandTest.testAddEdit_multipleDeleteGap | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_withMapping_noIntronsjalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_withMapping_noIntrons | 1PASS | ||
0.012738854
|
jalview.io.StockholmFileTest.dbrefOutputjalview.io.StockholmFileTest.dbrefOutput | 1PASS | ||
0.012738854
|
jalview.viewmodel.OverviewDimensionsShowHiddenTest.testConstructorjalview.viewmodel.OverviewDimensionsShowHiddenTest.testConstructor | 1PASS | ||
0.012738854
|
jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testFindPositionMapjalview.datamodel.SequenceTest.testFindPositionMap | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testEqualsjalview.datamodel.SearchResultsTest.testEquals | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testLocateVisibleStartofSequencejalview.datamodel.SequenceTest.testLocateVisibleStartofSequence | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testAlignAs_dnaAsDnajalview.datamodel.AlignmentTest.testAlignAs_dnaAsDna | 1PASS | ||
0.012738854
|
jalview.io.StockholmFileTest.descriptionLineOutputjalview.io.StockholmFileTest.descriptionLineOutput | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testMapEditCommandjalview.util.MappingUtilsTest.testMapEditCommand | 1PASS | ||
0.012738854
|
jalview.io.AnnotationFileIOTest.testAnnotateAlignmentViewjalview.io.AnnotationFileIOTest.testAnnotateAlignmentView | 1PASS | ||
0.012738854
|
jalview.structure.StructureSelectionManagerTest.testRegisterMappingjalview.structure.StructureSelectionManagerTest.testRegisterMapping | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.012738854
|
jalview.gui.ScalePanelTest.testPreventNegativeStartColumnjalview.gui.ScalePanelTest.testPreventNegativeStartColumn | 1PASS | ||
0.012738854
|
jalview.schemes.ClustalxColourSchemeTest.testFindColour_ignoreGapsjalview.schemes.ClustalxColourSchemeTest.testFindColour_ignoreGaps | 1PASS | ||
0.012738854
|
jalview.analysis.ConservationTest.testCountConservationAndGapsjalview.analysis.ConservationTest.testCountConservationAndGaps | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testShowOrHideSequenceAnnotationsjalview.analysis.AlignmentUtilsTests.testShowOrHideSequenceAnnotations | 1PASS | ||
0.012738854
|
jalview.commands.EditCommandTest.testPriorState_multipleInsertsjalview.commands.EditCommandTest.testPriorState_multipleInserts | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testGetPrimaryDBRefs_peptidejalview.datamodel.SequenceTest.testGetPrimaryDBRefs_peptide | 1PASS | ||
0.012738854
|
jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip | 1PASS | ||
0.012738854
|
jalview.gui.ColourMenuHelperTest.testAddMenuItems_forAlignFramejalview.gui.ColourMenuHelperTest.testAddMenuItems_forAlignFrame | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testGetMappedCodonsjalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons | 1PASS | ||
0.012738854
|
jalview.analysis.AlignSeqTest.testGlobalAlignmentjalview.analysis.AlignSeqTest.testGlobalAlignment | 1PASS | ||
0.012738854
|
jalview.analysis.AnnotationSorterTest.testSort_timingPresortedjalview.analysis.AnnotationSorterTest.testSort_timingPresorted | 1PASS | ||
0.012738854
|
jalview.commands.EditCommandTest.testPriorState_removeGappedColsjalview.commands.EditCommandTest.testPriorState_removeGappedCols | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testIsRealisableWithjalview.datamodel.AlignedCodonFrameTest.testIsRealisableWith | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_withMapping_withIntronsjalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_withMapping_withIntrons | 1PASS | ||
0.012738854
|
jalview.io.ClustalFileTest.testParse_noNumberingjalview.io.ClustalFileTest.testParse_noNumbering | 1PASS | ||
0.012738854
|
jalview.gui.AlignViewportTest.testUpdateConservation_qualityOnlyjalview.gui.AlignViewportTest.testUpdateConservation_qualityOnly | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testExpandContextjalview.analysis.AlignmentUtilsTests.testExpandContext | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceGroupTest.testContainsjalview.datamodel.SequenceGroupTest.testContains | 1PASS | ||
0.012738854
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scaleAbovejalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scaleAbove | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testToStringjalview.datamodel.SearchResultsTest.testToString | 1PASS | ||
0.012738854
|
jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructurejalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testVerifyAlignmentDatasetRefsjalview.datamodel.AlignmentTest.testVerifyAlignmentDatasetRefs | 1PASS | ||
0.012738854
|
jalview.gui.AlignViewportTest.testSetGetHasSearchResultsjalview.gui.AlignViewportTest.testSetGetHasSearchResults | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testDeleteSequenceByIndexjalview.datamodel.AlignmentTest.testDeleteSequenceByIndex | 1PASS | ||
0.012738854
|
jalview.schemes.ColourSchemesTest.testGetColourSchemejalview.schemes.ColourSchemesTest.testGetColourScheme | 1PASS | ||
0.012738854
|
jalview.datamodel.ColumnSelectionTest.testHideSelectedColumnsjalview.datamodel.ColumnSelectionTest.testHideSelectedColumns | 1PASS | ||
0.012738854
|
jalview.gui.ColourMenuHelperTest.testAddMenuItems_peptidejalview.gui.ColourMenuHelperTest.testAddMenuItems_peptide | 1PASS | ||
0.012738854
|
jalview.gui.AlignViewportTest.testGetSelectionAsNewSequences_withContactMatricesjalview.gui.AlignViewportTest.testGetSelectionAsNewSequences_withContactMatrices | 1PASS | ||
0.012738854
|
jalview.datamodel.ColumnSelectionTest.testInvertColumnSelectionjalview.datamodel.ColumnSelectionTest.testInvertColumnSelection | 1PASS | ||
0.012738854
|
jalview.viewmodel.ViewportRangesTest.testScrollToWrappedVisiblejalview.viewmodel.ViewportRangesTest.testScrollToWrappedVisible | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonIteratorTest.testNext_unmappedPeptidejalview.datamodel.AlignedCodonIteratorTest.testNext_unmappedPeptide | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAlignProteinAsDnajalview.analysis.AlignmentUtilsTests.testAlignProteinAsDna | 1PASS | ||
0.012738854
|
jalview.analysis.CrossRefTest.testFindXrefSequences_indirectDbrefToNucleotidejalview.analysis.CrossRefTest.testFindXrefSequences_indirectDbrefToNucleotide | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testFindPositionjalview.datamodel.SequenceTest.testFindPosition | 1PASS | ||
0.012738854
|
jalview.io.NewickFileTests.testTreeIOjalview.io.NewickFileTests.testTreeIO | 1PASS | ||
0.012738854
|
jalview.gui.AnnotationChooserTest.testSelectType_showForAlljalview.gui.AnnotationChooserTest.testSelectType_showForAll | 1PASS | ||
0.012738854
|
jalview.renderer.ResidueColourFinderTest.testGetResidueColour_userdefjalview.renderer.ResidueColourFinderTest.testGetResidueColour_userdef | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAddReferenceContactMapjalview.analysis.AlignmentUtilsTests.testAddReferenceContactMap | 1PASS | ||
0.012738854
|
jalview.project.Jalview2xmlTests.testMatrixToFloatsAndBackjalview.project.Jalview2xmlTests.testMatrixToFloatsAndBack | 1PASS | ||
0.012738854
|
jalview.renderer.ContactGeometryTest.testContactGeometryjalview.renderer.ContactGeometryTest.testContactGeometry | 1PASS | ||
0.012738854
|
jalview.renderer.ResidueShaderTest.testFindColour_gapColourjalview.renderer.ResidueShaderTest.testFindColour_gapColour | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testEquals_distinctSequencesjalview.datamodel.SearchResultsTest.testEquals_distinctSequences | 1PASS | ||
0.012738854
|
jalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_reverse_targetgffjalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_reverse_targetgff | 1PASS | ||
0.012738854
|
jalview.gui.QuitHandlerTest.testInstantQuitjalview.gui.QuitHandlerTest.testInstantQuit | 1PASS | ||
0.012738854
|
jalview.gui.ColourMenuHelperTest.testAddMenuItems_simpleOnlyjalview.gui.ColourMenuHelperTest.testAddMenuItems_simpleOnly | 1PASS | ||
0.012738854
|
jalview.commands.EditCommandTest.testAddEdit_multipleInsertGapjalview.commands.EditCommandTest.testAddEdit_multipleInsertGap | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonIteratorTest.testNext_withOffsetjalview.datamodel.AlignedCodonIteratorTest.testNext_withOffset | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testFindIndexjalview.datamodel.SequenceTest.testFindIndex | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.012738854
|
jalview.gui.SeqPanelTest.testSetStatusReturnsNearestResiduePositionjalview.gui.SeqPanelTest.testSetStatusReturnsNearestResiduePosition | 1PASS | ||
0.012738854
|
jalview.analysis.FinderTest.testFindAll_sequenceIdsjalview.analysis.FinderTest.testFindAll_sequenceIds | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.012738854
|
jalview.structure.StructureMappingTest.testEqualsjalview.structure.StructureMappingTest.testEquals | 1PASS | ||
0.012738854
|
jalview.io.BackupFilesTest.backupsEnabledNoRollMaxTestjalview.io.BackupFilesTest.backupsEnabledNoRollMaxTest | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons_dnaVariantsjalview.datamodel.AlignedCodonFrameTest.testGetMappedCodons_dnaVariants | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonIteratorTest.testNext_incompleteCodonjalview.datamodel.AlignedCodonIteratorTest.testNext_incompleteCodon | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testMatchAdjacentjalview.datamodel.SearchResultsTest.testMatchAdjacent | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testAlignAs_proteinAsCdnajalview.datamodel.AlignmentTest.testAlignAs_proteinAsCdna | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testAssertDatasetIsNormalisedjalview.datamodel.AlignmentTest.testAssertDatasetIsNormalised | 1PASS | ||
0.012738854
|
jalview.analysis.ConservationTest.testCalculate_thresholdjalview.analysis.ConservationTest.testCalculate_threshold | 1PASS | ||
0.012738854
|
jalview.schemes.ColourSchemePropertyTest.testGetColourSchemejalview.schemes.ColourSchemePropertyTest.testGetColourScheme | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testIsProteinWithXorNAmbiguityCodesjalview.datamodel.SequenceTest.testIsProteinWithXorNAmbiguityCodes | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testMatchConstructorjalview.datamodel.SearchResultsTest.testMatchConstructor | 1PASS | ||
0.012738854
|
jalview.io.BackupFilesTest.backupsEnabledReverseRollMaxTestjalview.io.BackupFilesTest.backupsEnabledReverseRollMaxTest | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testGetCharAtjalview.datamodel.SequenceTest.testGetCharAt | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.012738854
|
jalview.gui.AlignViewportTest.testDeregisterMapping_withReferencejalview.gui.AlignViewportTest.testDeregisterMapping_withReference | 1PASS | ||
0.012738854
|
jalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_zappojalview.renderer.OverviewResColourFinderTest.testGetResidueBoxColour_zappo | 1PASS | ||
0.012738854
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequencejalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequence | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testDeriveSequence_noDatasetGappedjalview.datamodel.SequenceTest.testDeriveSequence_noDatasetGapped | 1PASS | ||
0.012738854
|
jalview.analysis.TestAlignSeq.testPrintAlignmentjalview.analysis.TestAlignSeq.testPrintAlignment | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testEqualsjalview.datamodel.AlignmentTest.testEquals | 1PASS | ||
0.012738854
|
jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructurejalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure | 1PASS | ||
0.012738854
|
jalview.gui.SeqPanelTest.testAmbiguousAminoAcidGetsStatusMessagejalview.gui.SeqPanelTest.testAmbiguousAminoAcidGetsStatusMessage | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testAddMapjalview.datamodel.AlignedCodonFrameTest.testAddMap | 1PASS | ||
0.012738854
|
jalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_reverse_querygffjalview.io.gff.ExonerateHelperTest.testProcessGffSimilarity_protein2dna_reverse_querygff | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testCopyConstructorjalview.datamodel.AlignmentTest.testCopyConstructor | 1PASS | ||
0.012738854
|
jalview.analysis.AnnotationSorterTest.testSort_timingSemisortedjalview.analysis.AnnotationSorterTest.testSort_timingSemisorted | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testAppendjalview.datamodel.AlignmentTest.testAppend | 1PASS | ||
0.012738854
|
jalview.commands.EditCommandTest.testPriorState_singleDeletejalview.commands.EditCommandTest.testPriorState_singleDelete | 1PASS | ||
0.012738854
|
jalview.datamodel.MappedFeaturesTest.testFindProteinVariantsjalview.datamodel.MappedFeaturesTest.testFindProteinVariants | 1PASS | ||
0.012738854
|
jalview.analysis.DnaTest.testReverseCdnajalview.analysis.DnaTest.testReverseCdna | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testGetCoveringCodonMappingjalview.datamodel.AlignedCodonFrameTest.testGetCoveringCodonMapping | 1PASS | ||
0.012738854
|
jalview.gui.AlignViewportTest.testShowOrDontShowOccupancyjalview.gui.AlignViewportTest.testShowOrDontShowOccupancy | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceFeatureTest.testGetDetailsReportjalview.datamodel.SequenceFeatureTest.testGetDetailsReport | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testMapColumnSelection_hiddenColumnsjalview.util.MappingUtilsTest.testMapColumnSelection_hiddenColumns | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testSetNamejalview.datamodel.SequenceTest.testSetName | 1PASS | ||
0.012738854
|
jalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimportjalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimport | 1PASS | ||
0.012738854
|
jalview.analysis.AlignSeqTest.testIndexEncode_nucleotidejalview.analysis.AlignSeqTest.testIndexEncode_nucleotide | 1PASS | ||
0.012738854
|
jalview.datamodel.PAEContactMatrixTest.testSeqAssociatedPAEMatrixjalview.datamodel.PAEContactMatrixTest.testSeqAssociatedPAEMatrix | 1PASS | ||
0.012738854
|
jalview.analysis.AAFrequencyTest.testCalculate_withProfilejalview.analysis.AAFrequencyTest.testCalculate_withProfile | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.012738854
|
jalview.io.StockholmFileTest.stockholmFileRnaSSAlphaCharsjalview.io.StockholmFileTest.stockholmFileRnaSSAlphaChars | 1PASS | ||
0.012738854
|
jalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGapsjalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGaps | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceGroupTest.testCopyConstructorjalview.datamodel.SequenceGroupTest.testCopyConstructor | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testCreateDataset_updateDbrefMappingsjalview.datamodel.AlignmentTest.testCreateDataset_updateDbrefMappings | 1PASS | ||
0.012738854
|
jalview.datamodel.MatchTest.testToStringjalview.datamodel.MatchTest.testToString | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testMapColumnSelection_nulljalview.util.MappingUtilsTest.testMapColumnSelection_null | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_mappedProteinProteinjalview.analysis.AlignmentUtilsTests.testAlignSequenceAs_mappedProteinProtein | 1PASS | ||
0.012738854
|
jalview.io.WindowsFileLoadAndSaveTest.loadAndSaveAlignmentjalview.io.WindowsFileLoadAndSaveTest.loadAndSaveAlignment | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.012738854
|
jalview.gui.AlignViewportTest.testDeregisterMapping_withNoReferencejalview.gui.AlignViewportTest.testDeregisterMapping_withNoReference | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testBuildSearchResultsjalview.util.MappingUtilsTest.testBuildSearchResults | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testFindMappingsForSequenceAndOthersjalview.util.MappingUtilsTest.testFindMappingsForSequenceAndOthers | 1PASS | ||
0.012738854
|
jalview.datamodel.SearchResultsTest.testAppendResultjalview.datamodel.SearchResultsTest.testAppendResult | 1PASS | ||
0.012738854
|
jalview.io.StockholmFileTest.pfamFileDataExtractionjalview.io.StockholmFileTest.pfamFileDataExtraction | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testGetSequencejalview.datamodel.SequenceTest.testGetSequence | 1PASS | ||
0.012738854
|
jalview.gui.SeqPanelTest.testFindColumn_and_FindAlignmentColumn_wrappedjalview.gui.SeqPanelTest.testFindColumn_and_FindAlignmentColumn_wrapped | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAlignAs_alternateTranscriptsUngappedjalview.analysis.AlignmentUtilsTests.testAlignAs_alternateTranscriptsUngapped | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentAnnotationTests.testCopyConstructorjalview.datamodel.AlignmentAnnotationTests.testCopyConstructor | 1PASS | ||
0.012738854
|
jalview.schemes.ResidueColourSchemeTest.testGetNamejalview.schemes.ResidueColourSchemeTest.testGetName | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testDeleteCharsjalview.datamodel.SequenceTest.testDeleteChars | 1PASS | ||
0.012738854
|
jalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructurejalview.ws.dbsources.EBIAlphaFoldTest.checkImportPAEToStructure | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testMapSequenceGroup_sequencesjalview.util.MappingUtilsTest.testMapSequenceGroup_sequences | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testGetWidthjalview.datamodel.AlignmentTest.testGetWidth | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignmentTest.testFindGroupjalview.datamodel.AlignmentTest.testFindGroup | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonIteratorTest.testAnotherjalview.datamodel.AlignedCodonIteratorTest.testAnother | 1PASS | ||
0.012738854
|
jalview.util.MappingUtilsTest.testMapColumnSelection_dnaToProteinjalview.util.MappingUtilsTest.testMapColumnSelection_dnaToProtein | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceTest.testDeriveSequence_noDatasetUngappedjalview.datamodel.SequenceTest.testDeriveSequence_noDatasetUngapped | 1PASS | ||
0.012738854
|
jalview.analysis.AlignmentUtilsTests.testAlignAsSameSequencesjalview.analysis.AlignmentUtilsTests.testAlignAsSameSequences | 1PASS | ||
0.012738854
|
jalview.datamodel.SequenceFeatureTest.testGetDetailsReport_virtualFeaturejalview.datamodel.SequenceFeatureTest.testGetDetailsReport_virtualFeature | 1PASS | ||
0.012738854
|
jalview.datamodel.AlignedCodonFrameTest.testGetMappedRegion_eitherWayjalview.datamodel.AlignedCodonFrameTest.testGetMappedRegion_eitherWay | 1PASS | ||
0.012738854
|
jalview.analysis.AAFrequencyTest.testCompleteConsensus_includeGaps_showLogojalview.analysis.AAFrequencyTest.testCompleteConsensus_includeGaps_showLogo | 1PASS | ||
0.012738854
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.012738854
|
jalview.analysis.AverageDistanceEngineTest.testUPGMAEnginejalview.analysis.AverageDistanceEngineTest.testUPGMAEngine | 1PASS | ||
0.012738854
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jalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimportjalview.ws.dbsources.EBIAlphaFoldTest.checkPAEimport | 1PASS | ||
0.012738854
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jalview.datamodel.AlignmentTest.testAddSequencePreserveDatasetIntegrityjalview.datamodel.AlignmentTest.testAddSequencePreserveDatasetIntegrity | 1PASS | ||
0.012738854
|
jalview.renderer.ResidueColourFinderTest.testGetResidueColour_nonejalview.renderer.ResidueColourFinderTest.testGetResidueColour_none | 1PASS | ||
0.012738854
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jalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_splicedjalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_spliced | 1PASS | ||
0.012738854
|
jalview.io.FormatAdapterTest.testRoundTripjalview.io.FormatAdapterTest.testRoundTrip | 1PASS | ||
0.012738854
|
jalview.gui.AlignViewportTest.testGetConsensusSeqjalview.gui.AlignViewportTest.testGetConsensusSeq | 1PASS | ||
0.012738854
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jalview.gui.QuitHandlerTest.testUnsavedChangesjalview.gui.QuitHandlerTest.testUnsavedChanges | 1PASS | ||
0.012738854
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jalview.analysis.AlignmentUtilsTests.testIsMappablejalview.analysis.AlignmentUtilsTests.testIsMappable | 1PASS | ||
0.012738854
|
jalview.io.AnnotationExporterTest.testAnnotationExportAsCSVjalview.io.AnnotationExporterTest.testAnnotationExportAsCSV | 1PASS | ||
0.012738854
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jalview.gui.QuitHandlerTest.testNoGUIUnsavedChangesjalview.gui.QuitHandlerTest.testNoGUIUnsavedChanges | 1PASS | ||
0.012738854
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jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.012738854
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jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.012738854
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jalview.renderer.ResidueShaderTest.testApplyConservationjalview.renderer.ResidueShaderTest.testApplyConservation | 1PASS | ||
0.012738854
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jalview.io.NewickFileTests.testTreeIOjalview.io.NewickFileTests.testTreeIO | 1PASS |
1 | /* | ||||||
2 | * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) | ||||||
3 | * Copyright (C) $$Year-Rel$$ The Jalview Authors | ||||||
4 | * | ||||||
5 | * This file is part of Jalview. | ||||||
6 | * | ||||||
7 | * Jalview is free software: you can redistribute it and/or | ||||||
8 | * modify it under the terms of the GNU General Public License | ||||||
9 | * as published by the Free Software Foundation, either version 3 | ||||||
10 | * of the License, or (at your option) any later version. | ||||||
11 | * | ||||||
12 | * Jalview is distributed in the hope that it will be useful, but | ||||||
13 | * WITHOUT ANY WARRANTY; without even the implied warranty | ||||||
14 | * of MERCHANTABILITY or FITNESS FOR A PARTICULAR | ||||||
15 | * PURPOSE. See the GNU General Public License for more details. | ||||||
16 | * | ||||||
17 | * You should have received a copy of the GNU General Public License | ||||||
18 | * along with Jalview. If not, see <http://www.gnu.org/licenses/>. | ||||||
19 | * The Jalview Authors are detailed in the 'AUTHORS' file. | ||||||
20 | */ | ||||||
21 | package jalview.datamodel.features; | ||||||
22 | |||||||
23 | import java.util.ArrayList; | ||||||
24 | import java.util.Collections; | ||||||
25 | import java.util.HashSet; | ||||||
26 | import java.util.List; | ||||||
27 | import java.util.Map; | ||||||
28 | import java.util.Map.Entry; | ||||||
29 | import java.util.Set; | ||||||
30 | import java.util.TreeMap; | ||||||
31 | |||||||
32 | import intervalstore.api.IntervalI; | ||||||
33 | import jalview.datamodel.SequenceFeature; | ||||||
34 | import jalview.io.gff.SequenceOntologyFactory; | ||||||
35 | import jalview.io.gff.SequenceOntologyI; | ||||||
36 | |||||||
37 | /** | ||||||
38 | * A class that stores sequence features in a way that supports efficient | ||||||
39 | * querying by type and location (overlap). Intended for (but not limited to) | ||||||
40 | * storage of features for one sequence. | ||||||
41 | * | ||||||
42 | * @author gmcarstairs | ||||||
43 | * | ||||||
44 | */ | ||||||
|
|||||||
45 | public class SequenceFeatures implements SequenceFeaturesI | ||||||
46 | { | ||||||
47 | /* | ||||||
48 | * map from feature type to structured store of features for that type | ||||||
49 | * null types are permitted (but not a good idea!) | ||||||
50 | */ | ||||||
51 | private Map<String, FeatureStore> featureStore; | ||||||
52 | |||||||
53 | /** | ||||||
54 | * Constructor | ||||||
55 | */ | ||||||
|
|||||||
56 | 33331 | public SequenceFeatures()... | |||||
57 | { | ||||||
58 | /* | ||||||
59 | * use a TreeMap so that features are returned in alphabetical order of type | ||||||
60 | * ? wrap as a synchronized map for add and delete operations | ||||||
61 | */ | ||||||
62 | // featureStore = Collections | ||||||
63 | // .synchronizedSortedMap(new TreeMap<String, FeatureStore>()); | ||||||
64 | 33331 | featureStore = new TreeMap<>(); | |||||
65 | } | ||||||
66 | |||||||
67 | /** | ||||||
68 | * Constructor given a list of features | ||||||
69 | */ | ||||||
|
|||||||
70 | 46 | public SequenceFeatures(List<SequenceFeature> features)... | |||||
71 | { | ||||||
72 | 46 | this(); | |||||
73 | 46 | if (features != null) | |||||
74 | { | ||||||
75 | 43 | for (SequenceFeature feature : features) | |||||
76 | { | ||||||
77 | 423 | add(feature); | |||||
78 | } | ||||||
79 | } | ||||||
80 | } | ||||||
81 | |||||||
82 | /** | ||||||
83 | * {@inheritDoc} | ||||||
84 | */ | ||||||
|
|||||||
85 | 212376 | @Override... | |||||
86 | public boolean add(SequenceFeature sf) | ||||||
87 | { | ||||||
88 | 212376 | String type = sf.getType(); | |||||
89 | 212376 | if (type == null) | |||||
90 | { | ||||||
91 | 2 | jalview.bin.Console | |||||
92 | .errPrintln("Feature type may not be null: " + sf.toString()); | ||||||
93 | 2 | return false; | |||||
94 | } | ||||||
95 | |||||||
96 | 212374 | if (featureStore.get(type) == null) | |||||
97 | { | ||||||
98 | 2566 | featureStore.put(type, new FeatureStore()); | |||||
99 | } | ||||||
100 | 212374 | return featureStore.get(type).addFeature(sf); | |||||
101 | } | ||||||
102 | |||||||
103 | /** | ||||||
104 | * {@inheritDoc} | ||||||
105 | */ | ||||||
|
|||||||
106 | 222890 | @Override... | |||||
107 | public List<SequenceFeature> findFeatures(int from, int to, | ||||||
108 | String... type) | ||||||
109 | { | ||||||
110 | 222892 | List<SequenceFeature> result = new ArrayList<>(); | |||||
111 | |||||||
112 | 222912 | for (FeatureStore featureSet : varargToTypes(type)) | |||||
113 | { | ||||||
114 | 92419 | result.addAll(featureSet.findOverlappingFeatures(from, to)); | |||||
115 | } | ||||||
116 | |||||||
117 | 222817 | return result; | |||||
118 | } | ||||||
119 | |||||||
120 | /** | ||||||
121 | * {@inheritDoc} | ||||||
122 | */ | ||||||
|
|||||||
123 | 5749 | @Override... | |||||
124 | public List<SequenceFeature> getAllFeatures(String... type) | ||||||
125 | { | ||||||
126 | 5749 | List<SequenceFeature> result = new ArrayList<>(); | |||||
127 | |||||||
128 | 5749 | result.addAll(getPositionalFeatures(type)); | |||||
129 | |||||||
130 | 5749 | result.addAll(getNonPositionalFeatures()); | |||||
131 | |||||||
132 | 5749 | return result; | |||||
133 | } | ||||||
134 | |||||||
135 | /** | ||||||
136 | * {@inheritDoc} | ||||||
137 | */ | ||||||
|
|||||||
138 | 48 | @Override... | |||||
139 | public List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm) | ||||||
140 | { | ||||||
141 | 48 | if (ontologyTerm == null || ontologyTerm.length == 0) | |||||
142 | { | ||||||
143 | 3 | return new ArrayList<>(); | |||||
144 | } | ||||||
145 | |||||||
146 | 45 | Set<String> featureTypes = getFeatureTypes(ontologyTerm); | |||||
147 | 45 | if (featureTypes.isEmpty()) | |||||
148 | { | ||||||
149 | /* | ||||||
150 | * no features of the specified type or any sub-type | ||||||
151 | */ | ||||||
152 | 18 | return new ArrayList<>(); | |||||
153 | } | ||||||
154 | |||||||
155 | 27 | return getAllFeatures( | |||||
156 | featureTypes.toArray(new String[featureTypes.size()])); | ||||||
157 | } | ||||||
158 | |||||||
159 | /** | ||||||
160 | * {@inheritDoc} | ||||||
161 | */ | ||||||
|
|||||||
162 | 35 | @Override... | |||||
163 | public int getFeatureCount(boolean positional, String... type) | ||||||
164 | { | ||||||
165 | 35 | int result = 0; | |||||
166 | |||||||
167 | 35 | for (FeatureStore featureSet : varargToTypes(type)) | |||||
168 | { | ||||||
169 | 55 | result += featureSet.getFeatureCount(positional); | |||||
170 | } | ||||||
171 | 35 | return result; | |||||
172 | } | ||||||
173 | |||||||
174 | /** | ||||||
175 | * {@inheritDoc} | ||||||
176 | */ | ||||||
|
|||||||
177 | 22 | @Override... | |||||
178 | public int getTotalFeatureLength(String... type) | ||||||
179 | { | ||||||
180 | 22 | int result = 0; | |||||
181 | |||||||
182 | 22 | for (FeatureStore featureSet : varargToTypes(type)) | |||||
183 | { | ||||||
184 | 33 | result += featureSet.getTotalFeatureLength(); | |||||
185 | } | ||||||
186 | 22 | return result; | |||||
187 | } | ||||||
188 | |||||||
189 | /** | ||||||
190 | * {@inheritDoc} | ||||||
191 | */ | ||||||
|
|||||||
192 | 5899 | @Override... | |||||
193 | public List<SequenceFeature> getPositionalFeatures(String... type) | ||||||
194 | { | ||||||
195 | 5899 | List<SequenceFeature> result = new ArrayList<>(); | |||||
196 | |||||||
197 | 5899 | for (FeatureStore featureSet : varargToTypes(type)) | |||||
198 | { | ||||||
199 | 3732 | result.addAll(featureSet.getPositionalFeatures()); | |||||
200 | } | ||||||
201 | 5899 | return result; | |||||
202 | } | ||||||
203 | |||||||
204 | /** | ||||||
205 | * A convenience method that converts a vararg for feature types to an | ||||||
206 | * Iterable over matched feature sets. If no types are specified, all feature | ||||||
207 | * sets are returned. If one or more types are specified, feature sets for | ||||||
208 | * those types are returned, preserving the order of the types. | ||||||
209 | * | ||||||
210 | * @param type | ||||||
211 | * @return | ||||||
212 | */ | ||||||
|
|||||||
213 | 236175 | protected Iterable<FeatureStore> varargToTypes(String... type)... | |||||
214 | { | ||||||
215 | 236163 | if (type == null || type.length == 0) | |||||
216 | { | ||||||
217 | /* | ||||||
218 | * no vararg parameter supplied - return all | ||||||
219 | */ | ||||||
220 | 12714 | return featureStore.values(); | |||||
221 | } | ||||||
222 | |||||||
223 | 223449 | List<FeatureStore> types = new ArrayList<>(); | |||||
224 | 223446 | for (String theType : type) | |||||
225 | { | ||||||
226 | 223984 | if (theType != null && featureStore.containsKey(theType)) | |||||
227 | { | ||||||
228 | 92549 | types.add(featureStore.get(theType)); | |||||
229 | } | ||||||
230 | } | ||||||
231 | 223385 | return types; | |||||
232 | } | ||||||
233 | |||||||
234 | /** | ||||||
235 | * {@inheritDoc} | ||||||
236 | */ | ||||||
|
|||||||
237 | 25 | @Override... | |||||
238 | public List<SequenceFeature> getContactFeatures(String... type) | ||||||
239 | { | ||||||
240 | 25 | List<SequenceFeature> result = new ArrayList<>(); | |||||
241 | |||||||
242 | 25 | for (FeatureStore featureSet : varargToTypes(type)) | |||||
243 | { | ||||||
244 | 19 | result.addAll(featureSet.getContactFeatures()); | |||||
245 | } | ||||||
246 | 25 | return result; | |||||
247 | } | ||||||
248 | |||||||
249 | /** | ||||||
250 | * {@inheritDoc} | ||||||
251 | */ | ||||||
|
|||||||
252 | 5815 | @Override... | |||||
253 | public List<SequenceFeature> getNonPositionalFeatures(String... type) | ||||||
254 | { | ||||||
255 | 5815 | List<SequenceFeature> result = new ArrayList<>(); | |||||
256 | |||||||
257 | 5815 | for (FeatureStore featureSet : varargToTypes(type)) | |||||
258 | { | ||||||
259 | 3702 | result.addAll(featureSet.getNonPositionalFeatures()); | |||||
260 | } | ||||||
261 | 5815 | return result; | |||||
262 | } | ||||||
263 | |||||||
264 | /** | ||||||
265 | * {@inheritDoc} | ||||||
266 | */ | ||||||
|
|||||||
267 | 227 | @Override... | |||||
268 | public boolean delete(SequenceFeature sf) | ||||||
269 | { | ||||||
270 | 227 | for (FeatureStore featureSet : featureStore.values()) | |||||
271 | { | ||||||
272 | 327 | if (featureSet.delete(sf)) | |||||
273 | { | ||||||
274 | 225 | return true; | |||||
275 | } | ||||||
276 | } | ||||||
277 | 2 | return false; | |||||
278 | } | ||||||
279 | |||||||
280 | /** | ||||||
281 | * {@inheritDoc} | ||||||
282 | */ | ||||||
|
|||||||
283 | 661 | @Override... | |||||
284 | public boolean hasFeatures() | ||||||
285 | { | ||||||
286 | 661 | for (FeatureStore featureSet : featureStore.values()) | |||||
287 | { | ||||||
288 | 658 | if (!featureSet.isEmpty()) | |||||
289 | { | ||||||
290 | 650 | return true; | |||||
291 | } | ||||||
292 | } | ||||||
293 | 11 | return false; | |||||
294 | } | ||||||
295 | |||||||
296 | /** | ||||||
297 | * {@inheritDoc} | ||||||
298 | */ | ||||||
|
|||||||
299 | 968 | @Override... | |||||
300 | public Set<String> getFeatureGroups(boolean positionalFeatures, | ||||||
301 | String... type) | ||||||
302 | { | ||||||
303 | 968 | Set<String> groups = new HashSet<>(); | |||||
304 | |||||||
305 | 968 | for (FeatureStore featureSet : varargToTypes(type)) | |||||
306 | { | ||||||
307 | 2181 | groups.addAll(featureSet.getFeatureGroups(positionalFeatures)); | |||||
308 | } | ||||||
309 | |||||||
310 | 968 | return groups; | |||||
311 | } | ||||||
312 | |||||||
313 | /** | ||||||
314 | * {@inheritDoc} | ||||||
315 | */ | ||||||
|
|||||||
316 | 835 | @Override... | |||||
317 | public Set<String> getFeatureTypesForGroups(boolean positionalFeatures, | ||||||
318 | String... groups) | ||||||
319 | { | ||||||
320 | 835 | Set<String> result = new HashSet<>(); | |||||
321 | |||||||
322 | 835 | for (Entry<String, FeatureStore> featureType : featureStore.entrySet()) | |||||
323 | { | ||||||
324 | 4095 | Set<String> featureGroups = featureType.getValue() | |||||
325 | .getFeatureGroups(positionalFeatures); | ||||||
326 | 4095 | for (String group : groups) | |||||
327 | { | ||||||
328 | 4099 | if (featureGroups.contains(group)) | |||||
329 | { | ||||||
330 | /* | ||||||
331 | * yes this feature type includes one of the query groups | ||||||
332 | */ | ||||||
333 | 2106 | result.add(featureType.getKey()); | |||||
334 | 2106 | break; | |||||
335 | } | ||||||
336 | } | ||||||
337 | } | ||||||
338 | |||||||
339 | 835 | return result; | |||||
340 | } | ||||||
341 | |||||||
342 | /** | ||||||
343 | * {@inheritDoc} | ||||||
344 | */ | ||||||
|
|||||||
345 | 58 | @Override... | |||||
346 | public Set<String> getFeatureTypes(String... soTerm) | ||||||
347 | { | ||||||
348 | 58 | Set<String> types = new HashSet<>(); | |||||
349 | 58 | for (Entry<String, FeatureStore> entry : featureStore.entrySet()) | |||||
350 | { | ||||||
351 | 93 | String type = entry.getKey(); | |||||
352 | 93 | if (!entry.getValue().isEmpty() && isOntologyTerm(type, soTerm)) | |||||
353 | { | ||||||
354 | 65 | types.add(type); | |||||
355 | } | ||||||
356 | } | ||||||
357 | 58 | return types; | |||||
358 | } | ||||||
359 | |||||||
360 | /** | ||||||
361 | * Answers true if the given type matches one of the specified terms (or is a | ||||||
362 | * sub-type of one in the Sequence Ontology), or if no terms are supplied. | ||||||
363 | * Answers false if filter terms are specified and the given term does not | ||||||
364 | * match any of them. | ||||||
365 | * | ||||||
366 | * @param type | ||||||
367 | * @param soTerm | ||||||
368 | * @return | ||||||
369 | */ | ||||||
|
|||||||
370 | 99 | protected boolean isOntologyTerm(String type, String... soTerm)... | |||||
371 | { | ||||||
372 | 99 | if (soTerm == null || soTerm.length == 0) | |||||
373 | { | ||||||
374 | 20 | return true; | |||||
375 | } | ||||||
376 | 79 | SequenceOntologyI so = SequenceOntologyFactory.getInstance(); | |||||
377 | 79 | for (String term : soTerm) | |||||
378 | { | ||||||
379 | 88 | if (type.equals(term) || so.isA(type, term)) | |||||
380 | { | ||||||
381 | 51 | return true; | |||||
382 | } | ||||||
383 | } | ||||||
384 | 28 | return false; | |||||
385 | } | ||||||
386 | |||||||
387 | /** | ||||||
388 | * {@inheritDoc} | ||||||
389 | */ | ||||||
|
|||||||
390 | 2096 | @Override... | |||||
391 | public float getMinimumScore(String type, boolean positional) | ||||||
392 | { | ||||||
393 | 2096 | return featureStore.containsKey(type) | |||||
394 | ? featureStore.get(type).getMinimumScore(positional) | ||||||
395 | : Float.NaN; | ||||||
396 | } | ||||||
397 | |||||||
398 | /** | ||||||
399 | * {@inheritDoc} | ||||||
400 | */ | ||||||
|
|||||||
401 | 2070 | @Override... | |||||
402 | public float getMaximumScore(String type, boolean positional) | ||||||
403 | { | ||||||
404 | 2070 | return featureStore.containsKey(type) | |||||
405 | ? featureStore.get(type).getMaximumScore(positional) | ||||||
406 | : Float.NaN; | ||||||
407 | } | ||||||
408 | |||||||
409 | /** | ||||||
410 | * A convenience method to sort features by start position ascending (if on | ||||||
411 | * forward strand), or end position descending (if on reverse strand) | ||||||
412 | * | ||||||
413 | * @param features | ||||||
414 | * @param forwardStrand | ||||||
415 | */ | ||||||
|
|||||||
416 | 1002 | public static void sortFeatures(List<? extends IntervalI> features,... | |||||
417 | final boolean forwardStrand) | ||||||
418 | { | ||||||
419 | 1002 | Collections.sort(features, | |||||
420 | 1002 | forwardStrand ? IntervalI.COMPARE_BEGIN_ASC_END_DESC | |||||
421 | : IntervalI.COMPARE_END_DESC); | ||||||
422 | } | ||||||
423 | |||||||
424 | /** | ||||||
425 | * {@inheritDoc} This method is 'semi-optimised': it only inspects features | ||||||
426 | * for types that include the specified group, but has to inspect every | ||||||
427 | * feature of those types for matching feature group. This is efficient unless | ||||||
428 | * a sequence has features that share the same type but are in different | ||||||
429 | * groups - an unlikely case. | ||||||
430 | * <p> | ||||||
431 | * For example, if RESNUM feature is created with group = PDBID, then features | ||||||
432 | * would only be retrieved for those sequences associated with the target | ||||||
433 | * PDBID (group). | ||||||
434 | */ | ||||||
|
|||||||
435 | 498 | @Override... | |||||
436 | public List<SequenceFeature> getFeaturesForGroup(boolean positional, | ||||||
437 | String group, String... type) | ||||||
438 | { | ||||||
439 | 498 | List<SequenceFeature> result = new ArrayList<>(); | |||||
440 | 498 | for (FeatureStore featureSet : varargToTypes(type)) | |||||
441 | { | ||||||
442 | 122 | if (featureSet.getFeatureGroups(positional).contains(group)) | |||||
443 | { | ||||||
444 | 36 | result.addAll(featureSet.getFeaturesForGroup(positional, group)); | |||||
445 | } | ||||||
446 | } | ||||||
447 | 498 | return result; | |||||
448 | } | ||||||
449 | |||||||
450 | /** | ||||||
451 | * {@inheritDoc} | ||||||
452 | */ | ||||||
|
|||||||
453 | 39 | @Override... | |||||
454 | public boolean shiftFeatures(int fromPosition, int shiftBy) | ||||||
455 | { | ||||||
456 | 39 | boolean modified = false; | |||||
457 | 39 | for (FeatureStore fs : featureStore.values()) | |||||
458 | { | ||||||
459 | 40 | modified |= fs.shiftFeatures(fromPosition, shiftBy); | |||||
460 | } | ||||||
461 | 39 | return modified; | |||||
462 | } | ||||||
463 | |||||||
464 | /** | ||||||
465 | * {@inheritDoc} | ||||||
466 | */ | ||||||
|
|||||||
467 | 2 | @Override... | |||||
468 | public void deleteAll() | ||||||
469 | { | ||||||
470 | 2 | featureStore.clear(); | |||||
471 | } | ||||||
472 | } |