Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
Blosum62ColourScheme | 32 | 20 | 12 | 0.941176594.1% |
Class Blosum62ColourScheme |
20 |
12 |
0.941176594.1% |
|
---|---|---|---|---|
Blosum62ColourScheme() Blosum62ColourScheme() | 3838 | 1.01 | 1.01 | 1.0 1.0100% |
getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI getInstance(AlignViewportI,AnnotatedCollectionI) : ColourSchemeI | 4747 | 1.01 | 1.01 | 1.0 1.0100% |
findColour(char,int,SequenceI,String,float) : Color findColour(char,int,SequenceI,String,float) : Color | 5454 | 15.015 | 7.07 | 0.9130435 0.913043591.3% |
isPeptideSpecific() : boolean isPeptideSpecific() : boolean | 101101 | 1.01 | 1.01 | 1.0 1.0100% |
getSchemeName() : String getSchemeName() : String | 107107 | 1.01 | 1.01 | 1.0 1.0100% |
isSimple() : boolean isSimple() : boolean | 113113 | 1.01 | 1.01 | 1.0 1.0100% |
0.8235294
|
jalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjectsjalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjects | 1PASS | ||
0.8235294
|
jalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeightjalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeight | 1PASS | ||
0.7058824
|
jalview.project.Jalview2xmlTests.testColourByAnnotScoresjalview.project.Jalview2xmlTests.testColourByAnnotScores | 1PASS | ||
0.7058824
|
jalview.project.Jalview2xmlTests.testTCoffeeScoresjalview.project.Jalview2xmlTests.testTCoffeeScores | 1PASS | ||
0.7058824
|
jalview.schemes.Blosum62ColourSchemeTest.testFindColourjalview.schemes.Blosum62ColourSchemeTest.testFindColour | 1PASS | ||
0.23529412
|
jalview.schemes.ColourSchemesTest.testGetColourSchemejalview.schemes.ColourSchemesTest.testGetColourScheme | 1PASS | ||
0.1764706
|
jalview.project.Jalview2xmlTests.testCopyViewSettingsjalview.project.Jalview2xmlTests.testCopyViewSettings | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.1764706
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.1764706
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.1764706
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings | 1PASS | ||
0.1764706
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.1764706
|
jalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMol | 1PASS | ||
0.1764706
|
jalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMol | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.1764706
|
jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.1764706
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.1764706
|
jalview.project.Jalview2xmlTests.viewRefPdbAnnotationjalview.project.Jalview2xmlTests.viewRefPdbAnnotation | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.1764706
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.11764706
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scaleAbovejalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scaleAbove | 1PASS | ||
0.11764706
|
jalview.gui.AlignViewportTest.testDeregisterMapping_withNoReferencejalview.gui.AlignViewportTest.testDeregisterMapping_withNoReference | 1PASS | ||
0.11764706
|
jalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroup | 1PASS | ||
0.11764706
|
jalview.controller.AlignViewControllerTest.testSelectColumnsWithHighlightjalview.controller.AlignViewControllerTest.testSelectColumnsWithHighlight | 1PASS | ||
0.11764706
|
jalview.io.FeaturesFileTest.testParsejalview.io.FeaturesFileTest.testParse | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.gui.AlignViewportTest.testGetConsensusSeqjalview.gui.AlignViewportTest.testGetConsensusSeq | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation | 1PASS | ||
0.11764706
|
jalview.schemes.ResidueColourSchemeTest.testGetNamejalview.schemes.ResidueColourSchemeTest.testGetName | 1PASS | ||
0.11764706
|
jalview.renderer.ScaleRendererTest.testCalculateMarksjalview.renderer.ScaleRendererTest.testCalculateMarks | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.11764706
|
jalview.io.FeaturesFileTest.testParse_mixedJalviewGffjalview.io.FeaturesFileTest.testParse_mixedJalviewGff | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqsjalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqs | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverview | 1PASS | ||
0.11764706
|
jalview.gui.ScalePanelTest.testPreventNegativeStartColumnjalview.gui.ScalePanelTest.testPreventNegativeStartColumn | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testMergeDatasetsforManyViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforManyViews | 1PASS | ||
0.11764706
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModeljalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel | 1PASS | ||
0.11764706
|
jalview.gui.AnnotationLabelsTest2.testIdWidthNoChangesjalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges | 1PASS | ||
0.11764706
|
jalview.io.BackupFilesTest.backupsEnabledRollMaxTestjalview.io.BackupFilesTest.backupsEnabledRollMaxTest | 1PASS | ||
0.11764706
|
jalview.gui.QuitHandlerTest.testNoGUIUnsavedChangesjalview.gui.QuitHandlerTest.testNoGUIUnsavedChanges | 1PASS | ||
0.11764706
|
jalview.io.FeaturesFileTest.testPrintJalviewFormat_withFiltersjalview.io.FeaturesFileTest.testPrintJalviewFormat_withFilters | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.11764706
|
jalview.gui.QuitHandlerTest.testSavedProjectChangesjalview.gui.QuitHandlerTest.testSavedProjectChanges | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.datamodel.AlignmentViewTest.testGetVisibleContigsjalview.datamodel.AlignmentViewTest.testGetVisibleContigs | 1PASS | ||
0.11764706
|
jalview.schemes.ClustalxColourSchemeTest.testFindColour_ignoreGapsjalview.schemes.ClustalxColourSchemeTest.testFindColour_ignoreGaps | 1PASS | ||
0.11764706
|
jalview.gui.PopupMenuTest.testHideInsertionsjalview.gui.PopupMenuTest.testHideInsertions | 1PASS | ||
0.11764706
|
jalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGapsjalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGaps | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.gui.AlignViewportTest.testDeregisterMapping_withReferencejalview.gui.AlignViewportTest.testDeregisterMapping_withReference | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.11764706
|
jalview.gui.SeqPanelTest.testSetStatusReturnsNearestResiduePositionjalview.gui.SeqPanelTest.testSetStatusReturnsNearestResiduePosition | 1PASS | ||
0.11764706
|
jalview.gui.QuitHandlerTest.testUnsavedChangesjalview.gui.QuitHandlerTest.testUnsavedChanges | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.11764706
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFilterFeaturesForDisplayjalview.renderer.seqfeatures.FeatureRendererTest.testFilterFeaturesForDisplay | 1PASS | ||
0.11764706
|
jalview.gui.ScalePanelTest.testBuildPopupMenujalview.gui.ScalePanelTest.testBuildPopupMenu | 1PASS | ||
0.11764706
|
jalview.schemes.ResidueColourSchemeTest.testIsApplicableTojalview.schemes.ResidueColourSchemeTest.testIsApplicableTo | 1PASS | ||
0.11764706
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResiduejalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResidue | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColoursjalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColours | 1PASS | ||
0.11764706
|
jalview.gui.AlignFrameTest.testHideFeatureColumnsjalview.gui.AlignFrameTest.testHideFeatureColumns | 1PASS | ||
0.11764706
|
jalview.io.FeaturesFileTest.testPrintGffFormatjalview.io.FeaturesFileTest.testPrintGffFormat | 1PASS | ||
0.11764706
|
jalview.gui.FeatureSettingsTest.testSaveLoadjalview.gui.FeatureSettingsTest.testSaveLoad | 1PASS | ||
0.11764706
|
jalview.gui.AlignFrameTest.testChangeColour_background_groupsAndThresholdsjalview.gui.AlignFrameTest.testChangeColour_background_groupsAndThresholds | 1PASS | ||
0.11764706
|
jalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverviewjalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverview | 1PASS | ||
0.11764706
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_HiddenColumnsjalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_HiddenColumns | 1PASS | ||
0.11764706
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.11764706
|
jalview.structures.models.AAStructureBindingModelTest.testBuildColoursMapjalview.structures.models.AAStructureBindingModelTest.testBuildColoursMap | 1PASS | ||
0.11764706
|
jalview.ext.jmol.JmolParserTest.testAlignmentLoaderjalview.ext.jmol.JmolParserTest.testAlignmentLoader | 1PASS | ||
0.11764706
|
jalview.io.vcf.VCFLoaderTest.testDoLoad_reverseStrandjalview.io.vcf.VCFLoaderTest.testDoLoad_reverseStrand | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testMergeDatasetsforViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforViews | 1PASS | ||
0.11764706
|
jalview.schemes.ColourSchemePropertyTest.testGetColourSchemejalview.schemes.ColourSchemePropertyTest.testGetColourScheme | 1PASS | ||
0.11764706
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistancesjalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances | 1PASS | ||
0.11764706
|
jalview.renderer.seqfeatures.FeatureRendererTest.testIsVisiblejalview.renderer.seqfeatures.FeatureRendererTest.testIsVisible | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocusjalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocus | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.gui.AlignViewportTest.testDeregisterMapping_onCloseViewjalview.gui.AlignViewportTest.testDeregisterMapping_onCloseView | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.gui.ScalePanelTest.testSelectColumns_withHiddenjalview.gui.ScalePanelTest.testSelectColumns_withHidden | 1PASS | ||
0.11764706
|
jalview.schemes.ColourSchemesTest.testRegisterColourSchemejalview.schemes.ColourSchemesTest.testRegisterColourScheme | 1PASS | ||
0.11764706
|
jalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsqjalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsq | 1PASS | ||
0.11764706
|
jalview.gui.AlignViewportTest.testUpdateConservation_qualityOnlyjalview.gui.AlignViewportTest.testUpdateConservation_qualityOnly | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInBothSeqsjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInBothSeqs | 1PASS | ||
0.11764706
|
jalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotationjalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotation | 1PASS | ||
0.11764706
|
jalview.gui.AlignViewportTest.testSetSelectionGroupjalview.gui.AlignViewportTest.testSetSelectionGroup | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.11764706
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindFeatureAt_PointFeaturejalview.analysis.scoremodels.FeatureDistanceModelTest.testFindFeatureAt_PointFeature | 1PASS | ||
0.11764706
|
jalview.gui.AlignViewportTest.testShowOrDontShowOccupancyjalview.gui.AlignViewportTest.testShowOrDontShowOccupancy | 1PASS | ||
0.11764706
|
jalview.gui.QuitHandlerTest.testInstantQuitjalview.gui.QuitHandlerTest.testInstantQuit | 1PASS | ||
0.11764706
|
jalview.io.JSONFileTest.testGrpParsed_colourNonejalview.io.JSONFileTest.testGrpParsed_colourNone | 1PASS | ||
0.11764706
|
jalview.io.FeaturesFileTest.testParse_jalviewFeaturesOnlyjalview.io.FeaturesFileTest.testParse_jalviewFeaturesOnly | 1PASS | ||
0.11764706
|
jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withGapjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withGap | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholdsjalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholds | 1PASS | ||
0.11764706
|
jalview.io.AnnotationFileIOTest.testAnnotateAlignmentViewjalview.io.AnnotationFileIOTest.testAnnotateAlignmentView | 1PASS | ||
0.11764706
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances_withParamsjalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances_withParams | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.11764706
|
jalview.io.BackupFilesTest.backupsEnabledSingleFileBackupTestjalview.io.BackupFilesTest.backupsEnabledSingleFileBackupTest | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.controller.AlignViewControllerTest.testFindColumnsWithFeaturejalview.controller.AlignViewControllerTest.testFindColumnsWithFeature | 1PASS | ||
0.11764706
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.11764706
|
jalview.gui.SeqPanelTest.testFindColumn_and_FindAlignmentColumn_wrappedjalview.gui.SeqPanelTest.testFindColumn_and_FindAlignmentColumn_wrapped | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.11764706
|
jalview.gui.SeqPanelTest.testAmbiguousAminoAcidGetsStatusMessagejalview.gui.SeqPanelTest.testAmbiguousAminoAcidGetsStatusMessage | 1PASS | ||
0.11764706
|
jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice | 1PASS | ||
0.11764706
|
jalview.gui.DesktopTests.testInternalCopyPastejalview.gui.DesktopTests.testInternalCopyPaste | 1PASS | ||
0.11764706
|
jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery | 1PASS | ||
0.11764706
|
jalview.io.FeaturesFileTest.testPrintGffFormat_withFiltersjalview.io.FeaturesFileTest.testPrintGffFormat_withFilters | 1PASS | ||
0.11764706
|
jalview.gui.AlignViewportTest.testSetGetHasSearchResultsjalview.gui.AlignViewportTest.testSetGetHasSearchResults | 1PASS | ||
0.11764706
|
jalview.gui.ColourMenuHelperTest.testAddMenuItems_forAlignFramejalview.gui.ColourMenuHelperTest.testAddMenuItems_forAlignFrame | 1PASS | ||
0.11764706
|
jalview.renderer.seqfeatures.FeatureRendererTest.testGetColourjalview.renderer.seqfeatures.FeatureRendererTest.testGetColour | 1PASS | ||
0.11764706
|
jalview.gui.QuitHandlerTest.testForceQuitjalview.gui.QuitHandlerTest.testForceQuit | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.gui.SeqPanelTest.testFindColumn_unwrappedjalview.gui.SeqPanelTest.testFindColumn_unwrapped | 1PASS | ||
0.11764706
|
jalview.gui.ColourMenuHelperTest.testAddMenuItems_peptidejalview.gui.ColourMenuHelperTest.testAddMenuItems_peptide | 1PASS | ||
0.11764706
|
jalview.io.WindowsFileLoadAndSaveTest.loadAndSaveAlignmentjalview.io.WindowsFileLoadAndSaveTest.loadAndSaveAlignment | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.11764706
|
jalview.gui.AlignmentPanelTest.testSetOverviewTitlejalview.gui.AlignmentPanelTest.testSetOverviewTitle | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters | 1PASS | ||
0.11764706
|
jalview.io.FeaturesFileTest.testPrintJalviewFormatjalview.io.FeaturesFileTest.testPrintJalviewFormat | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.11764706
|
jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInEitherOneSeqjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInEitherOneSeq | 1PASS | ||
0.11764706
|
jalview.io.gff.GffTests.testResolveExonerateGffjalview.io.gff.GffTests.testResolveExonerateGff | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.11764706
|
jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.io.BackupFilesTest.noBackupsEnabledTestjalview.io.BackupFilesTest.noBackupsEnabledTest | 1PASS | ||
0.11764706
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequencejalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequence | 1PASS | ||
0.11764706
|
jalview.schemes.ColourSchemePropertyTest.testGetColourNamejalview.schemes.ColourSchemePropertyTest.testGetColourName | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.11764706
|
jalview.gui.AnnotationLabelsTest2.testIdWidthNoChangesjalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges | 1PASS | ||
0.11764706
|
jalview.schemes.ClustalxColourSchemeTest.testFindColourjalview.schemes.ClustalxColourSchemeTest.testFindColour | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.11764706
|
jalview.io.BackupFilesTest.backupsEnabledNoRollMaxTestjalview.io.BackupFilesTest.backupsEnabledNoRollMaxTest | 1PASS | ||
0.11764706
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumnjalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumn | 1PASS | ||
0.11764706
|
jalview.io.JalviewExportPropertiesTests.testImportExportPeriodGapsjalview.io.JalviewExportPropertiesTests.testImportExportPeriodGaps | 1PASS | ||
0.11764706
|
jalview.io.AnnotationExporterTest.testAnnotationExportAsCSVjalview.io.AnnotationExporterTest.testAnnotationExportAsCSV | 1PASS | ||
0.11764706
|
jalview.gui.AlignViewportTest.testSetGlobalColourSchemejalview.gui.AlignViewportTest.testSetGlobalColourScheme | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.11764706
|
jalview.io.FeaturesFileTest.testParse_pureGff3jalview.io.FeaturesFileTest.testParse_pureGff3 | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntryjalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntry | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.11764706
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_noAnnotationsjalview.gui.SeqPanelTest.testFindMousePosition_wrapped_noAnnotations | 1PASS | ||
0.11764706
|
jalview.io.gff.ExonerateHelperTest.testAddExonerateGffToAlignmentjalview.io.gff.ExonerateHelperTest.testAddExonerateGffToAlignment | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverOverview | 1PASS | ||
0.11764706
|
jalview.gui.QuitHandlerTest.testWaitForSaveQuitjalview.gui.QuitHandlerTest.testWaitForSaveQuit | 1PASS | ||
0.11764706
|
jalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_withSelectionGroup | 1PASS | ||
0.11764706
|
jalview.gui.AlignFrameTest.testNewView_dsRefPreservedjalview.gui.AlignFrameTest.testNewView_dsRefPreserved | 1PASS | ||
0.11764706
|
jalview.io.FeaturesFileTest.simpleGff3FileLoaderjalview.io.FeaturesFileTest.simpleGff3FileLoader | 1PASS | ||
0.11764706
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeaturesjalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeatures | 1PASS | ||
0.11764706
|
jalview.gui.PaintRefresherTest.testGetAssociatedPanelsjalview.gui.PaintRefresherTest.testGetAssociatedPanels | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMadejalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade | 1PASS | ||
0.11764706
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.11764706
|
jalview.ext.jmol.JmolCommandsTest.testGetColourBySequenceCommands_hiddenColumnsjalview.ext.jmol.JmolCommandsTest.testGetColourBySequenceCommands_hiddenColumns | 1PASS | ||
0.11764706
|
jalview.gui.AlignViewportTest.testGetSelectionAsNewSequences_withContactMatricesjalview.gui.AlignViewportTest.testGetSelectionAsNewSequences_withContactMatrices | 1PASS | ||
0.11764706
|
jalview.io.vcf.VCFLoaderTest.testDoLoadjalview.io.vcf.VCFLoaderTest.testDoLoad | 1PASS | ||
0.11764706
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.11764706
|
jalview.analysis.AverageDistanceEngineTest.testUPGMAEnginejalview.analysis.AverageDistanceEngineTest.testUPGMAEngine | 1PASS | ||
0.11764706
|
jalview.gui.AlignFrameTest.testNewView_colourThresholdsjalview.gui.AlignFrameTest.testNewView_colourThresholds | 1PASS | ||
0.11764706
|
jalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNonejalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNone | 1PASS | ||
0.11764706
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_annotationsjalview.gui.SeqPanelTest.testFindMousePosition_wrapped_annotations | 1PASS | ||
0.11764706
|
jalview.project.Jalview2xmlTests.testPAEsaveRestorejalview.project.Jalview2xmlTests.testPAEsaveRestore | 1PASS | ||
0.11764706
|
jalview.io.BackupFilesTest.backupsEnabledReverseRollMaxTestjalview.io.BackupFilesTest.backupsEnabledReverseRollMaxTest | 1PASS | ||
0.11764706
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_hiddenFirstColumnjalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_hiddenFirstColumn | 1PASS | ||
0.11764706
|
jalview.gui.ColourMenuHelperTest.testAddMenuItems_nucleotidejalview.gui.ColourMenuHelperTest.testAddMenuItems_nucleotide | 1PASS | ||
0.11764706
|
jalview.gui.QuitHandlerTest.testSavedAlignmentChangesjalview.gui.QuitHandlerTest.testSavedAlignmentChanges | 1PASS | ||
0.05882353
|
jalview.schemes.ColourSchemesTest.testGetColourSchemesjalview.schemes.ColourSchemesTest.testGetColourSchemes | 1PASS | ||
0.05882353
|
jalview.gui.ColourMenuHelperTest.testAddMenuItems_simpleOnlyjalview.gui.ColourMenuHelperTest.testAddMenuItems_simpleOnly | 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.schemes; | ||||||
22 | |||||||
23 | import jalview.analysis.scoremodels.ScoreModels; | ||||||
24 | import jalview.api.AlignViewportI; | ||||||
25 | import jalview.api.analysis.PairwiseScoreModelI; | ||||||
26 | import jalview.datamodel.AnnotatedCollectionI; | ||||||
27 | import jalview.datamodel.SequenceI; | ||||||
28 | import jalview.util.Comparison; | ||||||
29 | |||||||
30 | import java.awt.Color; | ||||||
31 | |||||||
|
|||||||
32 | public class Blosum62ColourScheme extends ResidueColourScheme | ||||||
33 | { | ||||||
34 | private static final Color LIGHT_BLUE = new Color(204, 204, 255); | ||||||
35 | |||||||
36 | private static final Color DARK_BLUE = new Color(154, 154, 255); | ||||||
37 | |||||||
|
|||||||
38 | 65 | public Blosum62ColourScheme()... | |||||
39 | { | ||||||
40 | 65 | super(); | |||||
41 | } | ||||||
42 | |||||||
43 | /** | ||||||
44 | * Returns a new instance of this colour scheme with which the given data may | ||||||
45 | * be coloured | ||||||
46 | */ | ||||||
|
|||||||
47 | 6 | @Override... | |||||
48 | public ColourSchemeI getInstance(AlignViewportI view, | ||||||
49 | AnnotatedCollectionI coll) | ||||||
50 | { | ||||||
51 | 6 | return new Blosum62ColourScheme(); | |||||
52 | } | ||||||
53 | |||||||
|
|||||||
54 | 22428 | @Override... | |||||
55 | public Color findColour(char res, int j, SequenceI seq, | ||||||
56 | String consensusResidue, float pid) | ||||||
57 | { | ||||||
58 | 22428 | PairwiseScoreModelI sm = ScoreModels.getInstance().getBlosum62(); | |||||
59 | |||||||
60 | /* | ||||||
61 | * compare as upper case; note consensusResidue is | ||||||
62 | * always computed as uppercase | ||||||
63 | */ | ||||||
64 | 22428 | if ('a' <= res && res <= 'z') | |||||
65 | { | ||||||
66 | 1 | res -= ('a' - 'A'); | |||||
67 | } | ||||||
68 | |||||||
69 | 22428 | if (Comparison.isGap(res) || consensusResidue == null) | |||||
70 | { | ||||||
71 | 0 | return Color.white; | |||||
72 | } | ||||||
73 | |||||||
74 | 22428 | Color colour; | |||||
75 | |||||||
76 | 22428 | if (consensusResidue.indexOf(res) > -1) | |||||
77 | { | ||||||
78 | 15764 | colour = DARK_BLUE; | |||||
79 | } | ||||||
80 | else | ||||||
81 | { | ||||||
82 | 6664 | float score = 0; | |||||
83 | |||||||
84 | 6664 | for (char consensus : consensusResidue.toCharArray()) | |||||
85 | { | ||||||
86 | 6987 | score += sm.getPairwiseScore(consensus, res); | |||||
87 | } | ||||||
88 | |||||||
89 | 6664 | if (score > 0) | |||||
90 | { | ||||||
91 | 2054 | colour = LIGHT_BLUE; | |||||
92 | } | ||||||
93 | else | ||||||
94 | { | ||||||
95 | 4610 | colour = Color.white; | |||||
96 | } | ||||||
97 | } | ||||||
98 | 22428 | return colour; | |||||
99 | } | ||||||
100 | |||||||
|
|||||||
101 | 844 | @Override... | |||||
102 | public boolean isPeptideSpecific() | ||||||
103 | { | ||||||
104 | 844 | return true; | |||||
105 | } | ||||||
106 | |||||||
|
|||||||
107 | 580 | @Override... | |||||
108 | public String getSchemeName() | ||||||
109 | { | ||||||
110 | 580 | return JalviewColourScheme.Blosum62.toString(); | |||||
111 | } | ||||||
112 | |||||||
|
|||||||
113 | 47 | @Override... | |||||
114 | public boolean isSimple() | ||||||
115 | { | ||||||
116 | 47 | return false; | |||||
117 | } | ||||||
118 | } |