Class |
Line # |
Actions |
|||
---|---|---|---|---|---|
Xfam | 39 | 14 | 7 | 0.2608695626.1% |
Class Xfam |
14 |
7 |
0.2608695626.1% |
|
---|---|---|---|---|
Xfam() Xfam() | 4141 | 1.01 | 1.01 | 1.0 1.0100% |
getSequenceRecords(String) : AlignmentI getSequenceRecords(String) : AlignmentI | 5858 | 10.010 | 3.03 | 0.0 0.00% |
getURL(String) : String getURL(String) : String | 8888 | 1.01 | 1.01 | 1.0 1.0100% |
isAlignmentSource() : boolean isAlignmentSource() : boolean | 9797 | 1.01 | 1.01 | 1.0 1.0100% |
getURLSuffix() : String getURLSuffix() : String | 108108 | 1.01 | 1.01 | 0.0 0.00% |
0.17391305
|
jalview.ws.dbsources.RfamSeedTest.testGetURLjalview.ws.dbsources.RfamSeedTest.testGetURL | 1PASS | ||
0.17391305
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.17391305
|
jalview.ws.dbsources.RfamFullTest.testGetURLjalview.ws.dbsources.RfamFullTest.testGetURL | 1PASS | ||
0.17391305
|
jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice | 1PASS | ||
0.17391305
|
jalview.ws.SequenceFetcherTest.testNoDuplicatesInFetchDbRefsjalview.ws.SequenceFetcherTest.testNoDuplicatesInFetchDbRefs | 1PASS | ||
0.17391305
|
jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges | 1PASS | ||
0.17391305
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testCopyViewSettingsjalview.project.Jalview2xmlTests.testCopyViewSettings | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.08695652
|
jalview.datamodel.AlignmentTest.testAssertDatasetIsNormalisedjalview.datamodel.AlignmentTest.testAssertDatasetIsNormalised | 1PASS | ||
0.08695652
|
jalview.controller.AlignViewControllerTest.testSelectColumnsWithHighlightjalview.controller.AlignViewControllerTest.testSelectColumnsWithHighlight | 1PASS | ||
0.08695652
|
jalview.gui.AlignViewportTest.testGetConsensusSeqjalview.gui.AlignViewportTest.testGetConsensusSeq | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.08695652
|
jalview.io.FeaturesFileTest.testParse_mixedJalviewGffjalview.io.FeaturesFileTest.testParse_mixedJalviewGff | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testMergeDatasetsforManyViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforManyViews | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjectsjalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjects | 1PASS | ||
0.08695652
|
jalview.io.BackupFilesTest.backupsEnabledRollMaxTestjalview.io.BackupFilesTest.backupsEnabledRollMaxTest | 1PASS | ||
0.08695652
|
jalview.gui.AnnotationColumnChooserTest.testResetjalview.gui.AnnotationColumnChooserTest.testReset | 1PASS | ||
0.08695652
|
jalview.gui.AlignViewportTest.testDeregisterMapping_withReferencejalview.gui.AlignViewportTest.testDeregisterMapping_withReference | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.08695652
|
jalview.gui.ScalePanelTest.testBuildPopupMenujalview.gui.ScalePanelTest.testBuildPopupMenu | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.08695652
|
jalview.gui.FeatureSettingsTest.testSaveLoadjalview.gui.FeatureSettingsTest.testSaveLoad | 1PASS | ||
0.08695652
|
jalview.gui.AlignFrameTest.testChangeColour_background_groupsAndThresholdsjalview.gui.AlignFrameTest.testChangeColour_background_groupsAndThresholds | 1PASS | ||
0.08695652
|
jalview.workers.AlignCalcManagerTest.testRemoveWorkerForAnnotationjalview.workers.AlignCalcManagerTest.testRemoveWorkerForAnnotation | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.08695652
|
jalview.datamodel.AlignmentTest.testFindAnnotation_byCalcIdjalview.datamodel.AlignmentTest.testFindAnnotation_byCalcId | 1PASS | ||
0.08695652
|
jalview.datamodel.AlignmentTest.testDeleteHiddenSequencejalview.datamodel.AlignmentTest.testDeleteHiddenSequence | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testMergeDatasetsforViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforViews | 1PASS | ||
0.08695652
|
jalview.io.SequenceAnnotationReportTest.testAppendFeature_colouredByAttributejalview.io.SequenceAnnotationReportTest.testAppendFeature_colouredByAttribute | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocusjalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocus | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.08695652
|
jalview.gui.AlignViewportTest.testDeregisterMapping_onCloseViewjalview.gui.AlignViewportTest.testDeregisterMapping_onCloseView | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08695652
|
jalview.util.CaseInsensitiveStringTest.testEqualsjalview.util.CaseInsensitiveStringTest.testEquals | 1PASS | ||
0.08695652
|
jalview.gui.ScalePanelTest.testSelectColumns_withHiddenjalview.gui.ScalePanelTest.testSelectColumns_withHidden | 1PASS | ||
0.08695652
|
jalview.datamodel.AlignmentTest.testCreateDatasetAlignmentWithMappedToSeqsjalview.datamodel.AlignmentTest.testCreateDatasetAlignmentWithMappedToSeqs | 1PASS | ||
0.08695652
|
jalview.io.TCoffeeScoreFileTest.testGetAsListjalview.io.TCoffeeScoreFileTest.testGetAsList | 1PASS | ||
0.08695652
|
jalview.schemes.ColourSchemesTest.testRegisterColourSchemejalview.schemes.ColourSchemesTest.testRegisterColourScheme | 1PASS | ||
0.08695652
|
jalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsqjalview.io.vcf.VCFLoaderTest.testDoLoad_vepCsq | 1PASS | ||
0.08695652
|
jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInBothSeqsjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInBothSeqs | 1PASS | ||
0.08695652
|
jalview.ws.dbsources.PfamFullTest.testGetURLjalview.ws.dbsources.PfamFullTest.testGetURL | 1PASS | ||
0.08695652
|
jalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotationjalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotation | 1PASS | ||
0.08695652
|
jalview.gui.AlignViewportTest.testSetSelectionGroupjalview.gui.AlignViewportTest.testSetSelectionGroup | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.08695652
|
jalview.gui.SeqCanvasTest.testCalculateWrappedGeometry_withAnnotationsjalview.gui.SeqCanvasTest.testCalculateWrappedGeometry_withAnnotations | 1PASS | ||
0.08695652
|
jalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMol | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholdsjalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholds | 1PASS | ||
0.08695652
|
jalview.io.BackupFilesTest.backupsEnabledSingleFileBackupTestjalview.io.BackupFilesTest.backupsEnabledSingleFileBackupTest | 1PASS | ||
0.08695652
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.08695652
|
jalview.gui.AnnotationChooserTest.testSelectType_showForSelectedjalview.gui.AnnotationChooserTest.testSelectType_showForSelected | 1PASS | ||
0.08695652
|
jalview.io.FeaturesFileTest.testPrintGffFormat_withFiltersjalview.io.FeaturesFileTest.testPrintGffFormat_withFilters | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.08695652
|
jalview.gui.AlignViewportTest.testSetGetHasSearchResultsjalview.gui.AlignViewportTest.testSetGetHasSearchResults | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.08695652
|
jalview.gui.AnnotationChooserTest.testDeselectType_showForSelectedjalview.gui.AnnotationChooserTest.testDeselectType_showForSelected | 1PASS | ||
0.08695652
|
jalview.structure.StructureSelectionManagerTest.testSetMapping_seqFeaturesjalview.structure.StructureSelectionManagerTest.testSetMapping_seqFeatures | 1PASS | ||
0.08695652
|
jalview.renderer.seqfeatures.FeatureRendererTest.testGetColourjalview.renderer.seqfeatures.FeatureRendererTest.testGetColour | 1PASS | ||
0.08695652
|
jalview.gui.QuitHandlerTest.testForceQuitjalview.gui.QuitHandlerTest.testForceQuit | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeightjalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeight | 1PASS | ||
0.08695652
|
jalview.io.SequenceAnnotationReportTest.testAppendFeature_statusjalview.io.SequenceAnnotationReportTest.testAppendFeature_status | 1PASS | ||
0.08695652
|
jalview.datamodel.AlignmentTest.testDeleteAllAnnotations_excludingAutocalculatedjalview.datamodel.AlignmentTest.testDeleteAllAnnotations_excludingAutocalculated | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.08695652
|
jalview.ws.dbsources.UniprotTest.testimportOfProblemEntriesjalview.ws.dbsources.UniprotTest.testimportOfProblemEntries | 1PASS | ||
0.08695652
|
jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.08695652
|
jalview.gui.AnnotationLabelsTest2.testIdWidthNoChangesjalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges | 1PASS | ||
0.08695652
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.08695652
|
jalview.datamodel.AlignmentTest.testCreateDataset_updateDbrefMappingsjalview.datamodel.AlignmentTest.testCreateDataset_updateDbrefMappings | 1PASS | ||
0.08695652
|
jalview.io.BackupFilesTest.backupsEnabledNoRollMaxTestjalview.io.BackupFilesTest.backupsEnabledNoRollMaxTest | 1PASS | ||
0.08695652
|
jalview.gui.StructureChooserTest.displayTDBQueryTestjalview.gui.StructureChooserTest.displayTDBQueryTest | 1PASS | ||
0.08695652
|
jalview.io.SequenceAnnotationReportTest.testAppendFeature_noScorejalview.io.SequenceAnnotationReportTest.testAppendFeature_noScore | 1PASS | ||
0.08695652
|
jalview.io.ScoreMatrixFileTest.testParseMatrix_aaindex_tooFewColumnsjalview.io.ScoreMatrixFileTest.testParseMatrix_aaindex_tooFewColumns | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.08695652
|
jalview.io.gff.ExonerateHelperTest.testAddExonerateGffToAlignmentjalview.io.gff.ExonerateHelperTest.testAddExonerateGffToAlignment | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.08695652
|
jalview.gui.AnnotationChooserTest.testDeselectType_hideForSelectedjalview.gui.AnnotationChooserTest.testDeselectType_hideForSelected | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.08695652
|
jalview.gui.AlignFrameTest.testNewView_dsRefPreservedjalview.gui.AlignFrameTest.testNewView_dsRefPreserved | 1PASS | ||
0.08695652
|
jalview.datamodel.AlignmentTest.testEqualsjalview.datamodel.AlignmentTest.testEquals | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMadejalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade | 1PASS | ||
0.08695652
|
jalview.schemes.ColourSchemesTest.testGetColourSchemejalview.schemes.ColourSchemesTest.testGetColourScheme | 1PASS | ||
0.08695652
|
jalview.gui.AlignViewportTest.testGetSelectionAsNewSequences_withContactMatricesjalview.gui.AlignViewportTest.testGetSelectionAsNewSequences_withContactMatrices | 1PASS | ||
0.08695652
|
jalview.io.SequenceAnnotationReportTest.testAppendFeature_disulfideBondjalview.io.SequenceAnnotationReportTest.testAppendFeature_disulfideBond | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08695652
|
jalview.gui.AlignFrameTest.testNewView_colourThresholdsjalview.gui.AlignFrameTest.testNewView_colourThresholds | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.08695652
|
jalview.datamodel.AlignmentTest.testDeleteSequenceBySeqjalview.datamodel.AlignmentTest.testDeleteSequenceBySeq | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.viewRefPdbAnnotationjalview.project.Jalview2xmlTests.viewRefPdbAnnotation | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testPAEsaveRestorejalview.project.Jalview2xmlTests.testPAEsaveRestore | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.08695652
|
jalview.gui.QuitHandlerTest.testSavedAlignmentChangesjalview.gui.QuitHandlerTest.testSavedAlignmentChanges | 1PASS | ||
0.08695652
|
jalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroup | 1PASS | ||
0.08695652
|
jalview.gui.AnnotationChooserTest.testSelectType_showForAlljalview.gui.AnnotationChooserTest.testSelectType_showForAll | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews | 1PASS | ||
0.08695652
|
jalview.io.FeaturesFileTest.testParsejalview.io.FeaturesFileTest.testParse | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08695652
|
jalview.gui.AnnotationChooserTest.testBuildShowHidePaneljalview.gui.AnnotationChooserTest.testBuildShowHidePanel | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation | 1PASS | ||
0.08695652
|
jalview.renderer.ScaleRendererTest.testCalculateMarksjalview.renderer.ScaleRendererTest.testCalculateMarks | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqsjalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqs | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverview | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testColourByAnnotScoresjalview.project.Jalview2xmlTests.testColourByAnnotScores | 1PASS | ||
0.08695652
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModeljalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel | 1PASS | ||
0.08695652
|
jalview.gui.AnnotationLabelsTest2.testIdWidthNoChangesjalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges | 1PASS | ||
0.08695652
|
jalview.gui.QuitHandlerTest.testNoGUIUnsavedChangesjalview.gui.QuitHandlerTest.testNoGUIUnsavedChanges | 1PASS | ||
0.08695652
|
jalview.io.TCoffeeScoreFileTest.testHeightAndWidthWithResidueNumbersjalview.io.TCoffeeScoreFileTest.testHeightAndWidthWithResidueNumbers | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.08695652
|
jalview.gui.QuitHandlerTest.testSavedProjectChangesjalview.gui.QuitHandlerTest.testSavedProjectChanges | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08695652
|
jalview.schemes.ClustalxColourSchemeTest.testFindColour_ignoreGapsjalview.schemes.ClustalxColourSchemeTest.testFindColour_ignoreGaps | 1PASS | ||
0.08695652
|
jalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGapsjalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGaps | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08695652
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.08695652
|
jalview.gui.SeqPanelTest.testSetStatusReturnsNearestResiduePositionjalview.gui.SeqPanelTest.testSetStatusReturnsNearestResiduePosition | 1PASS | ||
0.08695652
|
jalview.gui.QuitHandlerTest.testUnsavedChangesjalview.gui.QuitHandlerTest.testUnsavedChanges | 1PASS | ||
0.08695652
|
jalview.gui.ProgressBarTest.testSetProgressBarjalview.gui.ProgressBarTest.testSetProgressBar | 1PASS | ||
0.08695652
|
jalview.gui.AlignmentPanelTest.testCalculateIdWidth_noArgsjalview.gui.AlignmentPanelTest.testCalculateIdWidth_noArgs | 1PASS | ||
0.08695652
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResiduejalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResidue | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColoursjalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColours | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.08695652
|
jalview.io.FeaturesFileTest.testPrintGffFormatjalview.io.FeaturesFileTest.testPrintGffFormat | 1PASS | ||
0.08695652
|
jalview.gui.AnnotationChooserTest.testDeselectType_hideForAlljalview.gui.AnnotationChooserTest.testDeselectType_hideForAll | 1PASS | ||
0.08695652
|
jalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverviewjalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverview | 1PASS | ||
0.08695652
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_HiddenColumnsjalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_HiddenColumns | 1PASS | ||
0.08695652
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.08695652
|
jalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbsjalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbs | 1PASS | ||
0.08695652
|
jalview.ext.jmol.JmolParserTest.testAlignmentLoaderjalview.ext.jmol.JmolParserTest.testAlignmentLoader | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.08695652
|
jalview.gui.AlignmentPanelTest.testSetScrollValuesjalview.gui.AlignmentPanelTest.testSetScrollValues | 1PASS | ||
0.08695652
|
jalview.io.SequenceAnnotationReportTest.testAppendFeature_stripHtmljalview.io.SequenceAnnotationReportTest.testAppendFeature_stripHtml | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings | 1PASS | ||
0.08695652
|
jalview.gui.AlignViewportTest.testUpdateConservation_qualityOnlyjalview.gui.AlignViewportTest.testUpdateConservation_qualityOnly | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testTCoffeeScoresjalview.project.Jalview2xmlTests.testTCoffeeScores | 1PASS | ||
0.08695652
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.08695652
|
jalview.gui.PopupMenuTest.testBuildLinkMenujalview.gui.PopupMenuTest.testBuildLinkMenu | 1PASS | ||
0.08695652
|
jalview.datamodel.AlignmentTest.testDeleteSequenceByIndexjalview.datamodel.AlignmentTest.testDeleteSequenceByIndex | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.08695652
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindFeatureAt_PointFeaturejalview.analysis.scoremodels.FeatureDistanceModelTest.testFindFeatureAt_PointFeature | 1PASS | ||
0.08695652
|
jalview.gui.AlignViewportTest.testShowOrDontShowOccupancyjalview.gui.AlignViewportTest.testShowOrDontShowOccupancy | 1PASS | ||
0.08695652
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances_withParamsjalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances_withParams | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.08695652
|
jalview.gui.AnnotationChooserTest.testSelectType_hideForSelectedjalview.gui.AnnotationChooserTest.testSelectType_hideForSelected | 1PASS | ||
0.08695652
|
jalview.ext.jmol.JmolParserTest.testFileParserjalview.ext.jmol.JmolParserTest.testFileParser | 1PASS | ||
0.08695652
|
jalview.gui.DesktopTests.testInternalCopyPastejalview.gui.DesktopTests.testInternalCopyPaste | 1PASS | ||
0.08695652
|
jalview.io.ScoreMatrixFileTest.testParseMatrix_ncbiBadFloatjalview.io.ScoreMatrixFileTest.testParseMatrix_ncbiBadFloat | 1PASS | ||
0.08695652
|
jalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMol | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.08695652
|
jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInEitherOneSeqjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInEitherOneSeq | 1PASS | ||
0.08695652
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequencejalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequence | 1PASS | ||
0.08695652
|
jalview.ws.dbsources.PfamSeedTest.testGetURLjalview.ws.dbsources.PfamSeedTest.testGetURL | 1PASS | ||
0.08695652
|
jalview.io.TCoffeeScoreFileTest.testGetAsArrayjalview.io.TCoffeeScoreFileTest.testGetAsArray | 1PASS | ||
0.08695652
|
jalview.ext.pymol.PymolManagerTest.testGetPostRequestjalview.ext.pymol.PymolManagerTest.testGetPostRequest | 1PASS | ||
0.08695652
|
jalview.gui.StructureChooserTest.populateFilterComboBoxTestjalview.gui.StructureChooserTest.populateFilterComboBoxTest | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.08695652
|
jalview.io.AnnotationExporterTest.testAnnotationExportAsCSVjalview.io.AnnotationExporterTest.testAnnotationExportAsCSV | 1PASS | ||
0.08695652
|
jalview.gui.AlignViewportTest.testSetGlobalColourSchemejalview.gui.AlignViewportTest.testSetGlobalColourScheme | 1PASS | ||
0.08695652
|
jalview.io.FeaturesFileTest.testParse_pureGff3jalview.io.FeaturesFileTest.testParse_pureGff3 | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntryjalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntry | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.08695652
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverOverview | 1PASS | ||
0.08695652
|
jalview.gui.QuitHandlerTest.testWaitForSaveQuitjalview.gui.QuitHandlerTest.testWaitForSaveQuit | 1PASS | ||
0.08695652
|
jalview.math.SparseMatrixTest.testConstructorjalview.math.SparseMatrixTest.testConstructor | 1PASS | ||
0.08695652
|
jalview.datamodel.AlignmentTest.testCreateDatasetAlignmentjalview.datamodel.AlignmentTest.testCreateDatasetAlignment | 1PASS | ||
0.08695652
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeaturesjalview.renderer.seqfeatures.FeatureRendererTest.testFindAllFeatures | 1PASS | ||
0.08695652
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.08695652
|
jalview.io.SequenceAnnotationReportTest.testAppendFeature_virtualFeaturejalview.io.SequenceAnnotationReportTest.testAppendFeature_virtualFeature | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.08695652
|
jalview.analysis.AverageDistanceEngineTest.testUPGMAEnginejalview.analysis.AverageDistanceEngineTest.testUPGMAEngine | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.08695652
|
jalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNonejalview.io.JSONFileTest.testBioJSONRoundTripWithColourSchemeNone | 1PASS | ||
0.08695652
|
jalview.io.BackupFilesTest.backupsEnabledReverseRollMaxTestjalview.io.BackupFilesTest.backupsEnabledReverseRollMaxTest | 1PASS | ||
0.08695652
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_hiddenFirstColumnjalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_hiddenFirstColumn | 1PASS | ||
0.08695652
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.08695652
|
jalview.gui.ColourMenuHelperTest.testAddMenuItems_nucleotidejalview.gui.ColourMenuHelperTest.testAddMenuItems_nucleotide | 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.ws.dbsources; | ||||||
22 | |||||||
23 | import java.util.Locale; | ||||||
24 | |||||||
25 | import jalview.bin.Console; | ||||||
26 | import jalview.datamodel.AlignmentI; | ||||||
27 | import jalview.datamodel.DBRefEntry; | ||||||
28 | import jalview.io.DataSourceType; | ||||||
29 | import jalview.io.FileFormat; | ||||||
30 | import jalview.io.FormatAdapter; | ||||||
31 | import jalview.ws.seqfetcher.DbSourceProxyImpl; | ||||||
32 | |||||||
33 | /** | ||||||
34 | * Acts as a superclass for the Rfam and Pfam classes | ||||||
35 | * | ||||||
36 | * @author Lauren Michelle Lui | ||||||
37 | * | ||||||
38 | */ | ||||||
|
|||||||
39 | public abstract class Xfam extends DbSourceProxyImpl | ||||||
40 | { | ||||||
|
|||||||
41 | 56 | public Xfam()... | |||||
42 | { | ||||||
43 | 56 | super(); | |||||
44 | } | ||||||
45 | |||||||
46 | /** | ||||||
47 | * the base URL for this Xfam-like service | ||||||
48 | * | ||||||
49 | * @return | ||||||
50 | */ | ||||||
51 | protected abstract String getURLPrefix(); | ||||||
52 | |||||||
53 | @Override | ||||||
54 | public abstract String getDbVersion(); | ||||||
55 | |||||||
56 | abstract String getXfamSource(); | ||||||
57 | |||||||
|
|||||||
58 | 0 | @Override... | |||||
59 | public AlignmentI getSequenceRecords(String queries) throws Exception | ||||||
60 | { | ||||||
61 | // TODO: this is not a perfect implementation. We need to be able to add | ||||||
62 | // individual references to each sequence in each family alignment that's | ||||||
63 | // retrieved. | ||||||
64 | 0 | startQuery(); | |||||
65 | // TODO: trap HTTP 404 exceptions and return null | ||||||
66 | 0 | String xfamUrl = getURL(queries); | |||||
67 | |||||||
68 | 0 | Console.debug("XFAM URL for retrieval is: " + xfamUrl); | |||||
69 | |||||||
70 | 0 | AlignmentI rcds = new FormatAdapter().readFile(xfamUrl, | |||||
71 | DataSourceType.URL, FileFormat.Stockholm); | ||||||
72 | |||||||
73 | 0 | for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++) | |||||
74 | { | ||||||
75 | 0 | rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(), | |||||
76 | // getDbSource(), | ||||||
77 | getDbVersion(), queries.trim().toUpperCase(Locale.ROOT))); | ||||||
78 | 0 | if (!getDbSource().equals(getXfamSource())) | |||||
79 | { // add the specific ref too | ||||||
80 | 0 | rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getDbSource(), | |||||
81 | getDbVersion(), queries.trim().toUpperCase(Locale.ROOT))); | ||||||
82 | } | ||||||
83 | } | ||||||
84 | 0 | stopQuery(); | |||||
85 | 0 | return rcds; | |||||
86 | } | ||||||
87 | |||||||
|
|||||||
88 | 4 | String getURL(String queries)... | |||||
89 | { | ||||||
90 | 4 | return getURLPrefix() + "/family/" | |||||
91 | + queries.trim().toUpperCase(Locale.ROOT) + getURLSuffix(); | ||||||
92 | } | ||||||
93 | |||||||
94 | /** | ||||||
95 | * Pfam and Rfam provide alignments | ||||||
96 | */ | ||||||
|
|||||||
97 | 8085 | @Override... | |||||
98 | public boolean isAlignmentSource() | ||||||
99 | { | ||||||
100 | 8085 | return true; | |||||
101 | } | ||||||
102 | |||||||
103 | /** | ||||||
104 | * default suffix to append the retrieval URL for this source. | ||||||
105 | * | ||||||
106 | * @return "" for most Xfam sources | ||||||
107 | */ | ||||||
|
|||||||
108 | 0 | public String getURLSuffix()... | |||||
109 | { | ||||||
110 | 0 | return ""; | |||||
111 | } | ||||||
112 | |||||||
113 | } |