Class | Line # | Actions | |||
---|---|---|---|---|---|
SequenceFetcher | 44 | 20 | 5 | 1.0100% |
Class SequenceFetcher |
Line # 44 |
20 |
5 |
1.0100% |
---|---|---|---|---|
SequenceFetcher() SequenceFetcher() | 5252 | 8.08 | 1.01 | 1.0 1.0100% |
getNonAlignmentSources() : String[] getNonAlignmentSources() : String[] | 7474 | 12.012 | 4.04 | 1.0 1.0100% |
1.0
|
jalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwicejalview.io.CrossRef2xmlTests.openCrossrefsForEnsemblTwice | 1PASS | ||
1.0
|
jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges | 1PASS | ||
1.0
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
1.0
|
jalview.ws.SequenceFetcherTest.testNoDuplicatesInFetchDbRefsjalview.ws.SequenceFetcherTest.testNoDuplicatesInFetchDbRefs | 1PASS | ||
1.0
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.gui.AlignViewportTest.testDeregisterMapping_withNoReferencejalview.gui.AlignViewportTest.testDeregisterMapping_withNoReference | 1PASS | ||
0.6785714
|
jalview.io.vcf.VCFLoaderTest.testDoLoad_reverseStrandjalview.io.vcf.VCFLoaderTest.testDoLoad_reverseStrand | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettingsjalview.project.Jalview2xmlTests.testStoreAndRecoverReferenceSeqSettings | 1PASS | ||
0.6785714
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumnjalview.renderer.seqfeatures.FeatureRendererTest.testFindFeaturesAtColumn | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeightjalview.project.Jalview2xmlTests.testStoreAndRestoreIDwidthAndAnnotationHeight | 1PASS | ||
0.6785714
|
jalview.util.ColorUtilsTest.testGetAWTColorFromNamejalview.util.ColorUtilsTest.testGetAWTColorFromName | 1PASS | ||
0.6785714
|
jalview.gui.PopupMenuTest.testBuildLinkMenujalview.gui.PopupMenuTest.testBuildLinkMenu | 1PASS | ||
0.6785714
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.6785714
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_annotationsjalview.gui.SeqPanelTest.testFindMousePosition_wrapped_annotations | 1PASS | ||
0.6785714
|
jalview.util.ColorUtilsTest.testGetGraduatedColourjalview.util.ColorUtilsTest.testGetGraduatedColour | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testTCoffeeScoresjalview.project.Jalview2xmlTests.testTCoffeeScores | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.6785714
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistancesjalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances | 1PASS | ||
0.6785714
|
jalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerysjalview.gui.structurechooser.StructureChooserQuerySourceTest.cascadingThreeDBandPDBQuerys | 1PASS | ||
0.6785714
|
jalview.renderer.seqfeatures.FeatureRendererTest.testGetColourjalview.renderer.seqfeatures.FeatureRendererTest.testGetColour | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.gui.AlignViewportTest.testDeregisterMapping_onCloseViewjalview.gui.AlignViewportTest.testDeregisterMapping_onCloseView | 1PASS | ||
0.6785714
|
jalview.gui.ColourMenuHelperTest.testAddMenuItems_nucleotidejalview.gui.ColourMenuHelperTest.testAddMenuItems_nucleotide | 1PASS | ||
0.6785714
|
jalview.gui.QuitHandlerTest.testUnsavedChangesjalview.gui.QuitHandlerTest.testUnsavedChanges | 1PASS | ||
0.6785714
|
jalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverviewjalview.gui.AlignmentPanelTest.testSetOverviewTitle_automaticOverview | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.6785714
|
jalview.datamodel.VisibleRowsIteratorTest.testHasNextAndNextEndHiddenjalview.datamodel.VisibleRowsIteratorTest.testHasNextAndNextEndHidden | 1PASS | ||
0.6785714
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scaleAbovejalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scaleAbove | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.util.ColorUtilsTest.testCreateColourFromNamejalview.util.ColorUtilsTest.testCreateColourFromName | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFiltersjalview.project.Jalview2xmlTests.testSaveLoadFeatureColoursAndFilters | 1PASS | ||
0.6785714
|
jalview.gui.SeqCanvasTest.testCalculateWrappedGeometry_noAnnotationsjalview.gui.SeqCanvasTest.testCalculateWrappedGeometry_noAnnotations | 1PASS | ||
0.6785714
|
jalview.gui.AlignViewportTest.testSetGlobalColourSchemejalview.gui.AlignViewportTest.testSetGlobalColourScheme | 1PASS | ||
0.6785714
|
jalview.io.BackupFilesTest.backupsEnabledNoRollMaxTestjalview.io.BackupFilesTest.backupsEnabledNoRollMaxTest | 1PASS | ||
0.6785714
|
jalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_splicedjalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_spliced | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testPcaViewAssociationjalview.project.Jalview2xmlTests.testPcaViewAssociation | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.6785714
|
jalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGapsjalview.schemes.PIDColourSchemeTest.testFindColour_ignoreGaps | 1PASS | ||
0.6785714
|
jalview.gui.AlignViewportTest.testGetConsensusSeqjalview.gui.AlignViewportTest.testGetConsensusSeq | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.6785714
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_HiddenColumnsjalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_HiddenColumns | 1PASS | ||
0.6785714
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.6785714
|
jalview.gui.AssociatePDBFileTest.testAssociatePDBFilejalview.gui.AssociatePDBFileTest.testAssociatePDBFile | 1PASS | ||
0.6785714
|
jalview.io.BackupFilesTest.backupsEnabledRollMaxTestjalview.io.BackupFilesTest.backupsEnabledRollMaxTest | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColoursjalview.project.Jalview2xmlTests.testStoreAndRecoverAnnotationRowElementColours | 1PASS | ||
0.6785714
|
jalview.gui.QuitHandlerTest.testForceQuitjalview.gui.QuitHandlerTest.testForceQuit | 1PASS | ||
0.6785714
|
jalview.gui.AlignFrameTest.testNewView_colourThresholdsjalview.gui.AlignFrameTest.testNewView_colourThresholds | 1PASS | ||
0.6785714
|
jalview.gui.AnnotationLabelsTest2.testIdWidthChangesjalview.gui.AnnotationLabelsTest2.testIdWidthChanges | 1PASS | ||
0.6785714
|
jalview.datamodel.AlignmentViewTest.testGetVisibleAlignmentGapCharjalview.datamodel.AlignmentViewTest.testGetVisibleAlignmentGapChar | 1PASS | ||
0.6785714
|
jalview.gui.SeqPanelTest.testAmbiguousAminoAcidGetsStatusMessagejalview.gui.SeqPanelTest.testAmbiguousAminoAcidGetsStatusMessage | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjectsjalview.project.Jalview2xmlTests.testAutoShowOverviewForLegacyProjects | 1PASS | ||
0.6785714
|
jalview.io.cache.JvCacheableInputBoxTest.updateCacheTestjalview.io.cache.JvCacheableInputBoxTest.updateCacheTest | 1PASS | ||
0.6785714
|
jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInEitherOneSeqjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInEitherOneSeq | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntryjalview.project.Jalview2xmlTests.testStoreAndRecoverPDBEntry | 1PASS | ||
0.6785714
|
jalview.gui.ScalePanelTest.testPreventNegativeStartColumnjalview.gui.ScalePanelTest.testPreventNegativeStartColumn | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholdsjalview.project.Jalview2xmlTests.testStoreAndRecoverColourThresholds | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.6785714
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_noAnnotationsjalview.gui.SeqPanelTest.testFindMousePosition_wrapped_noAnnotations | 1PASS | ||
0.6785714
|
jalview.io.FeaturesFileTest.testParsejalview.io.FeaturesFileTest.testParse | 1PASS | ||
0.6785714
|
jalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotationjalview.io.AnnotatedPDBFileInputTest.testJalviewProjectRelocationAnnotation | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testMergeDatasetsforViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforViews | 1PASS | ||
0.6785714
|
jalview.urls.UrlLinkTableModelTest.testDeletablejalview.urls.UrlLinkTableModelTest.testDeletable | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testPAEsaveRestorejalview.project.Jalview2xmlTests.testPAEsaveRestore | 1PASS | ||
0.6785714
|
jalview.gui.ColourMenuHelperTest.testAddMenuItems_simpleOnlyjalview.gui.ColourMenuHelperTest.testAddMenuItems_simpleOnly | 1PASS | ||
0.6785714
|
jalview.datamodel.ColumnSelectionTest.testEqualsjalview.datamodel.ColumnSelectionTest.testEquals | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqsjalview.project.Jalview2xmlTests.testStoreAndRecoverGroupRepSeqs | 1PASS | ||
0.6785714
|
jalview.datamodel.SearchResultsTest.testMatchContainsjalview.datamodel.SearchResultsTest.testMatchContains | 1PASS | ||
0.6785714
|
jalview.ext.jmol.JmolParserTest.testAlignmentLoaderjalview.ext.jmol.JmolParserTest.testAlignmentLoader | 1PASS | ||
0.6785714
|
jalview.gui.AnnotationLabelsTest2.testIdWidthNoChangesjalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.io.gff.Gff3HelperTest.testGetDescriptionjalview.io.gff.Gff3HelperTest.testGetDescription | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverOverview | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.6785714
|
jalview.util.ColorUtilsTest.testParseColourStringjalview.util.ColorUtilsTest.testParseColourString | 1PASS | ||
0.6785714
|
jalview.gui.ProgressBarTest.testSetProgressBarjalview.gui.ProgressBarTest.testSetProgressBar | 1PASS | ||
0.6785714
|
jalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroupjalview.gui.PairwiseAlignmentPanelTest.testConstructor_noSelectionGroup | 1PASS | ||
0.6785714
|
jalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_forwardToReversejalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_forwardToReverse | 1PASS | ||
0.6785714
|
jalview.gui.AnnotationLabelsTest2.testIdWidthNoChangesjalview.gui.AnnotationLabelsTest2.testIdWidthNoChanges | 1PASS | ||
0.6785714
|
jalview.gui.StructureChooserTest.populateFilterComboBoxTestjalview.gui.StructureChooserTest.populateFilterComboBoxTest | 1PASS | ||
0.6785714
|
jalview.analysis.AverageDistanceEngineTest.testUPGMAEnginejalview.analysis.AverageDistanceEngineTest.testUPGMAEngine | 1PASS | ||
0.6785714
|
jalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testAddStrToSingleSeqViewJMol | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.6785714
|
jalview.io.FeaturesFileTest.testPrintJalviewFormat_withFiltersjalview.io.FeaturesFileTest.testPrintJalviewFormat_withFilters | 1PASS | ||
0.6785714
|
jalview.datamodel.AlignmentTest.testAlignAs_proteinAsCdnajalview.datamodel.AlignmentTest.testAlignAs_proteinAsCdna | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testCopyViewSettingsjalview.project.Jalview2xmlTests.testCopyViewSettings | 1PASS | ||
0.6785714
|
jalview.gui.SeqPanelTest.testFindColumn_and_FindAlignmentColumn_wrappedjalview.gui.SeqPanelTest.testFindColumn_and_FindAlignmentColumn_wrapped | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testColourByAnnotScoresjalview.project.Jalview2xmlTests.testColourByAnnotScores | 1PASS | ||
0.6785714
|
jalview.ext.pymol.PymolManagerTest.testGetPostRequestjalview.ext.pymol.PymolManagerTest.testGetPostRequest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.6785714
|
jalview.util.DBRefUtilsTest.testGetCanonicalNamejalview.util.DBRefUtilsTest.testGetCanonicalName | 1PASS | ||
0.6785714
|
jalview.io.FeaturesFileTest.testPrintGffFormat_withFiltersjalview.io.FeaturesFileTest.testPrintGffFormat_withFilters | 1PASS | ||
0.6785714
|
jalview.gui.SeqPanelTest.testFindColumn_unwrappedjalview.gui.SeqPanelTest.testFindColumn_unwrapped | 1PASS | ||
0.6785714
|
jalview.ext.jmol.JmolParserTest.testFileParserjalview.ext.jmol.JmolParserTest.testFileParser | 1PASS | ||
0.6785714
|
jalview.gui.FeatureSettingsTest.testSaveLoadjalview.gui.FeatureSettingsTest.testSaveLoad | 1PASS | ||
0.6785714
|
jalview.io.AnnotationExporterTest.testAnnotationExportAsCSVjalview.io.AnnotationExporterTest.testAnnotationExportAsCSV | 1PASS | ||
0.6785714
|
jalview.gui.AnnotationChooserTest.testResetOriginalStatejalview.gui.AnnotationChooserTest.testResetOriginalState | 1PASS | ||
0.6785714
|
jalview.gui.PopupMenuTest.testHideInsertionsjalview.gui.PopupMenuTest.testHideInsertions | 1PASS | ||
0.6785714
|
jalview.gui.AnnotationChooserTest.testSelectType_showForAlljalview.gui.AnnotationChooserTest.testSelectType_showForAll | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testRNAStructureRecoveryjalview.project.Jalview2xmlTests.testRNAStructureRecovery | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.io.BackupFilesTest.noBackupsEnabledTestjalview.io.BackupFilesTest.noBackupsEnabledTest | 1PASS | ||
0.6785714
|
jalview.util.CaseInsensitiveStringTest.testEqualsjalview.util.CaseInsensitiveStringTest.testEquals | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.6785714
|
jalview.workers.AlignCalcManagerTest.testRemoveWorkerForAnnotationjalview.workers.AlignCalcManagerTest.testRemoveWorkerForAnnotation | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.6785714
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.6785714
|
jalview.io.BackupFilesTest.backupsEnabledReverseRollMaxTestjalview.io.BackupFilesTest.backupsEnabledReverseRollMaxTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.6785714
|
jalview.schemes.ColourSchemesTest.testRegisterColourSchemejalview.schemes.ColourSchemesTest.testRegisterColourScheme | 1PASS | ||
0.6785714
|
jalview.gui.StructureViewerTest.testGetSequencesForPdbsjalview.gui.StructureViewerTest.testGetSequencesForPdbs | 1PASS | ||
0.6785714
|
jalview.datamodel.AlignmentViewTest.testGetVisibleContigsjalview.datamodel.AlignmentViewTest.testGetVisibleContigs | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.6785714
|
jalview.util.ColorUtilsTest.testBrighterThanjalview.util.ColorUtilsTest.testBrighterThan | 1PASS | ||
0.6785714
|
jalview.gui.ScalePanelTest.testSelectColumns_withHiddenjalview.gui.ScalePanelTest.testSelectColumns_withHidden | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviewsjalview.project.Jalview2xmlTests.testStoreAndRecoverExpandedviews | 1PASS | ||
0.6785714
|
jalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResiduejalview.renderer.seqfeatures.FeatureRendererTest.testFindComplementFeaturesAtResidue | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testMergeDatasetsforManyViewsjalview.project.Jalview2xmlTests.testMergeDatasetsforManyViews | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.gatherViewsHerejalview.project.Jalview2xmlTests.gatherViewsHere | 1PASS | ||
0.6785714
|
jalview.datamodel.SearchResultsTest.testAddResultjalview.datamodel.SearchResultsTest.testAddResult | 1PASS | ||
0.6785714
|
jalview.gui.AlignViewportTest.testDeregisterMapping_withReferencejalview.gui.AlignViewportTest.testDeregisterMapping_withReference | 1PASS | ||
0.6785714
|
jalview.urls.UrlLinkTableModelTest.testValuesjalview.urls.UrlLinkTableModelTest.testValues | 1PASS | ||
0.6785714
|
jalview.datamodel.AlignmentTest.testAppendjalview.datamodel.AlignmentTest.testAppend | 1PASS | ||
0.6785714
|
jalview.gui.AnnotationChooserTest.testBuildActionButtonsPaneljalview.gui.AnnotationChooserTest.testBuildActionButtonsPanel | 1PASS | ||
0.6785714
|
jalview.io.FeaturesFileTest.testPrintGffFormatjalview.io.FeaturesFileTest.testPrintGffFormat | 1PASS | ||
0.6785714
|
jalview.datamodel.SearchResultsTest.testToStringjalview.datamodel.SearchResultsTest.testToString | 1PASS | ||
0.6785714
|
jalview.datamodel.SearchResultsTest.testInvolvesSequencejalview.datamodel.SearchResultsTest.testInvolvesSequence | 1PASS | ||
0.6785714
|
jalview.datamodel.SequenceTest.testAddSequenceFeaturesjalview.datamodel.SequenceTest.testAddSequenceFeatures | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.6785714
|
jalview.structure.StructureSelectionManagerTest.testSetMapping_seqFeaturesjalview.structure.StructureSelectionManagerTest.testSetMapping_seqFeatures | 1PASS | ||
0.6785714
|
jalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInBothSeqsjalview.analysis.scoremodels.SecondaryStructureDistanceModelTest.testFindDistances_withSSUndefinedInBothSeqs | 1PASS | ||
0.6785714
|
jalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_reverseToForwardjalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_reverseToForward | 1PASS | ||
0.6785714
|
jalview.util.ColorUtilsTest.testBleachColourjalview.util.ColorUtilsTest.testBleachColour | 1PASS | ||
0.6785714
|
jalview.gui.AlignViewportTest.testSetSelectionGroupjalview.gui.AlignViewportTest.testSetSelectionGroup | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.gui.AnnotationChooserTest.testDeselectType_showForAlljalview.gui.AnnotationChooserTest.testDeselectType_showForAll | 1PASS | ||
0.6785714
|
jalview.io.WindowsFileLoadAndSaveTest.loadAndSaveAlignmentjalview.io.WindowsFileLoadAndSaveTest.loadAndSaveAlignment | 1PASS | ||
0.6785714
|
jalview.schemes.HydrophobicColourSchemeTest.testFindColourjalview.schemes.HydrophobicColourSchemeTest.testFindColour | 1PASS | ||
0.6785714
|
jalview.io.JSONFileTest.testGrpParsed_colourNonejalview.io.JSONFileTest.testGrpParsed_colourNone | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.6785714
|
jalview.gui.QuitHandlerTest.testWaitForSaveQuitjalview.gui.QuitHandlerTest.testWaitForSaveQuit | 1PASS | ||
0.6785714
|
jalview.math.SparseMatrixTest.testConstructorjalview.math.SparseMatrixTest.testConstructor | 1PASS | ||
0.6785714
|
jalview.util.ColorUtilsTest.testToTkCodejalview.util.ColorUtilsTest.testToTkCode | 1PASS | ||
0.6785714
|
jalview.datamodel.AlignmentTest.testAssertDatasetIsNormalisedjalview.datamodel.AlignmentTest.testAssertDatasetIsNormalised | 1PASS | ||
0.6785714
|
jalview.gui.DesktopTests.testInternalCopyPastejalview.gui.DesktopTests.testInternalCopyPaste | 1PASS | ||
0.6785714
|
jalview.gui.AlignFrameTest.testColourThresholdActionsjalview.gui.AlignFrameTest.testColourThresholdActions | 1PASS | ||
0.6785714
|
jalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequencejalview.gui.SeqPanelTest.testFindMousePosition_wrapped_scales_longSequence | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverviewjalview.project.Jalview2xmlTests.testStoreAndRecoverNoOverview | 1PASS | ||
0.6785714
|
jalview.gui.AlignmentPanelTest.testCalculateIdWidth_noArgsjalview.gui.AlignmentPanelTest.testCalculateIdWidth_noArgs | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMadejalview.project.Jalview2xmlTests.noDuplicatePdbMappingsMade | 1PASS | ||
0.6785714
|
jalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMoljalview.ext.jmol.JmolViewerTest.testSingleSeqViewJMol | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.6785714
|
jalview.controller.AlignViewControllerTest.testSelectColumnsWithHighlightjalview.controller.AlignViewControllerTest.testSelectColumnsWithHighlight | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.6785714
|
jalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_forwardToForwardjalview.io.gff.Gff3HelperTest.testProcessCdnaMatch_forwardToForward | 1PASS | ||
0.6785714
|
jalview.util.ColorUtilsTest.testDarkerThanjalview.util.ColorUtilsTest.testDarkerThan | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.6785714
|
jalview.gui.AnnotationChooserTest.testDeselectType_hideForSelectedjalview.gui.AnnotationChooserTest.testDeselectType_hideForSelected | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocusjalview.project.Jalview2xmlTests.testStoreAndRecoverGeneLocus | 1PASS | ||
0.6785714
|
jalview.io.vcf.VCFLoaderTest.testDoLoadjalview.io.vcf.VCFLoaderTest.testDoLoad | 1PASS | ||
0.6785714
|
jalview.io.ScoreMatrixFileTest.testParseMatrix_ncbiBadDelimiterjalview.io.ScoreMatrixFileTest.testParseMatrix_ncbiBadDelimiter | 1PASS | ||
0.6785714
|
jalview.gui.AlignViewportTest.testSetGetHasSearchResultsjalview.gui.AlignViewportTest.testSetGetHasSearchResults | 1PASS | ||
0.6785714
|
jalview.datamodel.SearchResultsTest.testMatchConstructorjalview.datamodel.SearchResultsTest.testMatchConstructor | 1PASS | ||
0.6785714
|
jalview.datamodel.SearchResultsTest.testAppendResultjalview.datamodel.SearchResultsTest.testAppendResult | 1PASS | ||
0.6785714
|
jalview.urls.UrlLinkTableModelTest.testEditablejalview.urls.UrlLinkTableModelTest.testEditable | 1PASS | ||
0.6785714
|
jalview.datamodel.SearchResultsTest.testMarkColumnsjalview.datamodel.SearchResultsTest.testMarkColumns | 1PASS | ||
0.6785714
|
jalview.project.Jalview2xmlTests.viewRefPdbAnnotationjalview.project.Jalview2xmlTests.viewRefPdbAnnotation | 1PASS | ||
0.6785714
|
jalview.gui.PopupMenuTest.testBuildAnnotationTypesMenusjalview.gui.PopupMenuTest.testBuildAnnotationTypesMenus | 1PASS | ||
0.6785714
|
jalview.gui.StructureChooserTest.displayTDBQueryTestjalview.gui.StructureChooserTest.displayTDBQueryTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest2.structureOpeningArgsTestjalview.bin.CommandsTest2.structureOpeningArgsTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.ws.dbsources.UniprotTest.testimportOfProblemEntriesjalview.ws.dbsources.UniprotTest.testimportOfProblemEntries | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.commandsOpenTestjalview.bin.CommandsTest.commandsOpenTest | 1PASS | ||
0.6785714
|
jalview.util.ShiftListTest.testParseMapjalview.util.ShiftListTest.testParseMap | 1PASS | ||
0.6785714
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances_withParamsjalview.analysis.scoremodels.FeatureDistanceModelTest.testFindDistances_withParams | 1PASS | ||
0.6785714
|
jalview.io.FeaturesFileTest.testParse_pureGff3jalview.io.FeaturesFileTest.testParse_pureGff3 | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.6785714
|
jalview.util.FormatTest.testFormat_scientificjalview.util.FormatTest.testFormat_scientific | 1PASS | ||
0.6785714
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.6785714
|
jalview.gui.StructureChooserTest.openStructureFileForSequenceTestjalview.gui.StructureChooserTest.openStructureFileForSequenceTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.6785714
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_hiddenFirstColumnjalview.analysis.scoremodels.FeatureDistanceModelTest.testFeatureScoreModel_hiddenFirstColumn | 1PASS | ||
0.6785714
|
jalview.gui.QuitHandlerTest.testSavedAlignmentChangesjalview.gui.QuitHandlerTest.testSavedAlignmentChanges | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.allLinkedIdsTestjalview.bin.CommandsTest.allLinkedIdsTest | 1PASS | ||
0.6785714
|
jalview.analysis.scoremodels.FeatureDistanceModelTest.testFindFeatureAt_PointFeaturejalview.analysis.scoremodels.FeatureDistanceModelTest.testFindFeatureAt_PointFeature | 1PASS | ||
0.6785714
|
jalview.math.RotatableMatrixTest.testPrintjalview.math.RotatableMatrixTest.testPrint | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageAnnotationsOutputTestjalview.bin.CommandsTest.structureImageAnnotationsOutputTest | 1PASS | ||
0.6785714
|
jalview.gui.QuitHandlerTest.testNoGUIUnsavedChangesjalview.gui.QuitHandlerTest.testNoGUIUnsavedChanges | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.structureImageOutputTestjalview.bin.CommandsTest.structureImageOutputTest | 1PASS | ||
0.6785714
|
jalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTestjalview.bin.CommandsTest.argFilesGlobAndSubstitutionsTest | 1PASS | ||
0.32142857
|
jalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbsjalview.ws.seqfetcher.DbRefFetcherTest.testStandardProtDbs | 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; | ||||||
22 | |||||||
23 | import jalview.ext.ensembl.EnsemblGene; | ||||||
24 | import jalview.ws.dbsources.EBIAlfaFold; | ||||||
25 | import jalview.ws.dbsources.EmblCdsSource; | ||||||
26 | import jalview.ws.dbsources.EmblSource; | ||||||
27 | import jalview.ws.dbsources.Pdb; | ||||||
28 | import jalview.ws.dbsources.PfamFull; | ||||||
29 | import jalview.ws.dbsources.PfamSeed; | ||||||
30 | import jalview.ws.dbsources.RfamSeed; | ||||||
31 | import jalview.ws.dbsources.TDBeacons; | ||||||
32 | import jalview.ws.dbsources.Uniprot; | ||||||
33 | import jalview.ws.seqfetcher.ASequenceFetcher; | ||||||
34 | import jalview.ws.seqfetcher.DbSourceProxy; | ||||||
35 | |||||||
36 | import java.util.ArrayList; | ||||||
37 | import java.util.Collections; | ||||||
38 | import java.util.List; | ||||||
39 | |||||||
40 | /** | ||||||
41 | * This implements the run-time discovery of sequence database clients. | ||||||
42 | * | ||||||
43 | */ | ||||||
|
|||||||
44 | public class SequenceFetcher extends ASequenceFetcher | ||||||
45 | { | ||||||
46 | /** | ||||||
47 | * Thread safe construction of database proxies TODO: extend to a configurable | ||||||
48 | * database plugin mechanism where classes are instantiated by reflection and | ||||||
49 | * queried for their DbRefSource and version association. | ||||||
50 | * | ||||||
51 | */ | ||||||
|
|||||||
52 | 16 | public SequenceFetcher()... | |||||
53 | { | ||||||
54 | 16 | addDBRefSourceImpl(EnsemblGene.class); | |||||
55 | // addDBRefSourceImpl(EnsemblGenomes.class); | ||||||
56 | 16 | addDBRefSourceImpl(EmblSource.class); | |||||
57 | 16 | addDBRefSourceImpl(EmblCdsSource.class); | |||||
58 | 16 | addDBRefSourceImpl(Uniprot.class); | |||||
59 | // not a sequence source yet | ||||||
60 | // addDBRefSourceImpl(TDBeacons.class); | ||||||
61 | 16 | addDBRefSourceImpl(Pdb.class); | |||||
62 | 16 | addDBRefSourceImpl(PfamFull.class); | |||||
63 | 16 | addDBRefSourceImpl(PfamSeed.class); | |||||
64 | 16 | addDBRefSourceImpl(RfamSeed.class); | |||||
65 | // Technically not a database cross reference we fetch directly | ||||||
66 | // Useful for AlphaFold debugging | ||||||
67 | // addDBRefSourceImpl(EBIAlfaFold.class); | ||||||
68 | } | ||||||
69 | |||||||
70 | /** | ||||||
71 | * return an ordered list of database sources excluding alignment only | ||||||
72 | * databases | ||||||
73 | */ | ||||||
|
|||||||
74 | 3465 | public String[] getNonAlignmentSources()... | |||||
75 | { | ||||||
76 | 3465 | String[] srcs = this.getSupportedDb(); | |||||
77 | 3465 | List<String> src = new ArrayList<>(); | |||||
78 | |||||||
79 | 31185 | for (int i = 0; i < srcs.length; i++) | |||||
80 | { | ||||||
81 | 27720 | boolean accept = true; | |||||
82 | 27720 | for (DbSourceProxy dbs : getSourceProxy(srcs[i])) | |||||
83 | { | ||||||
84 | // Skip the alignment databases for the moment - they're not useful for | ||||||
85 | // verifying a single sequence against its reference source | ||||||
86 | 27720 | if (dbs.isAlignmentSource()) | |||||
87 | { | ||||||
88 | 10395 | accept = false; | |||||
89 | 10395 | break; | |||||
90 | } | ||||||
91 | } | ||||||
92 | 27720 | if (accept) | |||||
93 | { | ||||||
94 | 17325 | src.add(srcs[i]); | |||||
95 | } | ||||||
96 | } | ||||||
97 | |||||||
98 | 3465 | Collections.sort(src, String.CASE_INSENSITIVE_ORDER); | |||||
99 | 3465 | return src.toArray(new String[src.size()]); | |||||
100 | } | ||||||
101 | } |