Class name	Method name	Groups
jalview.util.MathUtilsTest
@Test
	testGcd	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.SeqsetUtilsTest
@Test
	testSeqFeatureAddition	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.controller.AlignViewControllerTest
@Test
	testSelectColumnsWithHighlight	Functional
	testFindColumnsWithFeature	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.JSONUtilsTest
@Test
	testArrayToList	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.SequenceRendererTest
@Test
	testGetResidueColour_WithGroup	Functional
@BeforeClass
	setUpBeforeClass
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.ext.rbvi.chimera.ChimeraXCommandsTest
@Test
	testSetAttributes	Functional
	testSuperposeStructures	Functional
	testShowBackbone	Functional
	testGetResidueSpec	Functional
	testCloseViewer	Functional
	testColourByCharge	Functional
	testGetSelectedResidues	Functional
	testSaveSession	Functional
	testColourBySequence	Functional
	testStopNotifications	Functional
	testGetModelStartNo	Functional
	testGetAtomSpec	Functional
	testColourByChain	Functional
	testSetAttribute	Functional
	testGetAtomSpec_alphaOnly	Functional
	testOpenCommandFile	Functional
	testListResidueAttributes	Functional
	testFocusView	Functional
	testStartNotifications	Functional
	testGetColourCommand	Functional
	testOpenSession	Functional
	testSetBackgroundColour	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.schemes.ResiduePropertiesTest
@Test
	testGetResidues_peptide	Functional
	testPhysicoChemicalProperties	Functional
	testCodonTranslate	Functional
	testCodonTranslate_ambiguityCodes	Functional
	testGetResidues_nucleotide	Functional
	testGetSingleCharacterCode	Functional
	testGetDssp3State	Functional
	testGetCanonicalAminoAcid	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.PfamFormatInputTest
@Test
	testPfamFormatValidLimits	Functional
	testPfamFormatNoLimits	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ext.rbvi.chimera.ChimeraCommandsTest
@Test
	testGetResidueSpec	Functional
	testCloseViewer	Functional
	testSaveSession	Functional
	testGetResidueAttributes	Functional
	testColourBySequence	Functional
	testStopNotifications	Functional
	testGetModelStartNo	Functional
	testFocusView	Functional
	testStartNotifications	Functional
	testMakeAttributeName	Functional
	testSetAttributes	Functional
	testSuperposeStructures	Functional
	testShowBackbone	Functional
	testColourByCharge	Functional
	testGetSelectedResidues	Functional
	testGetAtomSpec	Functional
	testColourByChain	Functional
	testSetAttribute	Functional
	testGetAtomSpec_alphaOnly	Functional
	testOpenCommandFile	Functional
	testListResidueAttributes	Functional
	testGetColourCommand	Functional
	testLoadFile	Functional
	testOpenSession	Functional
	testSetBackgroundColour	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.commands.EditCommandTest
@Test
	testAddEdit_removeAllGaps	Functional
	testUndo_cut	Functional
	testPriorState_removeAllGaps	Functional
	testPriorState_removeGappedCols	Functional
	testAddEdit_multipleDeleteGap	Functional
	testReplace_withGaps	Functional
	testPriorState_singleInsertWithOffset	Functional
	testUndo_insertGap	Functional
	testReplace	Functional
	testAddEdit_multipleInsertGap	Functional
	testCut_withFeatures5prime	Functional
	testPriorState_multipleInserts	Functional
	testAppendEdit_insertGap	Functional
	testReplaceFirstResiduesWithGaps	Functional
	testPriorState_singleInsert	Functional
	testAddEdit_groupInsertGaps	Functional
	testPriorState_singleDelete	Functional
	testCut	Functional
	testPriorState_removeGapsMultipleSeqs	Functional
	testUndo_multipleInsertGaps	Functional
	testUndo_deleteGap	Functional
	testCut_withFeatures	Functional
	testPaste_undo_redo	Functional
	testAppendEdit_deleteGap	Functional
	testUndo_multipleCommands	Functional
	testCut_withFeatures_exhaustive	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.analysis.CrossRefTest
@Test
	testFindXrefSequences_indirectDbrefToNucleotide	Functional
	testFindXrefSequences_noDbrefs	Functional
	testSameSequence	Functional
	testFindXrefSequences_indirectDbrefToProtein	Functional
	testFindXrefSourcesForSequence_proteinToDna	Functional
	testFindXrefSequences_uniprotEmblManyToMany	Functional_Failing
	testFindXrefSequences_withFetch	Functional_Failing
	testFindXrefSequences_forGeneAndTranscripts	Functional_Failing
	testSearchDataset	Functional
	testFindXDbRefs	Functional
	testFindXrefSequences_fromDbRefMap	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDown
jalview.gui.FeatureSettingsTest
@Test
	testSaveLoad	Functional
	testGetColorTooltip	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.WindowsFileLoadAndSaveTest
@Test
	loadAndSaveAlignment	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	cleanupTmpFiles
jalview.math.SparseMatrixTest
@Test
	testPreMultiply_sparseProduct	Functional
	testTred_reproducible	Functional
	testTranspose	Functional
	testSign	Timing
	testConstructor	Functional
	testTqli_matchesMatrix	Functional
	testPreMultiply_tooFewColumns	Functional
	testGetValue
	testPreMultiply	Functional
	testTred_matchesMatrix	Functional
	testPreMultiply_tooManyColumns	Functional
	testPostMultiply	Functional
	testFillRatio	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.AlignmentAnnotationTests
@Test
	testCopyConstructor	Functional
	testAdjustForAlignment	Functional
	testLiftOver	Functional
	testIsQuantitative	Functional
	testGetDefaultRnaHelixSymbol	Functional
	testMakeVisibleAnnotation	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.BioJsHTMLOutputTest
@Test
	expectedNullPointerException	Functional
	getBioJsMSAVersions	Functional
	testBioJsUpdate	Network
	getJalviewAlignmentAsJsonString	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.bin.CommandLineOperations
@Test
	testAllInputOperations	Functional
	reportCurrentWorkingDirectory	Functional
	testHeadlessModeOutputOperations	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.StructureChooserTest
@Test
	sanitizeSeqNameTest	Functional
	populateFilterComboBoxTest	Functional
	fetchStructuresInfoTest	Network
	displayTDBQueryTest	Functional
	fetchStructuresInfoMockedTest	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
	tearDown
@AfterClass
jalview.ext.android.SparseIntArrayTest
@Test
	testAdd	Functional
	testCheckOverflow	Functional
	testPut	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.urls.UrlLinkTableModelTest
@Test
	testRowInsert	Functional
	testEditable	Functional
	testRowEditable	Functional
	testRowDelete	Functional
	testDeletable	Functional
	testInitialisation	Functional
	testCounts	Functional
	testColumns	Functional
	testValues	Functional
@BeforeClass
@BeforeMethod
	setup
@AfterMethod
@AfterClass
jalview.ws.dbsources.PfamFullTest
@Test
	testGetURL	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.structure.StructureCommandTest
@Test
	testEquals	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.SeqCigarTest
@Test
	testFindPosition	Functional
	testSomething	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.FeaturesFileTest
@Test
	testPrintGffFormat_withFilters	Functional
	testParse_mixedJalviewGff	Functional
	readGff3File	Functional
	testParse	Functional
	simpleGff3FileLoader	Functional
	testParse_pureGff3	Functional
	testPrintJalviewFormat	Functional
	testParse_jalviewFeaturesOnly	Functional
	testOutputFeatureFilters	Functional
	testPrintGffFormat	Functional
	testPrintJalviewFormat_withFilters	Functional
	simpleGff3FileClass	Functional
	testParseFilters	Functional
	simpleGff3RelaxedIdMatching	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.renderer.seqfeatures.FeatureRendererTest
@Test
	testGetColour	Functional
	testFindFeaturesAtColumn	Functional
	testFilterFeaturesForDisplay	Functional
	testFindAllFeatures	Functional
	testIsVisible	Functional
	testFindComplementFeaturesAtResidue	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.schemes.FeatureColourTest
@Test
	testGetColor_Graduated	Functional
	testParseJalviewFeatureColour	Functional
	testGetColor_colourByLabel	Functional
	testCopyConstructor	Functional
	testConstructors	Functional
	testGetColor_simpleColour	Functional
	testGetColor_colourByAttributeText	Functional
	testIsOutwithThreshold	Functional
	testGetDescription	Functional
	testGetColor_aboveBelowThreshold	Functional
	testToJalviewFormat	Functional
	testGetColor_GraduatedByAttributeValue	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.GeneticCodesTest
@Test
	testTranslate_standardTableAmbiguityCodes	Functional
	testTranslateCanonical	Functional
	testTranslate	Functional
	testGetCodeTables	Functional
	testTranslate_standardTable	Functional
	testTranslate_nonStandardTableAmbiguityCodes	Functional
	testGetCodeTable	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.viewmodel.OverviewDimensionsShowHiddenTest
@Test
	testFromMouseWithHiddenColsAtStart	Functional
	testSetBoxFromViewportHiddenColsAtEnd	Functional
	testFromMouseWithHiddenRowsInMiddle	Functional
	testSetBoxFromViewportHiddenColsInMiddle	Functional
	testFromMouseWithHiddenRowsAtStart	Functional
	testConstructor	Functional
	testPositionInBox	Functional
	testSetBoxFromViewportHiddenRowsAtStart	Functional
	testSetBoxFromViewportHiddenRowsAtEnd	Functional
	testDragging	Functional
	testFromMouseWithHiddenColsInMiddle	Functional
	testSetBoxFromViewport	Functional
	testFromMouseWithHiddenRowsAtStartWrapped	Functional
	testSetBoxFromMouseClick	Functional
	testSetBoxFromViewportHiddenRowsInMiddle	Functional
	testFromMouseWithHiddenColsAtEnd	Functional
	testSetBoxFromViewportHiddenColsAtStart	Functional
	testFromMouseWithHiddenRowsAtEnd	Functional
@BeforeClass
	setUpAlignment
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
	cleanUp
jalview.util.ComparisonTest
@Test
	testPID_includingGaps	Functional
	testIsNucleotideSequence	Functional
	testIsNucleotide_sequences	Functional
	testPID_ungappedOnly	Functional
	testIsSameResidue	Functional
	testIsNucleotide	Functional
	testIsGap	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
mc_view.BondTest
@Test
	testTranslate	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.ResidueCountTest
@Test
	test_unexpectedPeptide	Functional
	test_countNucleotide	Functional
	testPut	Functional
	testGetModalCount	Functional
	testGetSymbolCounts_nucleotide	Functional
	testGetSymbolCounts_peptide	Functional
	testOverflow	Functional
	test_countPeptide	Functional
	testToString	Functional
	testGetTooltip	Functional
	test_unexpectedNucleotide	Functional
	testAddGap	Functional
	testGetResiduesForCount	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.urls.AppletUrlProviderFactoryTest
@Test
	testCreateUrlProvider	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.MappingTest
@Test
	testIntersectVisContigs	Functional
	testCopyConstructor	Functional
	testToString	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.NewickFileTests
@Test
	testTreeIO	Functional
	testTreeIO	Functional
	testTreeIO	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.renderer.OverviewResColourFinderTest
@Test
	testGetResidueBoxColour_none	Functional
	testGetBoxColour
	testGetResidueBoxColour_zappo	Functional
	testGetResidueBoxColour_userdef	Functional
	testGetResidueBoxColour_group
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.structurechooser.StructureChooserQuerySourceTest
@Test
	cascadingThreeDBandPDBQuerys	Functional
	sanitizeSeqNameTest	Functional
	buildThreeDBQueryTest	Functional
	buildPDBQueryTest	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
	tearDown
@AfterClass
jalview.io.FileIOTester
@Test
	testGzipIo	Functional
	testNonGziplocalFileIO	Functional
	testGziplocalFileIO	Functional
	testIsGzipInputStream	Functional
	testStarsInFasta1	Functional
	testStarsInFasta2	Functional
	testNonGzipURLIO	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.structure.AtomSpecModelTest
@Test
	testGetRanges	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.CaseInsensitiveStringTest
@Test
	testHashcode	Functional
	testEquals	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.SequenceGroupTest
@Test
	testContains	Functional
	testAddOrRemove	Functional
	testConstructor_list	Functional
	testCopyConstructor	Functional
	testSetContext	Functional
	testGetColourScheme	Functional
	testAddSequence	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.gff.GffHelperBaseTest
@Test
	testParseAttributeMap	Functional
	testParseNameValuePairs	Functional
	testTrimMapping	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.SequenceFeatureTest
@Test
	testEqualsAndHashCode	Functional
	testGetValue	Functional
	testIsContactFeature	Functional
	testGetDetailsReport_virtualFeature	Functional
	testCopyConstructors	Functional
	testGetDetailsReport	Functional
	testGetStrand	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.PairwiseAlignmentPanelTest
@Test
	testConstructor_noSelectionGroup	Functional
	testConstructor_withSelectionGroup	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.StringUtilsTest
@Test
	testUrlEncode	Functional
	testStripHtmlTags	Functional
	testDeleteChars	Functional
	testArrayToSeparatorList	Functional
	testListToDelimitedString	Functional
	testSeparatorListToArray	Functional
	testGetLastToken	Functional
	testCompareVersions	Functional
	testUrlDecode	Functional
	testInsertCharAt	Functional
	testParseInt	Functional
	testToSentenceCase	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.CalculationChooserTest
@Test
	testGetApplicableScoreModels	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.schemes.ClustalxColourSchemeTest
@Test
	testFindColour_ignoreGaps	Functional
	testFindColour	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
mc_view.ResidueTest
@Test
	testFindAtom	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.UrlLinkTest
@Test
	testLinksWithTargets	Functional
	testUrlLinkCreationNoRegex	Functional
	testMakeUrlNoRegex	Functional
	testMakeUrlWithRegex	Functional
	testUrlLinkCreationWithRegex	Functional
	testCreateLinksFromSequence	Functional
	testCreateLinksForNonDynamic	Functional
	testCreateLinksFromNullSequence	Functional
	testLinkComparator	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.features.FeatureMatcherTest
@Test
	testMatches_byAttribute	Functional
	testGetAttribute	Functional
	testMatches_byLabel	Functional
	testGetMatcher	Functional
	testToString	Functional
	testIsByLabel	Functional
	testIsByScore	Functional
	testMatches_byScore	Functional
	testIsByAttribute	Functional
	testFromString	Functional
	testToStableString	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.SequenceIdMatcherTest
@Test
	test_seqIdNameEquals	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
mc_view.PDBChainTest
@Test
	testGetNewlineString	Functional
	testMakeBond	Functional
	testMakeCaBondList	Functional
	testMakeCaBondList_nucleotide	Functional
	testSetChainColours_colourScheme	Functional
	testMakeResidueList_withTempFactor	Functional
	testSetChainColours_colour	Functional
	testMakeResidueList_noAnnotation	Functional
	testMakeExactMapping	Functional
	testGetChargeColour	Functional
	testSetChargeColours	Functional
	testPrint	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.analysis.scoremodels.ScoreMatrixTest
@Test
	testBuildSymbolIndex	Functional
	testEqualsAndHashCode	Functional
	testSymmetric	Functional
	testBuildSymbolIndex_nonAscii	Functional
	testGetMaximumScore	Functional
	testComputePairwiseScores	Functional
	testConstructor_matrixTooSmall	Functional
	testGetMatrix	Functional
	testOutputMatrix_html	Functional
	testConstructor	Functional
	testConstructor_gapDash	Functional
	testOutputMatrix_roundTrip	Functional
	testGetMinimumScore	Functional
	testConstructor_matrixTooBig	Functional
	testcomputeSimilarity_matchShortestSequence	Functional
	testGetPairwiseScore	Functional
	testGetMatrixIndex	Functional
	testGetSize	Functional
	testIsSymmetric	Functional
	testBlosum62_values	Functional
	testConstructor_matrixNotSquare	Functional
	testcomputeSimilarity_matchLongestSequence	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.features.SequenceFeaturesTest
@Test
	testGetFeaturesForGroup	Functional
	testGetFeatureTypesForGroups	Functional
	testGetAllFeatures	Functional
	testVarargsToTypes	Functional
	testGetFeatureTypes_byOntology	Functional
	testGetTotalFeatureLength	Functional
	testSortFeatures	Functional
	testGetFeatureCount	Functional
	testGetFeaturesByOntology	Functional
	testIsOntologyTerm	Functional
	testGetNonPositionalFeatures	Functional
	testConstructor	Functional
	testDeleteAll	Functional
	testGetFeatureTypes	Functional
	testGetMinimumScore_getMaximumScore	Functional
	testDelete	Functional
	testFindFeatures	Functional
	testGetPositionalFeatures	Functional
	testGetFeatureGroups	Functional
	testHasFeatures	Functional
	testShiftFeatures	Functional
	testGetContactFeatures	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.SequenceDummyTest
@Test
	testBecome	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.FormatAdapterTest
@Test
	testRoundTrip	Functional
	testOneFormatRoundTrip	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.StructureViewerTest
@Test
	testGetSequencesForPdbs	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ws.SequenceFetcherTest
@Test
	testNoDuplicatesInFetchDbRefs	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.BackupFilesTest
@Test
	backupsEnabledNoRollMaxTest	Functional
	backupsEnabledReverseRollMaxTest	Functional
	noBackupsEnabledTest	Functional
	backupsEnabledRollMaxTest	Functional
	backupsEnabledSingleFileBackupTest	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	cleanupTmpFiles
jalview.schemes.ResidueColourSchemeTest
@Test
	testIsApplicableTo	Functional
	testGetName	Functional
	testIsApplicableTo_dynamicColourScheme	Functional
@BeforeClass
	setUp
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.urls.UrlProviderTest
@Test
	testSetDefaultUrl	Functional
	testSetDefaultUrlWrongly	Functional
	testInitUrlProvider	Functional
@BeforeClass
@BeforeMethod
	setup
@AfterMethod
@AfterClass
jalview.gui.AlignViewportTest
@Test
	testGetConsensusSeq	Functional
	testHideRevealSequences	Functional
	testDeregisterMapping_onCloseView	Functional
	testDeregisterMapping_withReference	Functional
	testDeregisterMapping_withNoReference	Functional
	testUpdateConservation_qualityOnly	Functional
	testSetGetHasSearchResults	Functional
	testSetSelectionGroup	Functional
	testShowOrDontShowOccupancy	Functional
	testSetGlobalColourScheme	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.analysis.TestAlignSeq
@Test
	testGetMappingForS1	Functional
	testPrintAlignment	Functional
	testExtractGaps	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.analysis.FinderTest
@Test
	testFind_findNext	Functional
	testFind_withHiddenColumns	Functional
	testFind_inDescription	Functional
	testFindAll	Functional
	testFindAll_sequenceIds	Functional
	testFindNext	Functional
	testFind_withHiddenColumnsAndSelection	Functional
	testFindAll_caseSensitive	Functional
	testFindAll_inSelection	Functional
	testFind_findAllInSelectionWithShortSequence	Functional
	testFind_ignoreHiddenColumns	Functional
	testFindNext_inSelection	Functional
	testFind_regex	Functional
	testFind_residueNumber	Functional
	testFind_findAll	Functional
	testFindAll_maximalResultOnly	Functional
@BeforeClass
	setUp	Functional
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
	tearDownAfterTest
@AfterClass
jalview.util.FormatTest
@Test
	testFormat_scientific_overflow	Functional
	testFormat_scientificTiming	Timing
	testForm_float	Functional
	testFormat_scientific	Functional
	testAppendPercentage	Functional
	testRepeat	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.PhylipFileTests
@Test
	testSequentialDataExtraction	Functional
	testInterleavedDataExtraction	Functional
	testSequentialIO	Functional
	testInterleavedIO	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.schemes.Blosum62ColourSchemeTest
@Test
	testFindColour	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
mc_view.AtomTest
@Test
	testStringConstructor_blankOccupancyTempFactor	Functional
	testStringConstructor	Functional
	testStringConstructor_malformed	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.StartRegionIteratorTest
@Test
	testBasicBoundsIterator	Functional
	testBoundsIteratorUsingNullCursor	Functional
	testBoundsIteratorUsingCursor	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.renderer.ResidueShaderTest
@Test
	testAboveThreshold	Functional
	testFindColour_gapColour	Functional
	testApplyConservation	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.fts.service.pdb.PDBFTSPanelTest
@Test
	populateCmbSearchTargetOptionsTest	Functional
	getFTSframeTitleTest
	testgetPDBIdwithSpecifiedChain	Functional
	testDecodeSearchTerm	Functional
	txt_search_ActionPerformedTest	External
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
	tearDown
@AfterClass
jalview.schemes.ColourSchemesTest
@Test
	testRegisterColourScheme	Functional
	testNameExists	Functional
	testGetColourScheme	Functional
	testGetColourSchemes	Functional
@BeforeClass
	setUpBeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.io.gff.GffHelperFactoryTest
@Test
	testGetHelper	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ws.dbsources.PfamSeedTest
@Test
	testGetURL	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.SparseCountTest
@Test
	testKeyAt_ValueAt	Functional
	testOverflow	Functional
	testUnderflow	Functional
	testAdd	Functional
	testPut	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.commands.TrimRegionCommandTest
@Test
	testTrimLeft_withUndoAndRedo	Functional
	testTrimLeft_noColumns	Functional
	testTrimRight_noColumns	Functional
	testTrimRight_oneColumn	Functional
	testTrimLeft_oneColumn	Functional
	testTrimRight_withUndoAndRedo	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.ext.htsjdk.TestHtsContigDb
@Test
	testGetSequenceProxy	Functional
	testGetSequenceProxy_indexed	Functional
	testCreateIndex
	testCreateFastaSequenceIndex	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ext.jmol.JmolCommandsTest
@Test
	testSuperposeStructures	Functional
	testShowBackbone	Functional
	testColourByCharge	Functional
	testSaveSession	Functional
	testColourBySequence	Functional
	testGetModelStartNo	Functional
	testGetColourBySequenceCommands_hiddenColumns	Functional
	testGetAtomSpec	Functional
	testColourByChain	Functional
	testFocusView	Functional
	testLoadFile	Functional
	testOpenSession	Functional
	testSetBackgroundColour	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.CodingUtilsTest
@Test
	testDecodeCodon	Functional
	testDecodeNucleotide	Functional
	testEncodeCodon	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.AnnotatedPDBFileInputTest
@Test
	checkNoDuplicates	Functional
	checkPDBSequenceFeatures	Functional
	checkAnnotationWiring	Functional
	testJalviewProjectRelocationAnnotation	Functional
	checkPDBannotationSource	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
	setup
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.fts.threedbeacons.TDBeaconsPanelTest
@Test
	populateCmbSearchTargetOptionsTest	Functional
	testgetUNIPROTid
	getFTSframeTitleTest
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
	tearDown
@AfterClass
jalview.structures.models.AAStructureBindingModelTest
@Test
	testImportPDBPreservesChainMappings	Functional
	testBuildColoursMap	Functional
	testFindSuperposableResidues_hiddenColumn	Functional
	testFindSuperposableResidues	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.datamodel.features.FeatureAttributesTest
@Test
	testAttributeNameComparator	Functional
	testDatatype	Functional
	testGetMinMax	Functional
	testGetDescription	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
	tearDown
@AfterClass
jalview.gui.HelpTest
@Test
	checkHelpTargets	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.AnnotationChooserTest
@Test
	testDeselectType_showForAll	Functional
	testBuildShowHidePanel	Functional
	testIsInActionScope_selectedScope	Functional
	testSelectType_hideForAll	Functional
	testSelectType_showForAll	Functional
	testDeselectType_hideForSelected	Functional
	testGetAnnotationTypes	Functional
	testBuildActionButtonsPanel	Functional
	testSelectType_hideForSelected	Functional
	testIsInActionScope_unselectedScope	Functional
	testBuildApplyToOptionsPanel_withSelectionGroup	Functional
	testBuildApplyToOptionsPanel_noSelectionGroup	Functional
	testResetOriginalState	Functional
	testBuildShowHideOptionsPanel	Functional
	testDeselectType_hideForAll	Functional
	testDeselectType_showForSelected	Functional
	testSelectType_showForSelected	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.analysis.DnaTest
@Test
	testCompareCodonPos_oneOnly	Functional
	testCompareCodonPos_isSymmetric	Functional
	testReverseCdna	Functional
	testCompareCodonPos	Functional
	testGetComplement	Functional
	testTranslateCdna_withUntranslatableCodons	Functional
	testTranslateCdna_simple	Functional
	testConvertCodon	Functional
	testTranslateCdna_hiddenColumns	Functional
	testTranslateCdna_sequenceOrderIndependent	Functional
	testTranslateCdna_withUntranslatableCodonsAndHiddenColumns	Functional
	testReverseSequence	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.renderer.seqfeatures.FeatureColourFinderTest
@Test
	testFindFeatureColour_graduatedFeatureColour	Functional
	testFindFeatureColour_featureTypeNotDisplayed	Functional
	testFindFeatureColour_singleFeatureNotAtPosition	Functional
	testFindFeatureColour_multipleFeaturesAtPositionNoTransparency	Functional
	testFindFeatureColour_noFeatures	Functional
	testFindFeatureColour_nestedFeatures	Functional
	testNoFeaturesDisplayed	Functional
	testFindFeatureColour_singleFeatureAtPosition	Functional
	testFindFeatureColour_transparencySingleFeature	Functional
	testFindFeatureColour_graduatedWithThreshold	Functional
	testFindFeatureColour_noFeaturesShown	Functional
	testFindFeatureColour_transparencyTwoFeatures	Functional
	testFindFeatureColour_gapPosition	Functional
	testFindFeatureColour_featureGroupNotDisplayed	Functional
	testFindFeatureColour_contactFeature	Functional
	testFindFeatureAtEnd	Functional
@BeforeClass
@BeforeMethod
	setUpBeforeTest
@AfterMethod
@AfterClass
jalview.schemes.UserColourSchemeTest
@Test
	testConstructor_coloursArray	Functional
	testToAppletParameter	Functional
	testParseAppletParameter	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ext.ensembl.EnsemblSeqProxyTest
@Test
	getGenomicRangesFromFeatures	Functional
	testReverseComplementAllele	Functional
	testGetSequenceRecords
	testReverseComplementAlleles	Functional
@BeforeClass
	setUp
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDown
jalview.gui.AppVarnaTest
@Test
	testReplaceOddGaps	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ext.ensembl.EnsemblGenomeTest
@Test
	testGetGenomicRangesFromFeatures	Functional
	testGetIdentifyingFeatures	Functional
	testRetainFeature	Functional
@BeforeClass
	setUp
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDown
jalview.ws.dbsources.RfamSeedTest
@Test
	testGetURL	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ext.ensembl.EnsemblCdnaTest
@Test
	testGetGenomicRangesFromFeatures	Functional
	testIsValidReference	Functional
	testGetGenomicRangesFromFeatures_mixedStrand	Functional
	testGetIdentifyingFeatures	Functional
	testGetGenomicRangesFromFeatures_reverseStrand	Functional
	testRetainFeature	Functional
@BeforeClass
	setUp
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDown
jalview.renderer.ScaleRendererTest
@Test
	testCalculateMarks	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.AnnotationFileIOTest
@Test
	exampleAnnotationFileIO	Functional
	testAnnotateAlignmentView	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.urls.DesktopUrlProviderFactoryTest
@Test
	testCreateUrlProvider	Functional
@BeforeClass
@BeforeMethod
	setup
@AfterMethod
@AfterClass
jalview.fts.service.pdb.PDBFTSRestClientTest
@Test
	parsePDBJsonResponseTest	External
	executeRequestTest	Network External
	getPDBDocFieldsAsCommaDelimitedStringTest	Functional
	getPDBIdColumIndexTest	Functional
	parsePDBJsonExceptionStringTest	External, Network
	testForExpectedRuntimeException	External
	externalServiceIntegrationTest	External
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
	tearDown
@AfterClass
jalview.util.MappingUtilsTest
@Test
	testFlattenRanges	Functional
	testRemoveStartPositions_reverseStrand	Functional
	testMapSequenceGroup_region	Functional
	testBuildSearchResults_withIntron	Functional
	testFindMappingsForSequence	Functional
	testMapSequenceGroup_sequences	Functional
	testMapEditCommand	Functional
	testFindOverlap	Functional
	testMapColumnSelection_hiddenColumns	Functional
	testRemoveEndPositions	Functional
	testMapColumnSelection_null	Functional
	testRemoveStartPositions	Functional
	testContains	Functional
	testMapSequenceGroup_columns	Functional
	testBuildSearchResults	Functional
	testFlattenRanges_reverseStrand	Functional
	testMapColumnSelection_dnaToProtein	Functional
	testFindMappingsForSequenceAndOthers	Functional
	testGetLength	Functional
	testMapSequenceGroup_sharedDataset	Functional
	testMapColumnSelection_proteinToDna	Functional
	testRangeContains	Functional
@BeforeClass
	setUp
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.AAFrequencyTest
@Test
	testCompleteConsensus_ignoreGaps_noLogo	Functional
	testExtractCdnaProfile_countGaps	Functional
	testCalculate_withProfile	Functional
	testExtractProfile_countGaps	Functional
	testCompleteConsensus_includeGaps_showLogo	Functional
	testExtractCdnaProfile	Functional
	testCalculate_noProfile	Functional
	testCalculate_withProfileTiming	Functional
	testExtractProfile	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.ProgressBarTest
@Test
	testConstructor_prematureInstantiation	Functional
	testSetProgressBar	Functional
	testConstructor_wrongLayout	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.structure.Mapping
@Test
	pdbEntryPositionMap	Functional
	testPDBentryMapping	Functional
	compareTransferredToRefPDBAnnot	Functional
	mapFer1From3W5V	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.urls.UrlLinkDisplayTest
@Test
	testGetSetValue	Functional
	getValue	Functional
	testDisplayColumnNames	Functional
	testIsEditable	Functional
	testUrl	Functional
	testDescription	Functional
	testName	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.SearchResultsTest
@Test
	testInvolvesSequence	Functional
	testMatchConstructor	Functional
	testToString	Functional
	testMatchContains	Functional
	testEquals_orderDiffers	Functional
	testAddResult	Functional
	testHashcode	Functional
	testMarkColumns	Functional
	testEquals	Functional
	testEquals_distinctSequences	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.AlignmentViewTest
@Test
	testGetVisibleAlignmentGapChar	Functional
	testGetVisibleContigs	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.RnaTest
@Test
	testIsCanonicalOrWobblePair	Functional
	testGetHelixMap_oneHelix	Functional
	testIsRnaSecondaryStructureSymbol	Functional
	testGetMatchingOpeningParenthesis	Functional
	testGetHelixMap_twoHelices	Functional
	testGetSimpleBPs_unmatchedOpener	Functional
	testGetRNASecStrucState	Functional
	testGetSimpleBPs	Functional
	testGetSimpleBPs_unmatchedCloser	Functional
	testIsCanonicalPair	Functional
	testIsOpeningParenthesis	Functional
	testIsClosingParenthesis	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.viewmodel.ViewportRangesTest
@Test
	testSetViewportWidth	Functional
	testPageUpDownWrapped	Functional
	testGetWrappedScrollPosition	Functional
	testGetAbsoluteAlignmentHeight	Functional
	testScrollRight	Functional
	testScrollUpWithHidden	Functional
	testSetEndSeq	Functional
	testViewportRanges	Functional
	testScrollRightWithHidden	Functional
	testSetViewportStartAndWidth	Functional
	testScrollUp	Functional
	testGetWrappedMaxScroll	Functional
	testGetAbsoluteAlignmentWidth	Functional
	testSetStartEndSeq	Functional
	testSetStartSeq	Functional
	testSetStartEndRes	Functional
	testSetStartRes	Functional
	testScrollUp_wrapped	Functional
	testEventFiring	Functional
	testSetStartEndResWrapped	Functional
	testScrollToWrappedVisible	Functional
	testScrollToVisible	Functional
	testSetStartResAndSeq	Functional
	testSetViewportStartAndHeight	Functional
	testPageUpDown	Functional
	testSetViewportHeight	Functional
	testSetViewportLocation	Functional
	testSetViewportStartAndWidthWrapped	Functional
@BeforeClass
	setUp
@BeforeMethod
	cleanUp
@AfterMethod
@AfterClass
jalview.ext.jmol.JmolViewerTest
@Test
	testAddStrToSingleSeqViewJMol	Functional
	testSingleSeqViewJMol	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.io.cache.AppCacheTest
@Test
	appCacheTest	Functional
	appCacheLimitTest	Functional
@BeforeClass
	setUpCache
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.GroupingTest
@Test
	testMakeGroupsWithBoth	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ext.htsjdk.VCFReaderTest
@Test
	testQuery_plain	Functional
	testReadVcf_plain	Functional
	testQuery_indexed
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.ConservationTest
@Test
	testRecordConservation	Functional
	testVerdict	Functional
	testCalculate_threshold	Functional
	testCountConservationAndGaps	Functional
	testCalculate_noThreshold	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.gff.GffTests
@Test
	testResolveExonerateGff	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.math.RotatableMatrixTest
@Test
	testPreMultiply	Functional
	testVectorMultiply	Functional
	testGetRotation	Functional
	testPrint	Functional
@BeforeClass
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.schemes.StrandColourSchemeTest
@Test
	testFindColour	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.ColorUtilsTest
@Test
	testBleachColour	Functional
	testDarkerThan	Functional
	testBrighterThan	Functional
	testParseColourString	Functional
	testGetGraduatedColour	Functional
	testToTkCode	Functional
	testGetAWTColorFromName	Functional
	testCreateColourFromName	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.MappingTypeTest
@Test
	testGetToRatio	Functional
	testGetInverse	Functional
	testGetFromRatio	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.SeqCanvasTest
@Test
	testCalculateWrappedGeometry_noAnnotations	Functional
	testClear_HighlightAndSelection	Functional
	testCalculateWrappedGeometry_fromScrolled	Functional_Failing
	testCalculateWrappedGeometry_withAnnotations	Functional
@BeforeClass
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.analysis.AlignSeqTest
@Test
	testIndexEncode_peptide	Functional
	testExtractGaps	Functional
	testIndexEncode_nucleotide	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.gff.Gff3HelperTest
@Test
	testProcessCdnaMatch_reverseToForward	Functional
	testProcessCdnaMatch_forwardToForward	Functional
	testProcessCdnaMatch_forwardToReverse	Functional
	testProcessCdnaMatch_spliced	Functional
	testGetDescription	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.DBRefUtilsTest
@Test
	testSelectRefs	Functional
	testSearchRefs_accessionid	Functional
	testSearchRefs_withMapping	Functional
	testParseToDbRef	Functional
	testGetCanonicalName	Functional
	testSearchRefs_noMapping	Functional
	testParseToDbRef_PDB	Functional
	testSearchRefs_wildcardAccessionid	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.AlignedCodonFrameTest
@Test
	testGetMappedRegion_eitherWay	Functional
	testGetMappedCodons	Functional
	testRealiseWith	Functional
	testGetCoveringMapping	Functional
	testIsRealisableWith	Functional
	testMarkMappedRegion	Functional
	testGetCoveringCodonMapping	Functional
	testFindAlignedSequence	Functional
	testGetMappedRegion	Functional
	testAddMap	Functional
	testGetMappedCodons_forSubSequences	Functional
	testGetMappedCodons_dnaVariants	Functional
	testCouldReplaceSequence	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.Log4jTest
@Test
	testLog4j	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ext.ensembl.EnsemblProteinTest
@Test
	testIsValidReference	Functional
	testGetAccesionIdFromQuery	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.AlignmentTest
@Test
	testDeleteSequenceByIndex	Functional
	testAddSequencePreserveDatasetIntegrity	Functional
	testAlignAs_dnaAsProtein_withIntrons	Functional
	testCreateDataset_updateDbrefMappings	Functional
	testAppend	Functional
	testFindAnnotations_bySeqLabelandorCalcId	Functional
	testAlignAs_proteinAsCdna	Functional
	testCopyConstructor	Functional
	testDeleteHiddenSequence	Functional
	testVerifyAlignmentDatasetRefs	Functional
	testAlignAs_cdnaAsProtein	Functional
	testCreateDatasetAlignment	Functional
	testAssertDatasetIsNormalised	Functional Asserts
	testAlignAs_dnaAsDna	Functional
	testPropagateInsertions	Functional
	testFindOrCreateForNullCalcId	Functional
	testAddCodonFrame	Functional
	testPadGaps	Functional
	testDeleteSequenceBySeq	Functional
	testPropagateInsertionsOverlap	Functional
	testCreateDatasetAlignmentWithMappedToSeqs	Functional
	testSetDataset_selfReference	Functional
	testGetWidth	Functional
	testDeleteAllAnnotations_includingAutocalculated	Functional
	testFindGroup	Functional
	testGetVisibleWidth	Functional
	testAlignAs_cdnaAsProtein_singleSequence	Functional
	testDeleteAllAnnotations_excludingAutocalculated	Functional
	testFindAnnotation_byCalcId	Functional
	testSetHiddenColumns	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.datamodel.HiddenSequencesTest
@Test
	testAdjustHeightSequenceAdded	Functional
	testFindIndexWithoutHiddenSeqs	Functional
	testAdjustHeightSequenceDeleted	Functional
	testGetHiddenSequence	Functional
	testHideShowSequence	Functional
	testIsHidden	Functional
	testHideShowSequence_withHiddenRepSequence	Functional
	testGetWidth	Functional
	testGetFullAlignment	Functional
	testFindIndexNFromRow	Functional
	testAdjustForHiddenSeqs	Functional
	testHideShowLastSequences	Functional
	testGetSize	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.MessageManagerTest
@Test
	testGetString_invalid	Functional
	testFormatMessage_invalid	Functional
	testGetStringOrReturn	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.SeqPanelTest
@Test
	testSetStatusReturnsNearestResiduePosition	Functional
	testFindMousePosition_wrapped_scales_longSequence	Functional
	testAmbiguousAminoAcidGetsStatusMessage	Functional
	testFindColumn_wrapped	Functional
	testFindMousePosition_wrapped_noAnnotations	Functional
	testFindColumn_unwrapped	Functional
	testGetEditStatusMessage_lockedEditing	Functional
	testGetEditStatusMessage	Functional
	testFindMousePosition_wrapped_annotations	Functional
	testFindMousePosition_wrapped_scaleAbove	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
	tearDown
@AfterClass
jalview.gui.ColourMenuHelperTest
@Test
	testAddMenuItems_nucleotide	Functional
	testAddMenuItems_peptide	Functional
	testAddMenuItems_forAlignFrame	Functional
	testAddMenuItems_simpleOnly	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.ScalePanelTest
@Test
	testBuildPopupMenu	Functional
	testPreventNegativeStartColumn	Functional
	testSelectColumns_withHidden	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.VisibleContigsIteratorTest
@Test
	testVisibleRegionsAtHiddenEdges	Functional
	testMultipleVisibleRegions	Functional
	testSimpleVisibleRegions	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.features.FeatureStoreTest
@Test
	testGetFeaturesForGroup	Functional
	testMax	Functional
	testGetTotalFeatureLength	Functional
	testFindFeatures_mixed	Functional
	testGetMinimumScore_getMaximumScore	Functional
	testContains	Functional
	testFindFeatures_contactFeatures	Functional
	testDelete	Functional
	testListContains	Functional
	testDelete_readd	Functional
	testIsEmpty	Functional
	testFindFeatures_nested	Functional
	testGetPositionalFeatures	Functional
	testMin	Functional
	testAddFeature	Functional
	testGetFeatureGroups	Functional
	testShiftFeatures	Functional
	testFindFeatures_nonNested	Functional
	testGetFeatureLength	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ext.ensembl.EnsemblGeneTest
@Test
	testGetGenomicRangesFromFeatures	Functional
	testGetFeatureColourScheme	Functional
	testGetIdentifyingFeatures	Functional
	testGetGeneIds	Network
	testRetainFeature	Functional
	testGetTranscriptFeatures	Functional
	testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand	Functional
@BeforeClass
	setUp
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDown
jalview.schemes.BuriedColourSchemeTest
@Test
	testFindColour	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.features.FeatureMatcherSetTest
@Test
	testMatches_byAttribute	Functional
	testOr	Functional
	testAnd	Functional
	testToString	Functional
	testMatches_compoundKey	Functional
	testIsEmpty	Functional
	testGetMatchers	Functional
	testFromString	Functional
	testToStableString	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.bin.HiDPISettingTest1
@Test
	testHiDPISettingInit	Functional
@BeforeClass
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
	tearDown
jalview.gui.AnnotationLabelsTest
@Test
	testGetTooltip	Functional
	testGetStatusMessage	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.bin.HiDPISettingTest2
@Test
	testHiDPISettings	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.ColumnSelectionTest
@Test
	testSetElementsFrom	Functional
	testHideColumns_withSelection	Functional
	testMarkColumns_toggle	Functional
	testGetSelected_isReadOnly	Functional
	testInvertColumnSelection	Functional
	testStretchGroup_shrink	Functional
	testMinColumnSelection	Functional
	testGetSelected	Functional
	testMarkColumns	Functional
	testFilterAnnotations	Functional
	testCopyConstructor	Functional
	testMarkColumns_extend	Functional
	testStretchGroup_expand	Functional
	testGetSelectedRanges	Functional
	testMaxColumnSelection	Functional
	testAddElement	Functional
	testHideSelectedColumns	Functional
	testMarkColumns_invert	Functional
	testGetSelected_concurrentModification	Functional
	testEquals	Functional
	testRemoveElement	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.CigarArrayTest
@Test
	testConstructor	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.ParseHtmlBodyAndLinksTest
@Test
	testParseHtml_noLinks	Functional
	testParseHtml_withLinksWithParameters	Functional
	testParseHtml_withLinks	Functional
	testParseHtml_withLinksWithEncoding	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.renderer.ResidueColourFinderTest
@Test
	testGetResidueColour_userdef	Functional
	testGetResidueColour_none	Functional
	testGetResidueColour_zappo	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.PDBEntryTest
@Test
	testTypeMatches	Functional
	testSetChainCode	Functional
	testGetType	Functional
	testConstructor_fromDbref	Functional
	testUpdateFrom	Functional
	testEquals	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
	tearDown
@AfterClass
jalview.datamodel.MatchTest
@Test
	testToString	Functional
	testEquals	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ws.rest.ShmmrRSBSService
@Test
	testShmmrServiceDataprep	Functional
	testShmmrService	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.AlignmentAnnotationUtilsTest
@Test
	testGetVisibleGraphGroups	Functional
	testGetShownHiddenTypes_noSequenceSelected	Functional
	testAsList	Functional
	testGetShownHiddenTypes_withGraphGroups	Functional
	testGetShownHiddenTypes_forSelectionGroup	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.schemes.ColourSchemePropertyTest
@Test
	testGetColourName	Functional
	testGetColourScheme	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.bin.JalviewLiteTest
@Test
	testSeparatorListToArray	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.project.Jalview2xmlTests
@Test
	testStoreAndRecoverReferenceSeqSettings	Functional
	testMergeDatasetsforViews	Functional
	testIsVersionStringLaterThan	Functional
	viewRefPdbAnnotation	Functional
	testStoreAndRecoverGroupRepSeqs	Functional
	testStoreAndRecoverColourThresholds	Functional
	testSaveLoadFeatureColoursAndFilters	Functional
	testPcaViewAssociation	Functional
	testStoreAndRecoverExpandedviews	Functional
	testStoreAndRecoverPDBEntry	Functional
	testColourByAnnotScores	Functional
	testMergeDatasetsforManyViews	Functional
	noDuplicatePdbMappingsMade	Functional
	testStoreAndRecoverGeneLocus	Functional
	testTCoffeeScores	Functional
	testCopyViewSettings	Functional
	testRNAStructureRecovery	Functional
	gatherViewsHere	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.viewmodel.styles.ViewStyleTest
@Test
	testCopyConstructor	Functional
	testEquals	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.DnaUtilsTest
@Test
	testParseLocation	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.scoremodels.FeatureDistanceModelTest
@Test
	testFeatureScoreModel_hiddenFirstColumn	Functional
	testFindFeatureAt_PointFeature	Functional
	testFeatureScoreModel	Functional
	testFeatureScoreModel_HiddenColumns	Functional
	testFindDistances_withParams	Functional
	testFindDistances	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.matcher.MatcherTest
@Test
	testMatches_long	Functional
	testToString	Functional
	testMatches_floatValueIntegerCondition	Functional
	testConstructor	Functional
	testHashCode	Functional
	testMatches_float	Functional
	testMatches_floatWithStringCondition	Functional
	testMatches_pattern	Functional
	testEquals	Functional
	testNumericMatch_nullOrInvalidValue	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.DBRefEntryTest
@Test
	testUpdateFrom	Functional
	testIsPrimaryCandidate	Functional
	testEqualRef	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ext.so.SequenceOntologyTest
@Test
	testIsA	Functional
	testIsSequenceVariant	Functional
	testIsCDS	Functional
@BeforeClass
	setUp
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ws.dbsources.EmblXmlSourceTest
@Test
	testGetEmblEntries	Functional
	testGetCdsRanges	Functional
	testGetSequence	Functional
	testAdjustForProteinLength	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.PaintRefresherTest
@Test
	testRegister	Functional
	testGetAssociatedPanels	Functional
	testRemoveComponent	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
	tearDown
@AfterClass
jalview.util.ArrayUtilsTest
@Test
	testReverseIntArray	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.schemes.HelixColourSchemeTest
@Test
	testFindColour	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.AnnotationPanelTest
@Test
	testGetRowIndex	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.structure.StructureSelectionManagerTest
@Test
	testAssociatedMappingToSubSeq	Network
	testSetMapping_seqFeatures	Functional
	testRegisterMapping	Functional
	testMapping_EqualsFeatures	Network
	testRegisterMappings	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.structure.StructureMappingTest
@Test
	testGetPDBResNumRanges	Functional
	testEquals	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.AnnotationColumnChooserTest
@Test
	testReset	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.ext.ensembl.EnsemblCdsTest
@Test
	testGetGenomicRangesFromFeatures	Functional
	testIsValidReference	Functional
	testGetIdentifyingFeatures	Functional
	testRetainFeature	Functional
@BeforeClass
	setUp
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDown
jalview.io.cache.JvCacheableInputBoxTest
@Test
	updateCacheTest	Functional
	getUserInputTest	Functional
@BeforeClass
	setUpCache
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.AlignmentUtilsTests
@Test
	testAlignSequenceAs_withTrailingPeptide	Functional
	testAddMappedPositions_withStopCodon	Functional
	testAlignSequenceAs_mappedProteinProtein	Functional
	testFindCdsPositions_reverseStrandThreePrimeIncomplete	Functional
	testFindCdsPositions_reverseStrand	Functional
	testMakeCdsAlignment	Functional
	testFindCdsPositions	Functional
	testMakeCdsAlignment_filterProducts	Functional
	testAlignProteinAsDna	Functional
	testTranslatesAs	Functional
	testShowOrHideSequenceAnnotations	Functional
	testIsMappable	Functional
	testExpandContext_annotation	Functional
	testTransferGeneLoci	Functional
	testFindCdsForProtein_noUTR
	testExpandContext	Functional
	testAlignSequenceAs_keepIntronGapsOnly	Functional
	testAlignSequenceAs_withMapping_withUnmappedProtein	Functional
	testMapProteinAlignmentToCdna_withStartAndStopCodons	Functional
	testFindCdsForProtein
	testAddMappedPositions	Functional
	testAlignSequenceAs_withMapping_noIntrons	Functional
	testAlignSequenceAs_withMapping_withIntrons	Functional
	testTransferFeatures	Functional
	testHaveCrossRef	Functional
	testAlignAsSameSequencesMultipleSubSeq	Functional
	testAlignAs_alternateTranscriptsUngapped	Functional
	testMapProteinAlignmentToCdna_withXrefs	Functional
	testAlignProteinAsDna_incompleteStartCodon	Functional
	testFindCdsPositions_fivePrimeIncomplete	Functional
	testAlignAsSameSequences	Functional
	testHasCrossRef	Functional
	testMapCdnaToProtein_forSubsequence	Functional
	testTransferFeatures_withOmit	Functional
	testMakeCdsAlignment_multipleProteins	Functional
	testTransferFeatures_withSelect	Functional
	testMapProteinAlignmentToCdna_prioritiseXrefs	Functional
	testMakeCdsAlignment_alternativeTranscripts	Functional
	testGetSequencesByName	Functional
	testMapCdsToProtein	Functional
	testMapProteinAlignmentToCdna_noXrefs	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.PlatformTest
@Test
	testIsControlDown_notMac	Functional
	testIsControlDown_mac	Functional
	testPathEquals	Functional
	testEscapeBackslashes	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.ParsePropertiesTest
@Test
	testGetScoresFromDescription_wordBoundaries	Functional
	testGetScoresFromDescription	Functional
	testGetScoresFromDescription_twoScores	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.datamodel.RangeElementsIteratorTest
@Test
	testHasNextAndNextNoHidden	Functional
	testHasNextAndNextWithHidden	Functional
	testLastNextWithHidden	Functional
	testRemove	Functional
	testHasNextAndNextStartHidden	Functional
	testLastNextStartHidden	Functional
	testHasNextAndNextEndHidden	Functional
	testLastNextEndHidden	Functional
	testLastNextNoHidden	Functional
@BeforeClass
	setup	Functional
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.SetUtilsTest
@Test
	testCountDisjunction	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.AlignmentSorterTest
@Test
	testSortByFeature_score	Functional
	testSortByFeature_density	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.IdentifyFileTest
@Test
	testIdentify_featureFile	Functional
	testLooksLikeFeatureData	Functional
	testIdentify	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.bin.MemorySettingTest
@Test
	testGetMemorySetting	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ext.jmol.JmolParserTest
@Test
	testParse_alternativeResidues	Functional
	testAlignmentLoader	Functional
	testSetSecondaryStructure	Functional
	testFileParser	Functional
	testParse_missingResidues	Functional
	testLocalPDBId	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.io.FileFormatsTest
@Test
	testGetFormats	Functional
	testIsIdentifiable	Functional
	testGetWritableFormats	Functional
	testGetReadableFormats	Functional
	testForName	Functional
	testDeregisterFileFormat	Functional
	testRegisterFileFormat	Functional
@BeforeClass
@BeforeMethod
	setUp
@AfterMethod
	tearDown
@AfterClass
jalview.ext.android.SparseShortArrayTest
@Test
	testAdd	Functional
	testPut	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.PopupMenuTest
@Test
	testBuildLinkMenu	Functional
	testAddFeatureDetails	Functional
	testConfigureReferenceAnnotationsMenu	Functional
	testConfigureReferenceAnnotationsMenu_alreadyAdded	Functional
	testBuildAnnotationTypesMenus_hideDisabled	Functional
	testConfigureReferenceAnnotationsMenu_noSequenceSelected	Functional
	testAddFeatureDetails_linkedFeatures	Functional
	testConfigureReferenceAnnotationsMenu_noReferenceAnnotations	Functional
	testBuildAnnotationTypesMenus_showDisabled	Functional
	testHideInsertions	Functional
	testConfigureReferenceAnnotationsMenu_twoViews	Functional
	testConfigureReferenceAnnotationsMenu_notOnAlignment	Functional
	testBuildAnnotationTypesMenus	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.fts.core.FTSRestClientTest
@Test
	getPrimaryKeyColumIndexTest	Functional
	coverageForEqualsAndHashFunction	Functional
	getSearchableDataColumns	Functional
	getDataColumnByNameOrCode	Functional
	getColumnPreferredWidthTest	Functional
	coverageForMiscellaneousBranches	Functional
	getColumnClassTest	Functional
	coverageForExceptionBranches	Functional
	getColumnMinWidthTest	Functional
	getDefaultResponsePageSize	Functional
	getAllFTSDataColumns	Functional
	getDataColumnsFieldsAsCommaDelimitedString	Functional
	getAllDefaulDisplayedDataColumns	Functional
	getDataColumnGroupById	Functional
	getColumnMaxWidthTest	Functional
	getPrimaryKeyColumn	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setup
@AfterMethod
@AfterClass
jalview.gui.AlignmentPanelTest
@Test
	testCalculateIdWidth_noArgs	Functional
	testUpdateLayout_endRes	Functional
	testGetVisibleWidth	Functional Not-bamboo
	testCalculateIdWidth_withMaxWidth	Functional
	testSetScrollValues	Functional
@BeforeClass
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.urls.CustomUrlProviderTest
@Test
	testUrlLinks	Functional
	testDefaultUrl	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ws.rest.RestClientTest
@Test
	testGetRestClient	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ws.dbsources.UniprotTest
@Test
	testGetUniprotSequence	Functional
	testGetUniprotEntryId	Functional
	testGetUniprotEntryDescription	Functional
	testGetDescription	Functional
	testGetUniprotEntries	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.gff.ExonerateHelperTest
@Test
	testAddExonerateGffToAlignment	Functional
	testProcessGffSimilarity_protein2dna_forward_targetgff	Functional
	testProcessGffSimilarity_protein2dna_reverse_targetgff	Functional
	testGetMappingType	Functional
	testProcessGffSimilarity_protein2dna_forward_querygff	Functional
	testProcessGffSimilarity_protein2dna_reverse_querygff	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.workers.AlignCalcManagerTest
@Test
	testRemoveWorkerForAnnotation	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.ws.dbsources.RfamFullTest
@Test
	testGetURL	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.math.MatrixTest
@Test
	testTred_reproducible	Functional
	testSign	Timing
	testFindMinMax	Functional
	testReverseRange_swapMinMax	Functional
	testConstructor	Functional
	testReverseRange_maxToZero	Functional
	testPreMultiply_timing	Timing
	testPreMultiply_tooFewColumns	Functional
	testPreMultiply	Functional
	testCopy	Functional
	testMultiply	Functional
	testPreMultiply_tooManyColumns	Functional
	testFindMinMax_timing	Functional Timing
	testPostMultiply	Functional
	testEquals	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.HiddenColumnsTest
@Test
	testVisibleContigsIterator	Functional
	testGetNextHiddenBoundary_Left	Functional
	testBoundedIterator	Functional
	testHideColumns_BitSet_range	Functional
	testGetRegionWithEdgeAtRes	Functional
	testAdjustForHiddenColumns	Functional
	testBoundedStartIterator	Functional
	testFindColumnPosition	Functional
	testHideInsertionsFor	Functional
	testCopyConstructor	Functional
	testHideColumns	Functional
	testCopyConstructor2	Functional
	testIsVisible	Functional
	testGetSize	Functional
	testRevealHiddenColumns	Functional
	testEquals	Functional
	testHasManyHiddenColumns	Functional
	testHideColumns_BitSet	Functional
	testHasHiddenColumns	Functional
	testGetVisibleColsIterator	Functional
	testHashCode	Functional
	testGetNextHiddenBoundary_Right	Functional
	testIterator	Functional
	testOffsetByVisibleColumns	Functional
	testRevealAllHiddenColumns	Functional
	testVisibleBlocksVisBoundsIterator	Functional
	testRegionsToString	Functional
	testGetVisibleStartAndEndIndex	Functional
	testHideColumns_subsumingHidden	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.SequenceTest
@Test
	testFindPositionMap	Functional
	testDeleteChars	Functional
	testCopyConstructor_withDataset	Functional
	testDeleteChars_withDbRefsAndFeatures	Functional
	testGetStartGetEnd	Functional
	testAddAlignmentAnnotation	Functional
	testCreateDatasetSequence	Functional
	testFindPosition_withCursorAndEdits	Functional
	testGetPrimaryDBRefs_nucleotide	Functional
	testInsertGapsAndGapmaps	Functional
	testGetAnnotation_forLabel	Functional
	testSetDatasetSequence_cascading	Functional
	testFindPositions	Functional
	testFindFeatures	Functional
	testReplace	Functional
	testUpdatePDBIds	Functional
	testDeriveSequence_noDatasetGapped	Functional
	testInsertCharAt	Functional
	testGetSequenceFeatures	Functional
	testCheckValidRange	Functional
	testFindPosition_withCursor	Functional
	testTransferAnnotation	Functional
	testGetSubsequence	Functional
	testAddSequenceFeatures	Functional
	testGetPrimaryDBRefs_peptide	Functional
	testGapBitset	Functional
	testSetDatasetSequence_toSelf	Functional
	testLocateVisibleStartofSequence	Functional
	testGapMap	Functional
	testDeleteChars_withGaps	Functional
	testGetAlignmentAnnotations_forCalcIdLabelAndDescription	Functional
	testAddDBRef	Functional
	testFindIndex	Functional
	testDeriveSequence_noDatasetUngapped	Functional
	testGetCharAt	Functional
	testFindPosition	Functional
	testGetAnnotation	Functional
	testIsProtein	Functional
	testCopyConstructor_noDataset	Functional
	testDeriveSequence_existingDataset	Functional
	testFindIndex_withCursor	Functional
	testAddPDBId	Functional
	testSetName	Functional
	testIsValidCursor
	testIsProteinWithXorNAmbiguityCodes	Functional
	testGetAlignmentAnnotations_forCalcIdAndLabel	Functional
	testGetSequence	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.schemes.AnnotationColourGradientTest
@Test
	testFindColour_noThreshold	Functional
	testShadeCalculation_belowThreshold	Functional
	testFindColour_belowThreshold	Functional
	testFindColour_aboveThreshold	Functional
	testShadeCalculation_aboveThreshold	Functional
	testShadeCalculation_noThreshold	Functional
	testFindColour_originalColours	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.schemes.TurnColourSchemeTest
@Test
	testFindColour	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.AlignedCodonTest
@Test
	testToString	Functional
	testEquals	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.GenBankFileTest
@Test
	testParse	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.AllRowsIteratorTest
@Test
	testHasNextAndNext	Functional
	testRemove	Functional
	testOneElement	Functional
	testLastNext	Functional
@BeforeClass
	setup
@BeforeMethod
@AfterMethod
@AfterClass
jalview.fts.threedbeacons.TDBeaconsFTSRestClientTest
@Test
	getPrimaryKeyColumIndexTest	Functional
	coverageForEqualsAndHashFunction	Functional
	testMockTDBRequest	Functional
	getTDBIdColumIndexTest	Functional
	getSearchableDataColumns	Functional
	getDataColumnByNameOrCode	Functional
	executeRequestTest	Network External
	verifyMockTDBRequest	Integration Network
	getColumnClassTest	Functional
	getColumnMinWidthTest	Functional
	getDefaultResponsePageSize	Functional
	getAllFTSDataColumns	Functional
	getDataColumnsFieldsAsCommaDelimitedString	Functional
	getAllDefaulDisplayedDataColumns
	getDataColumnGroupById	Functional
	getPrimaryKeyColumn	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
	tearDown
@AfterClass
jalview.ext.ensembl.EnsemblXrefTest
@Test
	testGetCrossReferences	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.bin.ArgsParserTest
@Test
	testContains	Functional
	testGetValue	Functional
	testGetValue_decoded	Functional
	testNextValue	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.QuickSortTest
@Test
	testSort_byFloatValues	Functional
	testSort_withDuplicates	Functional
	testSortByString	Functional
	testSortByInt	Functional
	testSort_timingTest	Timing
	testSort_byDoubleValues	Functional
	testSort_byIntValues	Functional
	testSort_charSortByInt_mostlyZeroValues	Functional
	testSort_byStringValues	Functional
	testSort_charSortByFloat_mostlyZeroValues	Functional
	testCharSortByFloat	Functional
	testCharSortByInt	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.ClustalFileTest
@Test
	testParse_withNumbering	Functional
	testParse_noNumbering	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.ShiftListTest
@Test
	testParseMap	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.RNAMLfileTest
@Test
	testRnamlToStockholmIO	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.schemes.PIDColourSchemeTest
@Test
	testFindColour_ignoreGaps	Functional
	testFindColour	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.JalviewFileViewTest
@Test
	testGetExtension	Functional
	testGetImageIcon	Functional
	testGetTypeDescription	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.ScoreMatrixFileTest
@Test
	testParseMatrix_ncbiMixedDelimiters	Functional
	testParseMatrix_aaindexFormat	Functional
	testParseMatrix_aaindex_rowColMismatch	Functional
	testParseMatrix_headerMissing	Functional
	testParseMatrix_ncbiBadFloat	Functional
	testParseMatrix_ncbiFormat	Functional
	testParseMatrix_ncbiNotEnoughRows	Functional
	testParseMatrix_ncbiBadDelimiter	Functional
	testParseMatrix_ncbiNameMissing	Functional
	testParseMatrix_ncbiHeaderRepeated	Functional
	testParseMatrix_aaindex_extraDataLines	Functional
	testParseMatrix_aaindex_mMissing	Functional
	testParseMatrix_ncbiTooManyRows	Functional
	testParseMatrix_aaindex_tooManyRows	Functional
	testParseMatrix_ncbiBadGuideCharacter	Functional
	testParse_ncbiFormat	Functional
	testParseMatrix_ncbiTooManyColumns	Functional
	testParseMatrix_aaIndexBlosum80	Functional
	testParseMatrix_aaindex_tooFewColumns	Functional
	testParseMatrix_ncbiNotEnoughColumns	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
	tearDownAfterTest
@AfterClass
jalview.io.JalviewExportPropertiesTests
@Test
	testImportExportPeriodGaps	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.io.StockholmFileTest
@Test
	pfamFileDataExtraction	Functional
	dbrefOutput	Functional
	detectWussBrackets	Functional
	curlyWUSSsecondaryStructureForRNASequence	Functional
	fullWUSSsecondaryStructureForRNASequence	Functional
	stockholmFileRnaSSSpaceChars	Functional
	pfamFileIO	Functional
	secondaryStructureForRNASequence	Functional
	stockholmFileRnaSSAlphaChars	Functional
	rfamFileIO	Functional
	testAnnotationEquivalence	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ext.pymol.PymolCommandsTest
@Test
	testSetAttributes	Functional
	testSuperposeStructures	Functional
	testShowBackbone	Functional
	testGetResidueSpec	Functional
	testCloseViewer	Functional
	testColourByCharge	Functional
	testSaveSession	Functional
	testColourBySequence	Functional
	testGetModelStartNo	Functional
	testGetAtomSpec	Functional
	testColourByChain	Functional
	testSetAttribute	Functional
	testGetAtomSpec_alphaOnly	Functional
	testOpenCommandFile	Functional
	testColourResidues	Functional
	testLoadFile	Functional
	testOpenSession	Functional
	testSetBackgroundColour	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.AnnotationSorterTest
@Test
	testNoSort_autocalcFirst	Functional
	testSort_timingSemisorted	Functional
	testSortBySequenceAndType_autocalcLast	Functional
	testSortByTypeAndSequence_autocalcFirst	Functional
	testSort_timingUnsorted	Functional
	testSortBySequenceAndType_autocalcFirst	Functional
	testSortByTypeAndSequence_autocalcLast	Functional
	testSort_timingPresorted	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.util.matcher.ConditionTest
@Test
	testGetStableName	Functional
	testToString	Functional
	testFromString	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.JvSwingUtilsTest
@Test
	testGetScrollValueForProportion	Functional
	testWrapTooltip_shortText	Functional
	testGetScrollBarProportion	Functional
	testWrapTooltip_multilineShortText	Functional
	testWrapTooltip_longText	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.AnnotationRowFilterTest
@Test
	testGetAnnotationItems	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.gff.InterProScanHelperTest
@Test
	testProcessProteinMatch	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.ws.ebi.EBIFetchClientTest
@Test
	testParseIds	Functional
	testBuildUrl	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.scoremodels.PIDModelTest
@Test
	testGetPairwiseScore	Functional
	testComputePID_matchesComparisonPID	Functional
	testComputePID_matchLongestSequence	Functional
	testComputePID_matchShortestSequence	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.AlignedCodonIteratorTest
@Test
	testNext_unmappedPeptide	Functional
	testNext	Functional
	testAnother	Functional
	testNext_withOffset	Functional
	testNext_incompleteCodon	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.AllColsIteratorTest
@Test
	testHasNextAndNext	Functional
	testRemove	Functional
	testOneElement	Functional
	testLastNext	Functional
@BeforeClass
	setup
@BeforeMethod
@AfterMethod
@AfterClass
jalview.viewmodel.OverviewDimensionsHideHiddenTest
@Test
	testFromMouseWithHiddenColsAtStart	Functional
	testSetBoxFromViewportHiddenColsAtEnd	Functional
	testFromMouseWithHiddenRowsInMiddle	Functional
	testSetBoxFromViewportHiddenColsInMiddle	Functional
	testFromMouseWithHiddenRowsAtStart	Functional
	testConstructor	Functional
	testPositionInBox	Functional
	testSetBoxFromViewportHiddenRowsAtStart	Functional
	testSetBoxFromViewportHiddenRowsAtEnd	Functional
	testDragging	Functional
	testFromMouseWithHiddenColsInMiddle	Functional
	testSetBoxFromViewport	Functional
	testSetBoxFromMouseClick	Functional
	testSetBoxFromViewportHiddenRowsInMiddle	Functional
	testFromMouseWithHiddenColsAtEnd	Functional
	testSetBoxFromViewportHiddenColsAtStart	Functional
	testFromMouseWithHiddenRowsAtEnd	Functional
@BeforeClass
	setUpAlignment
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
	cleanUp
jalview.io.EmblFlatFileTest
@Test
	testRemoveQuotes	Functional
	testParse_codonStartNot1	Functional
	testParseToRNA	Functional
	testParse_noUniprotXref	Functional
	testParse	Functional
	testAdjustForProteinLength	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.JvOptionPaneTest
@Test
	showInternalMessageDialogFamilyTest	Functional
	showInputDialogFamilyTest	Functional
	showMessageDialogFamilyTest	Functional
	showConfirmDialogFamilyTest	Functional
	showInternalConfirmDialogFamilyTest	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.schemes.JalviewColourSchemeTest
@Test
	testToString	Functional
	testGetSchemeClass	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.TCoffeeScoreFileTest
@Test
	testHeightAndWidthWithResidueNumbers	Functional
	testWrongFile	Functional
	testGetAsArray	Functional
	testGetAsList	Functional
	testReadHeader	Functional
	testReadBlock	Functional
	testParse	Functional
	testHeightAndWidth	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.VisibleRowsIteratorTest
@Test
	testHasNextAndNextNoHidden	Functional
	testHasNextAndNextWithHidden	Functional
	testLastNextWithHidden	Functional
	testRemove	Functional
	testHasNextAndNextStartHidden	Functional
	testLastNextStartHidden	Functional
	testHasNextAndNextEndHidden	Functional
	testLastNextEndHidden	Functional
	testLastNextNoHidden	Functional
@BeforeClass
	setup	Functional
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.SequenceAnnotationReportTest
@Test
	testAppendFeature_colouredByAttribute	Functional
	testAppendFeature_withScore	Functional
	testCreateSequenceAnnotationReport_withEllipsis	Functional
	testAppendFeatures_longText	Functional
	testCreateSequenceAnnotationReport	Functional
	testAppendFeature_noScore	Functional
	testAppendFeature_withScoreStatusAttribute	Functional
	testAppendFeature_virtualFeature	Functional
	testAppendFeature_DescEqualsType	Functional
	testAppendFeature_stripHtml	Functional
	testAppendFeature_status	Functional
	testAppendFeature_disulfideBond	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.analysis.scoremodels.ScoreModelsTest
@Test
	printAllMatrices_tabDelimited	none
	testConstructor	Functional
	printAllMatrices_asHtml	none
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.util.MapListTest
@Test
	testIsToForwardsStrand	Functional
	testLocateInFrom_noIntrons	Functional
	testGetOverlapsInFrom_withIntrons	Functional
	testLocateInFrom_withIntrons	Functional
	testGetMappedOffsetsForPositions	Functional
	testAddMapList_contiguous	Functional
	testConstructor	Functional
	testAddMapList_sameMap	Functional
	testGetRanges	Functional
	testLocateInFrom_reverseStrand	Functional
	testLocateInTo_withIntrons	Functional
	testCountPositions	Functional
	testLocateInTo_noIntrons	Functional
	testConstructor_withLists	Functional
	testCoalesceRanges	Functional
	testEquals	Functional
	testTraverseToPosition	Functional
	testAddMapList	Functional
	testAddRange	Functional
	testConstructor_mergeRanges	Functional
	testGetPositionsForOffsets	Functional
	testAddOffsetPositions	Functional
	testTraverse	Functional
	testToString	Functional
	testSomething	Functional
	testIsFromForwardStrand	Functional
	testLocateInFrom_withOverlap	Functional
	testGetInverse	Functional
	testGetOverlapsInTo_withIntrons	Functional
	testLocateInTo_withOverlap	Functional
@BeforeClass
	setUp
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
jalview.gui.AlignFrameTest
@Test
	testNewView_colourThresholds	Functional
	testChangeColour_background_groupsAndThresholds	Functional
	testNewView_dsRefPreserved	Functional
	testHideFeatureColumns	Functional
	testColourThresholdActions	Functional
@BeforeClass
	setUpBeforeClass
@BeforeMethod
	setUp
@AfterMethod
	tearDown
@AfterClass
jalview.io.JSONFileTest
@Test
	testSeqParsed	Functional
	roundTripTest	Functional
	hiddenColsTest	Functional
	testGrpParsed_colourNone	Functional
	isShowSeqFeaturesSet	Functional
	testGrpParsed	Functional
	testBioJSONRoundTripWithColourSchemeNone	Functional
	testAnnotationParsed	Functional
	hiddenSeqsTest	Functional
	colorSchemeTest	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	methodSetup
@AfterMethod
@AfterClass
jalview.io.vcf.VCFLoaderTest
@Test
	testDoLoad_vepCsq	Functional
	testDoLoad	Functional
	testDoLoad_reverseStrand	Functional
	testLoadVCFContig	Functional
@BeforeClass
	setUp
@BeforeMethod
@AfterMethod
@AfterClass
mc_view.PDBfileTest
@Test
	testParse_withJmol_noAnnotations	Functional
	testParse_withJmolAddAlignmentAnnotations	Functional
	testParse_withAnnotate3D	Functional
	testIsRna	Functional
	testParse	Functional
	testParse_withAnnotations_noSS	Functional
@BeforeClass
	setUpJvOptionPane
@BeforeMethod
	setUp
@AfterMethod
@AfterClass
jalview.ws.seqfetcher.DbRefFetcherTest
@Test
	checkUniprotCanonicalFlagSet	Network
	testStandardProtDbs	Functional
	testEmblUniprotProductRecovery	External
	testEmblCDSUniprotProductRecovery	External
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.ext.pymol.PymolManagerTest
@Test
	testGetPymolPaths	Functional
	testGetPostRequest	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.CrossRef2xmlTests
@Test
	openCrossrefsForEnsemblTwice	Functional
	testRetrieveAndShowCrossref	Operational
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.datamodel.MappedFeaturesTest
@Test
	testFindProteinVariants	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.io.gff.SequenceOntologyLiteTest
@Test
	testIsA_sequenceVariant	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.datamodel.HiddenColumnsCursorTest
@Test
	testFindRegionForColumn_Visible	Functional
	testFindRegionForColumn	Functional
	testConstructor	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.schemes.HydrophobicColourSchemeTest
@Test
	testFindColour	Functional
@BeforeClass
@BeforeMethod
@AfterMethod
@AfterClass
jalview.bin.CacheTest
@Test
	testSetDateProperty	Functional
	testVersionChecker	Functional
@BeforeClass
	setUpBeforeClass
	setUpJvOptionPane
@BeforeMethod
@AfterMethod
@AfterClass
	tearDownAfterClass
jalview.urls.IdentifiersUrlProviderTest
@Test
	testUrlLinks	Functional
	testDefaultUrl	Functional
@BeforeClass
	setup
@BeforeMethod
@AfterMethod
@AfterClass