TestNG Report

Test	# Passed	# Skipped	# Failed	Time (ms)	Included Groups	Excluded Groups
Jalview Release 2.7 by groups
GRP-Functional	738	6	18	173,946	Functional

Class	Method	Start	Time (ms)
Jalview Release 2.7 by groups
GRP-Functional — failed (configuration methods)
jalview.ws.jabaws.JpredJabaStructExportImport	setUpBeforeClass	1478592566009	0
jalview.ws.jabaws.RNAStructExportImport	setUpBeforeClass	1478592566194	0
GRP-Functional — failed
jalview.analysis.CrossRefTest	testFindXrefSequences_forGeneAndTranscripts	1478592566136	5
	testFindXrefSequences_uniprotEmblManyToMany	1478592566156	4
	testFindXrefSequences_withFetch	1478592566163	1
jalview.bin.CommandLineOperations	testHeadlessModeOutputOperations	1478592597577	3
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
jalview.io.RNAMLfileTest	testRnamlToStockholmIO	1478592517365	160
jalview.ws.seqfetcher.DasSequenceFetcher	testDasRegistryContact	1478592610822	87
jalview.ws.sifts.SiftsClientTest	getGreedyMappingTest	1478592605140	3
jalview.ws.sifts.SiftsClientTest	getSiftsStructureMappingTest	1478592605394	2
GRP-Functional — skipped
jalview.ws.jabaws.JpredJabaStructExportImport	testJPredStructExport	1478592566116	1
	testJPredStructOneSeqOnly	1478592566118	0
	testJpredwsSettingsRecovery	1478592566119	1
jalview.ws.jabaws.RNAStructExportImport	testRNAAliFoldValidStructure	1478592566299	1
	testRNAStructExport	1478592566301	1
	testRnaalifoldSettingsRecovery	1478592566303	1
GRP-Functional — passed
MCview.AtomTest	testStringConstructor	1478592564709	1
	testStringConstructor_blankOccupancyTempFactor	1478592564711	1
	testStringConstructor_malformed	1478592564713	1
MCview.BondTest	testTranslate	1478592517879	1
MCview.PDBChainTest	testGetChargeColour	1478592571246	1
	testGetNewlineString	1478592571249	1
	testMakeBond	1478592571251	1
	testMakeCaBondList	1478592571253	1
	testMakeCaBondList_nucleotide	1478592571255	1
	testMakeExactMapping	1478592571258	1
	testMakeResidueList_noAnnotation	1478592571260	1
	testMakeResidueList_withTempFactor	1478592571263	0
	testPrint	1478592571265	1
	testSetChainColours_colour	1478592571267	1
	testSetChainColours_colourScheme	1478592571269	1
	testSetChargeColours	1478592571271	2
MCview.PDBfileTest	testIsRna	1478592564730	2
	testParse	1478592564735	47
	testParse_withAnnotations_noSS	1478592564785	84
	testParse_withJmolAddAlignmentAnnotations	1478592564871	727
	testParse_withJmol_noAnnotations	1478592565601	407
MCview.ResidueTest	testFindAtom	1478592557409	3
jalview.analysis.AAFrequencyTest	testCalculate_noProfile	1478592507724	3
	testCalculate_withProfile	1478592507729	1
	testCompleteConsensus_ignoreGaps_noLogo	1478592507733	2
	testCompleteConsensus_includeGaps_showLogo	1478592507737	3
jalview.analysis.AlignSeqTest	testExtractGaps	1478592566313	4
jalview.analysis.AlignmentAnnotationUtilsTest	testAsList	1478592509263	56
	testGetShownHiddenTypes_forSelectionGroup	1478592509321	2
	testGetShownHiddenTypes_noSequenceSelected	1478592509327	2
	testGetShownHiddenTypes_withGraphGroups	1478592509342	9
	testGetVisibleGraphGroups	1478592509354	1
jalview.analysis.AlignmentUtilsTests	testAddMappedPositions	1478592574421	1
	testAddMappedPositions_withStopCodon	1478592574423	1
	testAlignAsSameSequences	1478592574425	1
	testAlignAsSameSequencesMultipleSubSeq	1478592574427	0
	testAlignAs_alternateTranscriptsUngapped	1478592574428	1
	testAlignProteinAsDna	1478592574429	2
	testAlignProteinAsDna_incompleteStartCodon	1478592574432	2
	testAlignSequenceAs_keepIntronGapsOnly	1478592574434	1
	testAlignSequenceAs_mappedProteinProtein	1478592574435	1
	testAlignSequenceAs_withMapping_noIntrons	1478592574437	1
	testAlignSequenceAs_withMapping_withIntrons	1478592574438	1
	testAlignSequenceAs_withMapping_withUnmappedProtein	1478592574440	1
	testAlignSequenceAs_withTrailingPeptide	1478592574442	0
	testBuildDnaVariantsMap	1478592574443	1
	testComputePeptideVariants	1478592574445	1
	testExpandContext	1478592574447	5
	testExpandContext_annotation	1478592574453	1
	testFindCdsPositions	1478592574454	1
	testFindCdsPositions_fivePrimeIncomplete	1478592574456	0
	testGetSequencesByName	1478592574457	0
	testHasCrossRef	1478592574458	1
	testHaveCrossRef	1478592574459	1
	testIsMappable	1478592574461	1
	testMakeCdsAlignment	1478592574463	2
	testMakeCdsAlignment_alternativeTranscripts	1478592574466	1
	testMakeCdsAlignment_filterProducts	1478592574468	1
	testMakeCdsAlignment_multipleProteins	1478592574469	2
	testMapCdnaToProtein_forSubsequence	1478592574472	0
	testMapProteinAlignmentToCdna_noXrefs	1478592574473	1
	testMapProteinAlignmentToCdna_prioritiseXrefs	1478592574475	1
	testMapProteinAlignmentToCdna_withStartAndStopCodons	1478592574476	1
	testMapProteinAlignmentToCdna_withXrefs	1478592574478	1
	testShowOrHideSequenceAnnotations	1478592574480	1
	testTransferFeatures	1478592574482	1
	testTransferFeatures_withOmit	1478592574484	1
	testTransferFeatures_withSelect	1478592574486	1
	testTranslatesAs	1478592574488	1
jalview.analysis.AnnotationSorterTest	testNoSort_autocalcFirst	1478592567978	0
	testSortBySequenceAndType_autocalcFirst	1478592567979	1
	testSortBySequenceAndType_autocalcLast	1478592567981	1
	testSortByTypeAndSequence_autocalcFirst	1478592567984	1
	testSortByTypeAndSequence_autocalcLast	1478592567986	1
	testSort_timingPresorted	1478592567989	209
	testSort_timingSemisorted	1478592568201	366
	testSort_timingUnsorted	1478592568569	176
jalview.analysis.CodingUtilsTest	testDecodeCodon	1478592574490	2
	testDecodeNucleotide	1478592574493	0
	testEncodeCodon	1478592574494	1
jalview.analysis.ConservationTest	testCalculate_noThreshold	1478592517866	2
	testCalculate_threshold	1478592517869	2
	testCountConservationAndGaps	1478592517872	2
	testRecordConservation	1478592517875	0
	testVerdict	1478592517876	3
jalview.analysis.CrossRefTest	testFindXDbRefs	1478592566131	1
	testFindXrefSequences_fromDbRefMap	1478592566142	2
	testFindXrefSequences_indirectDbrefToNucleotide	1478592566145	1
	testFindXrefSequences_indirectDbrefToProtein	1478592566147	2
	testFindXrefSequences_noDbrefs	1478592566151	3
	testFindXrefSourcesForSequence_proteinToDna	1478592566166	2
	testSameSequence	1478592566169	2
	testSearchDataset	1478592566172	2
jalview.analysis.DnaTest	testCompareCodonPos	1478592610910	3
	testCompareCodonPos_isSymmetric	1478592610914	2
	testCompareCodonPos_oneOnly	1478592610917	1
	testConvertCodon	1478592610918	1
	testGetComplement	1478592610919	1
	testReverseCdna	1478592610920	1
	testReverseSequence	1478592610922	1
	testTranslateCdna_hiddenColumns	1478592610924	2
	testTranslateCdna_sequenceOrderIndependent	1478592610926	5
	testTranslateCdna_simple	1478592610932	1
	testTranslateCdna_withUntranslatableCodons	1478592610934	6
	testTranslateCdna_withUntranslatableCodonsAndHiddenColumns	1478592610941	27
jalview.analysis.GroupingTest	testMakeGroupsWithBoth	1478592508954	5
jalview.analysis.ParsePropertiesTest	testGetScoresFromDescription	1478592574538	2
	testGetScoresFromDescription_twoScores	1478592574541	2
	testGetScoresFromDescription_wordBoundaries	1478592574544	2
jalview.analysis.RnaTest	testGetMatchingOpeningParenthesis	1478592566814	1
	testGetRNASecStrucState	1478592566816	0
	testGetSimpleBPs	1478592566817	1
	testGetSimpleBPs_unmatchedCloser	1478592566819	1
	testGetSimpleBPs_unmatchedOpener	1478592566821	1
	testIsCanonicalOrWobblePair	1478592566822	1
	testIsCanonicalPair	1478592566824	0
	testIsClosingParenthesis	1478592566825	20
	testIsOpeningParenthesis	1478592566846	19
	testIsRnaSecondaryStructureSymbol	1478592566866	15
jalview.analysis.SeqsetUtilsTest	testSeqFeatureAddition	1478592507533	8
jalview.analysis.SequenceIdMatcherTest	test_seqIdNameEquals	1478592610803	0
jalview.analysis.TestAlignSeq	testExtractGaps	1478592667016	0
	testGetMappingForS1	1478592667017	0
	testPrintAlignment	1478592667018	0
jalview.analysis.scoremodels.FeatureScoreModelTest	testFeatureScoreModel	1478592610973	507
	testFeatureScoreModel_HiddenColumns	1478592611480	506
	testFeatureScoreModel_hiddenFirstColumn	1478592611987	507
jalview.bin.ArgsParserTest	testContains	1478592507704	4
	testGetValue	1478592507710	2
	testGetValue_decoded	1478592507715	2
	testNextValue	1478592507720	2
jalview.bin.CacheTest	testSetDateProperty	1478592571283	1
jalview.bin.CommandLineOperations	testAllInputOperations	1478592579204	0
	testAllInputOperations
	testAllInputOperations
	testAllInputOperations
	testAllInputOperations
	testAllInputOperations
	testAllInputOperations
	testAllInputOperations
	testAllInputOperations
	testAllInputOperations
	testAllInputOperations
	testAllInputOperations
	testHeadlessModeOutputOperations	1478592591479	3056
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
	testHeadlessModeOutputOperations
jalview.bin.JalviewLiteTest	testSeparatorListToArray	1478592507791	5
jalview.commands.EditCommandTest	testAddEdit_groupInsertGaps	1478592517933	3
	testAddEdit_multipleDeleteGap	1478592517938	1
	testAddEdit_multipleInsertGap	1478592517941	1
	testAddEdit_removeAllGaps	1478592517945	0
	testAppendEdit_deleteGap	1478592517946	1
	testAppendEdit_insertGap	1478592517949	1
	testCut	1478592517951	1
	testPriorState_multipleInserts	1478592517953	1
	testPriorState_removeAllGaps	1478592517955	2
	testPriorState_removeGappedCols	1478592517958	1
	testPriorState_removeGapsMultipleSeqs	1478592517961	1
	testPriorState_singleDelete	1478592517963	1
	testPriorState_singleInsert	1478592517966	1
	testPriorState_singleInsertWithOffset	1478592517968	1
	testReplace	1478592517970	1
	testUndo_cut	1478592517972	1
	testUndo_deleteGap	1478592517975	1
	testUndo_insertGap	1478592517978	1
	testUndo_multipleCommands	1478592517981	1
	testUndo_multipleInsertGaps	1478592517983	1
jalview.commands.TrimRegionCommandTest	testTrimLeft_noColumns	1478592566801	1
	testTrimLeft_oneColumn	1478592566803	2
	testTrimLeft_withUndoAndRedo	1478592566807	1
	testTrimRight_noColumns	1478592566809	1
	testTrimRight_oneColumn	1478592566811	0
	testTrimRight_withUndoAndRedo	1478592566812	1
jalview.controller.AlignViewControllerTest	testFindColumnsWithFeature	1478592507780	2
jalview.datamodel.AlignedCodonFrameTest	testAddMap	1478592571227	1
	testCouldReplaceSequence	1478592571229	1
	testFindAlignedSequence	1478592571231	1
	testGetMappedCodons	1478592571233	1
	testGetMappedCodons_dnaVariants	1478592571235	0
	testGetMappedCodons_forSubSequences	1478592571236	1
	testGetMappedRegion	1478592571238	1
	testGetMappedRegion_eitherWay	1478592571240	1
	testIsRealisableWith	1478592571243	0
	testRealiseWith	1478592571244	1
jalview.datamodel.AlignedCodonIteratorTest	testAnother	1478592610804	0
	testNext	1478592610805	0
	testNext_incompleteCodon	1478592610805	1
	testNext_unmappedPeptide	1478592610807	0
	testNext_withOffset	1478592610808	1
jalview.datamodel.AlignedCodonTest	testEquals	1478592662612	1
jalview.datamodel.AlignedCodonTest	testToString	1478592662613	1
jalview.datamodel.AlignmentAnnotationTests	testAdjustForAlignment	1478592571291	1
	testCopyConstructor	1478592571293	1
	testGetDefaultRnaHelixSymbol	1478592571296	1
	testLiftOver	1478592571298	2
jalview.datamodel.AlignmentTest	getVisibleStartAndEndIndexTest	1478592599876	0
	testAddCodonFrame	1478592599879	1
	testAddSequencePreserveDatasetIntegrity	1478592599883	1
	testAlignAs_cdnaAsProtein	1478592599888	2
	testAlignAs_cdnaAsProtein_singleSequence	1478592599894	2
	testAlignAs_dnaAsDna	1478592599900	3
	testAlignAs_proteinAsCdna	1478592599912	1
	testAssertDatasetIsNormalised	1478592599917	3
	testCopyConstructor	1478592599926	6
	testCreateDatasetAlignment	1478592599941	1
	testCreateDatasetAlignmentWithMappedToSeqs	1478592599949	2
	testCreateDataset_updateDbrefMappings	1478592599957	1
	testDeleteAllAnnotations_excludingAutocalculated	1478592599961	2
	testDeleteAllAnnotations_includingAutocalculated	1478592599966	1
	testFindAnnotation_byCalcId	1478592599971	0
	testVerifyAlignmentDatasetRefs	1478592599977	3
jalview.datamodel.AlignmentViewTest	testGetVisibleAlignmentGapChar	1478592566121	2
jalview.datamodel.ColumnSelectionTest	testAddElement	1478592616384	2
	testCopyConstructor	1478592616387	1
	testEquals	1478592616389	1
	testFindColumnPosition	1478592616393	0
	testGetSelected	1478592616394	2
	testGetSelectedRanges	1478592616397	0
	testGetSelected_concurrentModification	1478592616400	5
	testGetSelected_isReadOnly	1478592616410	1
	testGetVisibleContigs	1478592616413	1
	testHideColumns	1478592616415	0
	testHideColumns_withSelection	1478592616416	1
	testHideSelectedColumns	1478592616418	1
	testInvertColumnSelection	1478592616420	0
	testIsVisible	1478592616421	1
	testLocateVisibleBoundsPathologicals	1478592616423	0
	testLocateVisibleBoundsofSequence	1478592616424	1
	testMarkColumns	1478592616426	0
	testMarkColumns_extend	1478592616427	1
	testMarkColumns_invert	1478592616428	2
	testMarkColumns_toggle	1478592616431	1
	testMaxColumnSelection	1478592616433	1
	testMinColumnSelection	1478592616435	1
	testRemoveElement	1478592616436	5
	testRevealAllHiddenColumns	1478592616442	1
	testRevealHiddenColumns	1478592616444	1
jalview.datamodel.DBRefEntryTest	testEqualRef	1478592517353	2
	testIsPrimaryCandidate	1478592517357	1
	testUpdateFrom	1478592517361	1
jalview.datamodel.HiddenSequencesTest	testAdjustForHiddenSeqs	1478592605417	1
	testAdjustHeightSequenceAdded	1478592605419	0
	testAdjustHeightSequenceDeleted	1478592605420	0
	testFindIndexWithoutHiddenSeqs	1478592605421	0
	testGetFullAlignment	1478592605422	0
	testGetHiddenSequence	1478592605423	0
	testGetSize	1478592605423	1
	testGetWidth	1478592605424	1
	testHideShowSequence	1478592605425	1
	testHideShowSequence_withHiddenRepSequence	1478592605426	1
	testIsHidden	1478592605428	1
jalview.datamodel.MappingTest	testCopyConstructor	1478592508961	3
	testIntersectVisContigs	1478592508968	2
	testToString	1478592508972	2
jalview.datamodel.MappingTypeTest	testGetFromRatio	1478592564722	1
	testGetInverse	1478592564724	1
	testGetToRatio	1478592564727	1
jalview.datamodel.MatchTest	testEquals	1478592507783	2
	testGetCharacters	1478592507786	1
	testToString	1478592507789	1
jalview.datamodel.PDBEntryTest	testConstructor_fromDbref	1478592507545	2
	testEquals	1478592507550	3
	testGetType	1478592507556	2
	testSetChainCode	1478592507561	2
	testTypeMatches	1478592507566	2
	testUpdateFrom	1478592507571	1
jalview.datamodel.ResidueCountTest	testAddGap	1478592661338	1
	testGetModalCount	1478592661340	1
	testGetResiduesForCount	1478592661342	0
	testGetSymbolCounts_nucleotide	1478592661343	7
	testGetSymbolCounts_peptide	1478592661352	0
	testGetTooltip	1478592661353	1
	testOverflow	1478592661355	0
	testPut	1478592661356	1
	testToString	1478592661358	0
	test_countNucleotide	1478592661360	0
	test_countPeptide	1478592661362	2
	test_unexpectedNucleotide	1478592661365	1
	test_unexpectedPeptide	1478592661367	1
jalview.datamodel.SearchResultsTest	testEquals	1478592564158	2
	testEquals_distinctSequences	1478592564162	1
	testEquals_orderDiffers	1478592564164	1
	testGetCharacters	1478592564166	2
	testHashcode	1478592564169	1
	testMatchConstructor	1478592564171	1
	testToString	1478592564173	1
jalview.datamodel.SeqCigarTest	testFindPosition	1478592610812	1
jalview.datamodel.SeqCigarTest	testSomething	1478592610813	9
jalview.datamodel.SequenceDummyTest	testBecome	1478592616350	1
jalview.datamodel.SequenceFeatureTest	testCopyConstructor	1478592566175	1
	testEqualsAndHashCode	1478592566176	1
	testGetStrand	1478592566178	0
	testGetValue	1478592566179	1
jalview.datamodel.SequenceTest	testAddAlignmentAnnotation	1478592662558	1
	testAddDBRef	1478592662560	2
	testAddPDBId	1478592662563	1
	testCopyConstructor_noDataset	1478592662565	1
	testCopyConstructor_withDataset	1478592662567	1
	testCreateDatasetSequence	1478592662570	0
	testDeleteChars	1478592662571	1
	testDeriveSequence_existingDataset	1478592662572	2
	testDeriveSequence_noDatasetGapped	1478592662574	1
	testDeriveSequence_noDatasetUngapped	1478592662576	0
	testFindIndex	1478592662577	1
	testFindPosition	1478592662579	0
	testFindPositionMap	1478592662580	1
	testGapMap	1478592662582	1
	testGetAlignmentAnnotations_forCalcIdAndLabel	1478592662584	0
	testGetAnnotation	1478592662585	1
	testGetAnnotation_forLabel	1478592662587	0
	testGetCharAt	1478592662588	0
	testGetPrimaryDBRefs_nucleotide	1478592662589	1
	testGetPrimaryDBRefs_peptide	1478592662591	1
	testGetSequenceFeatures	1478592662593	1
	testGetStartGetEnd	1478592662595	1
	testGetSubsequence	1478592662597	0
	testInsertCharAt	1478592662598	0
	testInsertGapsAndGapmaps	1478592662599	1
	testIsProtein	1478592662601	1
	testSetDatasetSequence_cascading	1478592662603	1
	testSetDatasetSequence_toSelf	1478592662605	1
	testUpdatePDBIds	1478592662607	1
jalview.datamodel.xdb.embl.EmblEntryTest	testAdjustForProteinLength	1478592517528	11
	testGetCdsRanges	1478592517541	4
	testParseCodingFeature	1478592517547	312
jalview.datamodel.xdb.embl.EmblFileTest	testGetEmblFile	1478592662517	10
jalview.ext.android.SparseIntArrayTest	testAdd	1478592610799	1
	testCheckOverflow	1478592610800	1
	testPut	1478592610801	1
jalview.ext.android.SparseShortArrayTest	testAdd	1478592612496	1
jalview.ext.android.SparseShortArrayTest	testPut	1478592612498	1
jalview.ext.ensembl.EnsemblCdnaTest	testGetGenomicRangesFromFeatures	1478592616373	1
	testGetGenomicRangesFromFeatures_mixedStrand	1478592616375	1
	testGetGenomicRangesFromFeatures_reverseStrand	1478592616377	0
	testIdentifiesSequence	1478592616378	1
	testIsValidReference	1478592616379	1
	testRetainFeature	1478592616381	1
jalview.ext.ensembl.EnsemblCdsTest	testGetGenomicRangesFromFeatures	1478592567969	2
	testIdentifiesSequence	1478592567972	0
	testIsValidReference	1478592567973	1
	testRetainFeature	1478592567975	1
jalview.ext.ensembl.EnsemblGeneTest	testGetFeatureColourScheme	1478592616332	10
	testGetGenomicRangesFromFeatures	1478592616343	1
	testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand	1478592616345	0
	testGetTranscriptFeatures	1478592616346	1
	testIdentifiesSequence	1478592616347	1
	testRetainFeature	1478592616348	1
jalview.ext.ensembl.EnsemblGenomeTest	testGetGenomicRangesFromFeatures	1478592616352	3
	testIdentifiesSequence	1478592616356	0
	testRetainFeature	1478592616357	1
jalview.ext.ensembl.EnsemblProteinTest	testGetAccesionIdFromQuery	1478592574503	1
jalview.ext.ensembl.EnsemblProteinTest	testIsValidReference	1478592574518	12
jalview.ext.ensembl.EnsemblSeqProxyTest	getGenomicRangesFromFeatures	1478592616230	1
	testIsGeneIdentifier	1478592616232	1
	testIsTranscriptIdentifier	1478592616233	1
	testReverseComplementAllele	1478592616235	1
	testReverseComplementAlleles	1478592616236	1
	testSortFeatures	1478592616238	1
jalview.ext.ensembl.EnsemblXrefTest	testGetCrossReferences	1478592667019	1
jalview.ext.htsjdk.TestHtsContigDb	testHTSReferenceSequence	1478592566912	98
jalview.ext.jmol.JmolCommandsTest	testGetColourBySequenceCommand_noFeatures	1478592571304	67
jalview.ext.jmol.JmolParserTest	testAlignmentLoader	1478592606398	2521
	testFileParser	1478592608920	938
	testLocalPDBId	1478592609859	358
	testParse_alternativeResidues	1478592610219	341
	testParse_missingResidues	1478592610562	207
	testSetSecondaryStructure	1478592610771	1
jalview.ext.jmol.JmolViewerTest	testSingleSeqViewJMol	1478592568814	2008
jalview.ext.rbvi.chimera.ChimeraCommandsTest	testAddColourRange	1478592519224	4
jalview.ext.rbvi.chimera.ChimeraCommandsTest	testBuildColourCommands	1478592519229	3
jalview.ext.rbvi.chimera.ChimeraConnect	testLaunchAndExit	1478592567011	935
jalview.ext.rbvi.chimera.JalviewChimeraView	testSingleSeqViewChimera	1478592557636	5333
jalview.ext.so.SequenceOntologyTest	testIsA	1478592518977	1
jalview.ext.so.SequenceOntologyTest	testIsCDS	1478592518979	1
jalview.fts.core.FTSRestClientTest	coverageForEqualsAndHashFunction	1478592616172	8
	coverageForExceptionBranches	1478592616181	3
	coverageForMiscellaneousBranches	1478592616185	2
	getAllDefaulDisplayedDataColumns	1478592616188	3
	getAllFTSDataColumns	1478592616191	3
	getColumnClassTest	1478592616195	2
	getColumnMaxWidthTest	1478592616198	2
	getColumnMinWidthTest	1478592616201	2
	getColumnPreferredWidthTest	1478592616204	2
	getDataColumnByNameOrCode	1478592616207	2
	getDataColumnGroupById	1478592616210	2
	getDataColumnsFieldsAsCommaDelimitedString	1478592616213	2
	getDefaultResponsePageSize	1478592616216	2
	getPrimaryKeyColumIndexTest	1478592616219	2
	getPrimaryKeyColumn	1478592616223	2
	getSearchableDataColumns	1478592616227	2
jalview.fts.service.pdb.PDBFTSPanelTest	populateCmbSearchTargetOptionsTest	1478592517988	256
	testDecodeSearchTerm	1478592518245	1
	testgetPDBIdwithSpecifiedChain	1478592518247	1
jalview.fts.service.pdb.PDBFTSRestClientTest	getPDBDocFieldsAsCommaDelimitedStringTest	1478592662247	1
jalview.fts.service.pdb.PDBFTSRestClientTest	getPDBIdColumIndexTest	1478592662251	1
jalview.gui.AlignFrameTest	testHideFeatureColumns	1478592517889	32
jalview.gui.AlignViewportTest	testCollateForPdb	1478592662704	1
	testDeregisterMapping_onCloseView	1478592662706	925
	testDeregisterMapping_withNoReference	1478592663633	1180
	testDeregisterMapping_withReference	1478592664814	1189
	testSetGlobalColourScheme	1478592666004	506
	testUpdateConservation_qualityOnly	1478592666511	504
jalview.gui.AnnotationChooserTest	testBuildActionButtonsPanel	1478592612533	24
	testBuildApplyToOptionsPanel_noSelectionGroup	1478592612610	19
	testBuildApplyToOptionsPanel_withSelectionGroup	1478592612684	19
	testBuildShowHideOptionsPanel	1478592612751	23
	testBuildShowHidePanel	1478592612830	21
	testDeselectType_hideForAll	1478592612906	24
	testDeselectType_hideForSelected	1478592613036	26
	testDeselectType_showForAll	1478592613190	34
	testDeselectType_showForSelected	1478592613380	56
	testGetAnnotationTypes	1478592613559	29
	testIsInActionScope_selectedScope	1478592613678	18
	testIsInActionScope_unselectedScope	1478592613827	17
	testResetOriginalState	1478592613932	29
	testSelectType_hideForAll	1478592614041	19
	testSelectType_hideForSelected	1478592614116	16
	testSelectType_showForAll	1478592614247	14
	testSelectType_showForSelected	1478592614310	18
jalview.gui.AppVarnaTest	testReplaceOddGaps	1478592616325	5
jalview.gui.HelpTest	checkHelpTargets	1478592610772	23
jalview.gui.JvSwingUtilsTest	testGetScrollBarProportion	1478592571274	1
	testGetScrollValueForProportion	1478592571276	1
	testWrapTooltip_longText	1478592571278	0
	testWrapTooltip_multilineShortText	1478592571279	1
	testWrapTooltip_shortText	1478592571281	1
jalview.gui.PaintRefresherTest	testGetAssociatedPanels	1478592519234	49
	testRegister	1478592519286	2
	testRemoveComponent	1478592519290	1
jalview.gui.PopupMenuTest	testAddFeatureLinks	1478592614594	278
	testBuildAnnotationTypesMenus	1478592614920	3
	testBuildAnnotationTypesMenus_hideDisabled	1478592614971	2
	testBuildAnnotationTypesMenus_showDisabled	1478592615016	3
	testConfigureReferenceAnnotationsMenu	1478592615060	6
	testConfigureReferenceAnnotationsMenu_alreadyAdded	1478592615103	1
	testConfigureReferenceAnnotationsMenu_noReferenceAnnotations	1478592615134	1
	testConfigureReferenceAnnotationsMenu_noSequenceSelected	1478592615171	0
	testConfigureReferenceAnnotationsMenu_notOnAlignment	1478592615220	1
	testConfigureReferenceAnnotationsMenu_twoViews	1478592615280	1
jalview.gui.ProgressBarTest	testConstructor_prematureInstantiation	1478592508910	2
	testConstructor_wrongLayout	1478592508914	1
	testSetProgressBar	1478592508917	24
jalview.gui.SequenceRendererTest	testGetResidueBoxColour_zappo	1478592507884	2
jalview.gui.StructureChooserTest	buildQueryTest	1478592605513	20
	fetchStructuresInfoTest	1478592605534	696
	populateFilterComboBoxTest	1478592606232	161
	sanitizeSeqNameTest	1478592606395	1
jalview.gui.StructureViewerTest	testGetUniquePdbFiles	1478592661368	2
jalview.io.AnnotatedPDBFileInputTest	checkAnnotationWiring	1478592575141	1
	checkNoDuplicates	1478592575644	2
	checkPDBSequenceFeatures	1478592576148	1
	checkPDBannotationSource	1478592576651	1
	testJalviewProjectRelocationAnnotation	1478592577158	1745
jalview.io.AnnotationFileIOTest	exampleAnnotationFileIO	1478592661371	357
jalview.io.BioJsHTMLOutputTest	expectedNullPointerException	1478592571385	1
	getBioJsMSAVersions	1478592571388	3
	getJalviewAlignmentAsJsonString	1478592571393	3026
jalview.io.FeaturesFileTest	readGff3File	1478592615294	2
	simpleGff3FileClass	1478592615297	2
	simpleGff3FileLoader	1478592615299	504
	simpleGff3RelaxedIdMatching	1478592615804	2
	testParse	1478592615806	54
	testParse_jalviewFeaturesOnly	1478592615861	31
	testParse_mixedJalviewGff	1478592615893	111
	testParse_pureGff3	1478592616005	132
	testPrintJalviewFormat	1478592616138	33
jalview.io.FileIOTester	testGzipIo	1478592508978	6
	testGziplocalFileIO	1478592508986	2
	testNonGzipURLIO	1478592508990	5
	testNonGziplocalFileIO	1478592508996	2
	testStarsInFasta1	1478592508999	5
	testStarsInFasta2	1478592509006	6
jalview.io.FormatAdapterTest	testRoundTrip	1478592616454	3
	testRoundTrip
	testRoundTrip
	testRoundTrip
	testRoundTrip
	testRoundTrip
	testRoundTrip
	testRoundTrip
	testRoundTrip
	testRoundTrip
jalview.io.IdentifyFileTest	testIdentify	1478592605462	3
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify
	testIdentify_featureFile	1478592605504	1
	testLooksLikeFeatureData	1478592605505	0
jalview.io.JSONFileTest	colorSchemeTest	1478592518249	1
	hiddenColsTest	1478592518251	1
	hiddenSeqsTest	1478592518253	0
	isShowSeqFeaturesSet	1478592518254	1
	roundTripTest	1478592518256	0
	testAnnotationParsed	1478592518257	1
	testGrpParsed	1478592518259	1
	testSeqParsed	1478592518261	1
jalview.io.Jalview2xmlTests	gatherViewsHere	1478592616605	6095
	testColourByAnnotScores	1478592622701	1988
	testCopyViewSettings	1478592624690	3708
	testIsVersionStringLaterThan	1478592628398	1
	testRNAStructureRecovery	1478592628400	2293
	testStoreAndRecoverExpandedviews	1478592630693	12179
	testStoreAndRecoverGroupRepSeqs	1478592642873	3228
	testStoreAndRecoverPDBEntry	1478592646102	1638
	testStoreAndRecoverReferenceSeqSettings	1478592647741	8032
	testTCoffeeScores	1478592655774	1197
	viewRefPdbAnnotation	1478592656972	3238
jalview.io.JalviewExportPropertiesTests	testImportExportPeriodGaps	1478592563359	507
jalview.io.NewickFileTests	testTreeIO	1478592507574	34
	testTreeIO
	testTreeIO
jalview.io.PfamFormatInputTest	testPfamFormatNoLimits	1478592517344	5
jalview.io.PfamFormatInputTest	testPfamFormatValidLimits	1478592517351	1
jalview.io.PhylipFileTests	testInterleavedDataExtraction	1478592508699	91
	testInterleavedIO	1478592508794	51
	testSequentialDataExtraction	1478592508847	14
	testSequentialIO	1478592508893	14
jalview.io.SequenceAnnotationReportTest	testAppendFeature_DescEqualsType	1478592507838	2
	testAppendFeature_clinicalSignificance	1478592507843	2
	testAppendFeature_disulfideBond	1478592507847	1
	testAppendFeature_noScore	1478592507850	1
	testAppendFeature_status	1478592507854	1
	testAppendFeature_stripHtml	1478592507856	2
	testAppendFeature_withScore	1478592507861	1
	testAppendFeature_withScoreStatusClinicalSignificance	1478592507865	2
jalview.io.StockholmFileTest	pfamFileDataExtraction	1478592564194	97
	pfamFileIO	1478592564293	234
	rfamFileIO	1478592564529	178
jalview.io.TCoffeeScoreFileTest	testGetAsArray	1478592662494	7
	testGetAsList	1478592662501	1
	testHeightAndWidth	1478592662503	1
	testHeightAndWidthWithResidueNumbers	1478592662505	3
	testParse	1478592662508	1
	testReadBlock	1478592662510	0
	testReadHeader	1478592662511	1
	testWrongFile	1478592662512	3
jalview.io.gff.ExonerateHelperTest	testAddExonerateGffToAlignment	1478592661734	506
	testGetMappingType	1478592662240	1
	testProcessGffSimilarity_protein2dna_forward_querygff	1478592662242	1
	testProcessGffSimilarity_protein2dna_forward_targetgff	1478592662243	1
	testProcessGffSimilarity_protein2dna_reverse_querygff	1478592662244	1
	testProcessGffSimilarity_protein2dna_reverse_targetgff	1478592662246	0
jalview.io.gff.Gff3HelperTest	testProcessCdnaMatch_forwardToForward	1478592566888	1
	testProcessCdnaMatch_forwardToReverse	1478592566890	1
	testProcessCdnaMatch_reverseToForward	1478592566891	1
	testProcessCdnaMatch_spliced	1478592566893	1
jalview.io.gff.GffHelperBaseTest	testParseNameValuePairs	1478592563258	2
jalview.io.gff.GffHelperBaseTest	testTrimMapping	1478592563261	2
jalview.io.gff.GffHelperFactoryTest	testGetHelper	1478592518981	8
jalview.io.gff.GffTests	testResolveExonerateGff	1478592518269	512
jalview.io.gff.InterProScanHelperTest	testProcessProteinMatch	1478592605412	1
jalview.schemes.DnaCodonTests	regenerateCodonTable	1478592517881	4
	testAmbiguityCodeGeneration	1478592517886	0
	testAmbiguityCodon	1478592517887	1
jalview.schemes.FeatureColourTest	testCopyConstructor	1478592616242	0
	testGetColor_Graduated	1478592616243	1
	testGetColor_belowThreshold	1478592616245	0
	testGetColor_colourByLabel	1478592616246	1
	testGetColor_simpleColour	1478592616247	1
	testIsColored_aboveThreshold	1478592616248	1
	testIsColored_colourByLabel	1478592616250	0
	testIsColored_simpleColour	1478592616251	1
	testParseJalviewFeatureColour	1478592616252	2
	testToJalviewFormat	1478592616254	2
jalview.schemes.ResidueColourSchemeTest	testAboveThreshold	1478592662609	1
jalview.schemes.ResidueColourSchemeTest	testApplyConservation	1478592662610	1
jalview.schemes.ResiduePropertiesTest	testCodonTranslate	1478592509188	2
	testCodonTranslate_ambiguityCodes	1478592509195	2
	testGetCanonicalAminoAcid	1478592509199	3
	testGetResidues_nucleotide	1478592509218	3
	testGetResidues_peptide	1478592509229	6
	testGetSingleCharacterCode	1478592509237	1
	testPhysicoChemicalProperties	1478592509240	3
jalview.schemes.ScoreMatrixPrinter	printAllMatrices	1478592614331	1
jalview.schemes.ScoreMatrixPrinter	printHTMLMatrices	1478592614333	2
jalview.schemes.UserColourSchemeTest	testGetColourFromString	1478592615282	1
jalview.structure.Mapping	compareTransferredToRefPDBAnnot	1478592509367	2900
jalview.structure.Mapping	mapFer1From3W5V	1478592512268	5059
jalview.structure.StructureSelectionManagerTest	testRegisterMapping	1478592566318	1
	testRegisterMappings	1478592566320	1
	testSetMapping_seqFeatures	1478592566323	475
jalview.structures.models.AAStructureBindingModelTest	testFindSuperposableResidues	1478592598727	1
jalview.structures.models.AAStructureBindingModelTest	testFindSuperposableResidues_hiddenColumn	1478592599869	0
jalview.util.ArrayUtilsTest	testReverseIntArray	1478592564190	3
jalview.util.CaseInsensitiveStringTest	testEquals	1478592517985	0
jalview.util.CaseInsensitiveStringTest	testHashcode	1478592517986	1
jalview.util.ColorUtilsTest	testBleachColour	1478592564181	0
	testBrighterThan	1478592564183	1
	testDarkerThan	1478592564185	1
	testGetGraduatedColour	1478592564187	0
	testToTkCode	1478592564188	1
jalview.util.ComparisonTest	compareCharsTest	1478592616360	0
	testIsGap	1478592616361	1
	testIsNucleotide	1478592616362	1
	testIsNucleotideSequence	1478592616364	0
	testIsNucleotide_sequences	1478592616365	1
	testPID_includingGaps	1478592616367	1
	testPID_ungappedOnly	1478592616368	1
jalview.util.DBRefUtilsTest	testGetCanonicalName	1478592567954	1
	testIsDasCoordinateSystem	1478592567959	1
	testParseToDbRef	1478592567960	1
	testParseToDbRef_PDB	1478592567962	1
	testSearchRefs_accessionid	1478592567964	0
	testSearchRefs_noMapping	1478592567965	0
	testSearchRefs_wildcardAccessionid	1478592567966	0
	testSearchRefs_withMapping	1478592567967	0
	testSelectRefs	1478592567968	1
jalview.util.DnaUtilsTest	testParseLocation	1478592509357	4
jalview.util.FormatTest	testAppendPercentage	1478592509014	2
	testForm_float	1478592509018	4
	testRepeat	1478592509024	2
jalview.util.MapListTest	testAddMapList	1478592509028	3
	testAddMapList_contiguous	1478592509033	2
	testAddMapList_sameMap	1478592509037	1
	testAddRange	1478592509040	4
	testCoalesceRanges	1478592509047	8
	testCoalesceRanges_withOverlap	1478592509056	2
	testConstructor	1478592509061	2
	testConstructor_mergeRanges	1478592509065	3
	testConstructor_withLists	1478592509070	2
	testEquals	1478592509076	6
	testGetInverse	1478592509085	2
	testGetRanges	1478592509089	1
	testIsFromForwardStrand	1478592509092	2
	testLocateInFrom_noIntrons	1478592509103	2
	testLocateInFrom_withIntrons	1478592509107	3
	testLocateInTo_noIntrons	1478592509112	3
	testLocateInTo_withIntrons	1478592509117	4
	testSomething	1478592509123	45
	testToString	1478592509170	1
jalview.util.MappingUtilsTest	testBuildSearchResults	1478592662528	1
	testBuildSearchResults_withIntron	1478592662530	1
	testContains	1478592662531	1
	testFindMappingsForSequence	1478592662532	1
	testFindMappingsForSequenceAndOthers	1478592662533	1
	testFlattenRanges	1478592662534	1
	testFlattenRanges_reverseStrand	1478592662535	1
	testGetLength	1478592662537	0
	testMapColumnSelection_dnaToProtein	1478592662538	1
	testMapColumnSelection_hiddenColumns	1478592662540	2
	testMapColumnSelection_null	1478592662542	1
	testMapColumnSelection_proteinToDna	1478592662544	1
	testMapEditCommand	1478592662546	1
	testMapSequenceGroup_columns	1478592662547	2
	testMapSequenceGroup_region	1478592662549	2
	testMapSequenceGroup_sequences	1478592662552	1
	testRemoveStartPositions	1478592662554	0
	testRemoveStartPositions_reverseStrand	1478592662556	0
jalview.util.ParseHtmlBodyAndLinksTest	testParseHtml_noLinks	1478592661729	1
	testParseHtml_withLinks	1478592661730	1
	testParseHtml_withLinksWithEncoding	1478592661732	0
	testParseHtml_withLinksWithParameters	1478592661733	0
jalview.util.PlatformTest	testIsControlDown_mac	1478592571301	1
jalview.util.PlatformTest	testIsControlDown_notMac	1478592571303	0
jalview.util.QuickSortTest	testCharSortByFloat	1478592507798	4
	testCharSortByInt	1478592507805	1
	testSortByInt	1478592507807	3
	testSortByString	1478592507811	4
	testSort_byDoubleValues	1478592507817	1
	testSort_byFloatValues	1478592507820	1
	testSort_byIntValues	1478592507822	2
	testSort_byStringValues	1478592507827	1
	testSort_charSortByFloat_mostlyZeroValues	1478592507830	2
	testSort_charSortByInt_mostlyZeroValues	1478592507834	2
jalview.util.ShiftListTest	testParseMap	1478592509363	2
jalview.util.SparseCountTest	testAdd	1478592566181	0
	testKeyAt_ValueAt	1478592566184	1
	testOverflow	1478592566186	2
	testPut	1478592566190	1
	testUnderflow	1478592566192	1
jalview.util.StringUtilsTest	testArrayToSeparatorList	1478592566895	1
	testCompareVersions	1478592566897	1
	testDeleteChars	1478592566900	1
	testGetLastToken	1478592566901	1
	testInsertCharAt	1478592566903	0
	testListToDelimitedString	1478592566904	1
	testParseInt	1478592566906	1
	testSeparatorListToArray	1478592566908	2
	testToSentenceCase	1478592566911	1
jalview.util.UrlLinkTest	testCreateLinksForNonDynamic	1478592597603	2
	testCreateLinksFromNullSequence	1478592597606	0
	testCreateLinksFromSequence	1478592597607	1
	testMakeUrlNoRegex	1478592597609	1
	testMakeUrlWithRegex	1478592597610	2
	testUrlLinkCreationNoRegex	1478592597613	1
	testUrlLinkCreationWithRegex	1478592597614	1
jalview.viewmodel.styles.ViewStyleTest	testCopyConstructor	1478592508688	3
jalview.viewmodel.styles.ViewStyleTest	testEquals	1478592508693	3
jalview.workers.AlignCalcManagerTest	testRemoveWorkerForAnnotation	1478592662386	108
jalview.ws.dbsources.UniprotTest	testGetUniprotEntries	1478592616256	34
	testGetUniprotEntryDescription	1478592616291	9
	testGetUniprotEntryId	1478592616301	11
	testGetUniprotSequence	1478592616313	11
jalview.ws.ebi.EBIFetchClientTest	testBuildUrl	1478592605506	3
jalview.ws.ebi.EBIFetchClientTest	testParseIds	1478592605510	0
jalview.ws.jws2.ParameterUtilsTest	testCopyOption	1478592555295	257
	testCopyParameter	1478592555554	244
	testWriteParameterSet	1478592555800	1607
jalview.ws.rest.RestClientTest	testGetRestClient	1478592616370	2
jalview.ws.rest.ShmmrRSBSService	testShmmrService	1478592507888	16
jalview.ws.rest.ShmmrRSBSService	testShmmrServiceDataprep	1478592507906	781
jalview.ws.seqfetcher.DbRefFetcherTest	testStandardProtDbs	1478592518990	223
jalview.ws.sifts.SiftsClientTest	downloadSiftsFileTest	1478592599981	396
	getAllMappingAccessionTest	1478592600378	0
	getAtomIndexNullTest	1478592600379	0
	getAtomIndexTest	1478592600380	0
	getDbAccessionIdTest	1478592600381	0
	getDbCoordSysTest	1478592600382	0
	getDbSourceTest	1478592600383	1
	getDbVersionTest	1478592600384	1
	getEntityByMostOptimalMatchedIdTest1	1478592600386	4291
	getEntityByMostOptimalMatchedIdTest2	1478592604678	460
	getEntityCountTest	1478592605139	0
	getSIFTsFileTest	1478592605144	249
	getValidSourceDBRefExceptionTest	1478592605397	2
	getValidSourceDBRefExceptionXTest	1478592605401	1
	getValidSourceDBRefTest	1478592605404	0
	isValidDBRefEntryTest	1478592605405	1
	padWithGapsTest	1478592605407	1
	populateAtomPositionsNullTest1	1478592605408	1
	populateAtomPositionsNullTest2	1478592605410	0

GRP-Functional

jalview.ws.jabaws.JpredJabaStructExportImport#setUpBeforeClass

Exception
java.lang.AssertionError: Failed to discover any services at expected [true] but found [false] at org.testng.Assert.fail(Assert.java:94) at org.testng.Assert.failNotEquals(Assert.java:513) at org.testng.Assert.assertTrue(Assert.java:42) at jalview.ws.jabaws.JalviewJabawsTestUtils.getJabawsDiscoverer(JalviewJabawsTestUtils.java:103) at jalview.ws.jabaws.JpredJabaStructExportImport.setUpBeforeClass(JpredJabaStructExportImport.java:71) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeConfigurationMethod(Invoker.java:515) at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:216) at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:143) at org.testng.internal.TestMethodWorker.invokeBeforeClassMethods(TestMethodWorker.java:169) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Exception

java.lang.AssertionError: Failed to discover any services at expected [true] but found [false] at org.testng.Assert.fail(Assert.java:94) at org.testng.Assert.failNotEquals(Assert.java:513) at org.testng.Assert.assertTrue(Assert.java:42) at jalview.ws.jabaws.JalviewJabawsTestUtils.getJabawsDiscoverer(JalviewJabawsTestUtils.java:103) at jalview.ws.jabaws.JpredJabaStructExportImport.setUpBeforeClass(JpredJabaStructExportImport.java:71) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeConfigurationMethod(Invoker.java:515) at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:216) at org.testng.internal.Invoker.invokeConfigurations(Invoker.java:143) at org.testng.internal.TestMethodWorker.invokeBeforeClassMethods(TestMethodWorker.java:169) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Parameter #1	Parameter #2	Parameter #3	Parameter #4	Parameter #5	Parameter #6
headless -open examples/uniref50.fa	-pileup	test_uniref50_out.aln	true	2096	3000
Exception
java.lang.AssertionError: Jalview did not exit after -pileup generation (try running test again to verify - timeout at 9000ms). [headless -open examples/uniref50.fa] at org.testng.Assert.fail(Assert.java:94) at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:205) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1137) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Parameter #1	Parameter #2	Parameter #3	Parameter #4	Parameter #5	Parameter #6
headless -open examples/uniref50.fa	-pfam	test_uniref50_out.pfam	true	2096	3000
Exception
java.lang.AssertionError: Jalview did not exit after -pfam generation (try running test again to verify - timeout at 9000ms). [headless -open examples/uniref50.fa] at org.testng.Assert.fail(Assert.java:94) at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:205) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1137) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Parameter #1	Parameter #2	Parameter #3	Parameter #4	Parameter #5	Parameter #6
headless -open examples/uniref50.fa	-svg	test_uniref50_out.svg	false	4096	3000
Exception
java.lang.AssertionError: Jalview did not exit after -svg generation (try running test again to verify - timeout at 9000ms). [headless -open examples/uniref50.fa] at org.testng.Assert.fail(Assert.java:94) at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:205) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1137) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Parameter #1	Parameter #2	Parameter #3	Parameter #4	Parameter #5	Parameter #6
headless -open examples/uniref50.fa	-jalview	test_uniref50_out.jvp	true	2096	3000
Exception
java.lang.AssertionError: Jalview did not exit after -jalview generation (try running test again to verify - timeout at 9000ms). [headless -open examples/uniref50.fa] at org.testng.Assert.fail(Assert.java:94) at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:205) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1137) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Parameter #1	Parameter #2	Parameter #3	Parameter #4	Parameter #5	Parameter #6
headless -open examples/uniref50.fa	-png	test_uniref50_out.png	true	4096	3000
Exception
java.lang.AssertionError: Jalview did not exit after -png generation (try running test again to verify - timeout at 9000ms). [headless -open examples/uniref50.fa] at org.testng.Assert.fail(Assert.java:94) at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:205) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1137) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Parameter #1	Parameter #2	Parameter #3	Parameter #4	Parameter #5	Parameter #6
headless -open examples/uniref50.fa	-clustal	test_uniref50_out.aln	true	2096	3000
Exception
java.lang.AssertionError: Jalview did not exit after -clustal generation (try running test again to verify - timeout at 9000ms). [headless -open examples/uniref50.fa] at org.testng.Assert.fail(Assert.java:94) at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:205) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1137) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Parameter #1	Parameter #2	Parameter #3	Parameter #4	Parameter #5	Parameter #6
headless -open examples/uniref50.fa	-html	test_uniref50_out.html	true	4096	3000
Exception
java.lang.AssertionError: Jalview did not exit after -html generation (try running test again to verify - timeout at 9000ms). [headless -open examples/uniref50.fa] at org.testng.Assert.fail(Assert.java:94) at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:205) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1137) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Parameter #1	Parameter #2	Parameter #3	Parameter #4	Parameter #5	Parameter #6
headless -open examples/uniref50.fa	-pir	test_uniref50_out.pir	true	2096	3000
Exception
java.lang.AssertionError: Jalview did not exit after -pir generation (try running test again to verify - timeout at 9000ms). [headless -open examples/uniref50.fa] at org.testng.Assert.fail(Assert.java:94) at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:205) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1137) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Parameter #1	Parameter #2	Parameter #3	Parameter #4	Parameter #5	Parameter #6
headless -open examples/uniref50.fa	-msf	test_uniref50_out.msf	true	2096	3000
Exception
java.lang.AssertionError: Jalview did not exit after -msf generation (try running test again to verify - timeout at 9000ms). [headless -open examples/uniref50.fa] at org.testng.Assert.fail(Assert.java:94) at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:205) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1137) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Parameter #1	Parameter #2	Parameter #3	Parameter #4	Parameter #5	Parameter #6
headless -open examples/uniref50.fa	-blc	test_uniref50_out.blc	true	2096	3000
Exception
java.lang.AssertionError: Jalview did not exit after -blc generation (try running test again to verify - timeout at 9000ms). [headless -open examples/uniref50.fa] at org.testng.Assert.fail(Assert.java:94) at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:205) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1137) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

Parameter #1	Parameter #2	Parameter #3	Parameter #4	Parameter #5	Parameter #6
headless -open examples/uniref50.fa	-fasta	test_uniref50_out.mfa	true	2096	3000
Exception
java.lang.AssertionError: Jalview did not exit after -fasta generation (try running test again to verify - timeout at 9000ms). [headless -open examples/uniref50.fa] at org.testng.Assert.fail(Assert.java:94) at jalview.bin.CommandLineOperations.testHeadlessModeOutputOperations(CommandLineOperations.java:205) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:100) at org.testng.internal.Invoker.invokeMethod(Invoker.java:646) at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:811) at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1137) at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:129) at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:112) at org.testng.TestRunner.privateRun(TestRunner.java:753) at org.testng.TestRunner.run(TestRunner.java:607) at org.testng.SuiteRunner.runTest(SuiteRunner.java:368) at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:363) at org.testng.SuiteRunner.privateRun(SuiteRunner.java:321) at org.testng.SuiteRunner.run(SuiteRunner.java:270) at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52) at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86) at org.testng.TestNG.runSuitesSequentially(TestNG.java:1284) at org.testng.TestNG.runSuitesLocally(TestNG.java:1209) at org.testng.TestNG.runSuites(TestNG.java:1124) at org.testng.TestNG.run(TestNG.java:1096) at org.testng.remote.AbstractRemoteTestNG.run(AbstractRemoteTestNG.java:132) at org.testng.remote.RemoteTestNG.initAndRun(RemoteTestNG.java:236) at org.testng.remote.RemoteTestNG.main(RemoteTestNG.java:81)

GRP-Functional

jalview.ws.jabaws.JpredJabaStructExportImport#setUpBeforeClass

jalview.ws.jabaws.RNAStructExportImport#setUpBeforeClass

jalview.analysis.CrossRefTest#testFindXrefSequences_forGeneAndTranscripts

jalview.analysis.CrossRefTest#testFindXrefSequences_uniprotEmblManyToMany

jalview.analysis.CrossRefTest#testFindXrefSequences_withFetch

jalview.bin.CommandLineOperations#testHeadlessModeOutputOperations

jalview.bin.CommandLineOperations#testHeadlessModeOutputOperations

jalview.bin.CommandLineOperations#testHeadlessModeOutputOperations

jalview.bin.CommandLineOperations#testHeadlessModeOutputOperations

jalview.bin.CommandLineOperations#testHeadlessModeOutputOperations

jalview.bin.CommandLineOperations#testHeadlessModeOutputOperations

jalview.bin.CommandLineOperations#testHeadlessModeOutputOperations

jalview.bin.CommandLineOperations#testHeadlessModeOutputOperations

jalview.bin.CommandLineOperations#testHeadlessModeOutputOperations

jalview.bin.CommandLineOperations#testHeadlessModeOutputOperations

jalview.bin.CommandLineOperations#testHeadlessModeOutputOperations

jalview.io.RNAMLfileTest#testRnamlToStockholmIO

jalview.ws.seqfetcher.DasSequenceFetcher#testDasRegistryContact

jalview.ws.sifts.SiftsClientTest#getGreedyMappingTest

jalview.ws.sifts.SiftsClientTest#getSiftsStructureMappingTest

jalview.ws.jabaws.JpredJabaStructExportImport#testJPredStructExport

jalview.ws.jabaws.JpredJabaStructExportImport#testJPredStructOneSeqOnly

jalview.ws.jabaws.JpredJabaStructExportImport#testJpredwsSettingsRecovery

jalview.ws.jabaws.RNAStructExportImport#testRNAAliFoldValidStructure

jalview.ws.jabaws.RNAStructExportImport#testRNAStructExport

jalview.ws.jabaws.RNAStructExportImport#testRnaalifoldSettingsRecovery

MCview.AtomTest#testStringConstructor

MCview.AtomTest#testStringConstructor_blankOccupancyTempFactor

MCview.AtomTest#testStringConstructor_malformed

MCview.BondTest#testTranslate

MCview.PDBChainTest#testGetChargeColour

MCview.PDBChainTest#testGetNewlineString

MCview.PDBChainTest#testMakeBond

MCview.PDBChainTest#testMakeCaBondList

MCview.PDBChainTest#testMakeCaBondList_nucleotide

MCview.PDBChainTest#testMakeExactMapping

MCview.PDBChainTest#testMakeResidueList_noAnnotation

MCview.PDBChainTest#testMakeResidueList_withTempFactor

MCview.PDBChainTest#testPrint

MCview.PDBChainTest#testSetChainColours_colour

MCview.PDBChainTest#testSetChainColours_colourScheme

MCview.PDBChainTest#testSetChargeColours

MCview.PDBfileTest#testIsRna

MCview.PDBfileTest#testParse

MCview.PDBfileTest#testParse_withAnnotations_noSS

MCview.PDBfileTest#testParse_withJmolAddAlignmentAnnotations

MCview.PDBfileTest#testParse_withJmol_noAnnotations

MCview.ResidueTest#testFindAtom

jalview.analysis.AAFrequencyTest#testCalculate_noProfile

jalview.analysis.AAFrequencyTest#testCalculate_withProfile

jalview.analysis.AAFrequencyTest#testCompleteConsensus_ignoreGaps_noLogo

jalview.analysis.AAFrequencyTest#testCompleteConsensus_includeGaps_showLogo

jalview.analysis.AlignSeqTest#testExtractGaps

jalview.analysis.AlignmentAnnotationUtilsTest#testAsList

jalview.analysis.AlignmentAnnotationUtilsTest#testGetShownHiddenTypes_forSelectionGroup

jalview.analysis.AlignmentAnnotationUtilsTest#testGetShownHiddenTypes_noSequenceSelected

jalview.analysis.AlignmentAnnotationUtilsTest#testGetShownHiddenTypes_withGraphGroups

jalview.analysis.AlignmentAnnotationUtilsTest#testGetVisibleGraphGroups

jalview.analysis.AlignmentUtilsTests#testAddMappedPositions

jalview.analysis.AlignmentUtilsTests#testAddMappedPositions_withStopCodon

jalview.analysis.AlignmentUtilsTests#testAlignAsSameSequences

jalview.analysis.AlignmentUtilsTests#testAlignAsSameSequencesMultipleSubSeq

jalview.analysis.AlignmentUtilsTests#testAlignAs_alternateTranscriptsUngapped

jalview.analysis.AlignmentUtilsTests#testAlignProteinAsDna

jalview.analysis.AlignmentUtilsTests#testAlignProteinAsDna_incompleteStartCodon

jalview.analysis.AlignmentUtilsTests#testAlignSequenceAs_keepIntronGapsOnly

jalview.analysis.AlignmentUtilsTests#testAlignSequenceAs_mappedProteinProtein

jalview.analysis.AlignmentUtilsTests#testAlignSequenceAs_withMapping_noIntrons

jalview.analysis.AlignmentUtilsTests#testAlignSequenceAs_withMapping_withIntrons

jalview.analysis.AlignmentUtilsTests#testAlignSequenceAs_withMapping_withUnmappedProtein

jalview.analysis.AlignmentUtilsTests#testAlignSequenceAs_withTrailingPeptide

jalview.analysis.AlignmentUtilsTests#testBuildDnaVariantsMap

jalview.analysis.AlignmentUtilsTests#testComputePeptideVariants

jalview.analysis.AlignmentUtilsTests#testExpandContext

jalview.analysis.AlignmentUtilsTests#testExpandContext_annotation

jalview.analysis.AlignmentUtilsTests#testFindCdsPositions

jalview.analysis.AlignmentUtilsTests#testFindCdsPositions_fivePrimeIncomplete

jalview.analysis.AlignmentUtilsTests#testGetSequencesByName

jalview.analysis.AlignmentUtilsTests#testHasCrossRef