Build #132

Build: #132 failed

Job: Default Job failed

Stages & jobs

  1. Default Stage

Build log

The build generated 18,447 lines of output.The output is too long and has been truncated to the last 1,000 lines. Download or view full build log

20-Apr-2019 08:30:42    [testng] PASSED: testPrintGffFormat_withFilters
20-Apr-2019 08:30:42    [testng] PASSED: testPrintJalviewFormat
20-Apr-2019 08:30:42    [testng] PASSED: testPrintJalviewFormat_withFilters
20-Apr-2019 08:30:42    [testng] PASSED: testDeregisterFileFormat
20-Apr-2019 08:30:42    [testng] PASSED: testForName
20-Apr-2019 08:30:42    [testng] PASSED: testGetFormats
20-Apr-2019 08:30:42    [testng] PASSED: testGetReadableFormats
20-Apr-2019 08:30:42    [testng] PASSED: testGetWritableFormats
20-Apr-2019 08:30:42    [testng] PASSED: testIsIdentifiable
20-Apr-2019 08:30:42    [testng] PASSED: testRegisterFileFormat
20-Apr-2019 08:30:42    [testng] PASSED: testGzipIo
20-Apr-2019 08:30:42    [testng] PASSED: testGziplocalFileIO
20-Apr-2019 08:30:42    [testng] PASSED: testNonGzipURLIO
20-Apr-2019 08:30:42    [testng] PASSED: testNonGziplocalFileIO
20-Apr-2019 08:30:42    [testng] PASSED: testStarsInFasta1
20-Apr-2019 08:30:42    [testng] PASSED: testStarsInFasta2
20-Apr-2019 08:30:42    [testng] PASSED: testFindAll_sequenceIds
20-Apr-2019 08:30:42    [testng] PASSED: testFindNext
20-Apr-2019 08:30:42    [testng] PASSED: testFind_findAll
20-Apr-2019 08:30:42    [testng] PASSED: testFind_findAllCaseSensitive
20-Apr-2019 08:30:42    [testng] PASSED: testFind_findAllInSelection
20-Apr-2019 08:30:42    [testng] PASSED: testFind_findAllInSelectionWithShortSequence
20-Apr-2019 08:30:42    [testng] PASSED: testFind_findNext
20-Apr-2019 08:30:42    [testng] PASSED: testFind_inDescription
20-Apr-2019 08:30:42    [testng] PASSED: testFind_inSelection
20-Apr-2019 08:30:42    [testng] PASSED: testFind_maximalResultOnly
20-Apr-2019 08:30:42    [testng] PASSED: testFind_regex
20-Apr-2019 08:30:42    [testng] PASSED: testFind_residueNumber
20-Apr-2019 08:30:42    [testng] PASSED: testFind_withHiddenColumns
20-Apr-2019 08:30:42    [testng] PASSED: testFind_withHiddenColumnsAndSelection
20-Apr-2019 08:30:42    [testng] PASSED: testRoundTrip(Fasta)
20-Apr-2019 08:30:42    [testng] PASSED: testRoundTrip(Pfam)
20-Apr-2019 08:30:42    [testng] PASSED: testRoundTrip(Stockholm)
20-Apr-2019 08:30:42    [testng] PASSED: testRoundTrip(PIR)
20-Apr-2019 08:30:42    [testng] PASSED: testRoundTrip(BLC)
20-Apr-2019 08:30:42    [testng] PASSED: testRoundTrip(AMSA)
20-Apr-2019 08:30:42    [testng] PASSED: testRoundTrip(Json)
20-Apr-2019 08:30:42    [testng] PASSED: testRoundTrip(Pileup)
20-Apr-2019 08:30:42    [testng] PASSED: testRoundTrip(MSF)
20-Apr-2019 08:30:42    [testng] PASSED: testRoundTrip(Clustal)
20-Apr-2019 08:30:42    [testng] PASSED: testRoundTrip(Phylip)
20-Apr-2019 08:30:42    [testng] PASSED: testAppendPercentage
20-Apr-2019 08:30:42    [testng] PASSED: testForm_float
20-Apr-2019 08:30:42    [testng] PASSED: testFormat_scientific
20-Apr-2019 08:30:42    [testng] PASSED: testFormat_scientific_overflow
20-Apr-2019 08:30:42    [testng] PASSED: testRepeat
20-Apr-2019 08:30:42    [testng] PASSED: testGetCodeTable
20-Apr-2019 08:30:42    [testng] PASSED: testGetCodeTables
20-Apr-2019 08:30:42    [testng] PASSED: testTranslate
20-Apr-2019 08:30:42    [testng] PASSED: testTranslateCanonical
20-Apr-2019 08:30:42    [testng] PASSED: testTranslate_nonStandardTableAmbiguityCodes
20-Apr-2019 08:30:42    [testng] PASSED: testTranslate_standardTable
20-Apr-2019 08:30:42    [testng] PASSED: testTranslate_standardTableAmbiguityCodes
20-Apr-2019 08:30:42    [testng] PASSED: testGetDescription
20-Apr-2019 08:30:42    [testng] PASSED: testProcessCdnaMatch_forwardToForward
20-Apr-2019 08:30:42    [testng] PASSED: testProcessCdnaMatch_forwardToReverse
20-Apr-2019 08:30:42    [testng] PASSED: testProcessCdnaMatch_reverseToForward
20-Apr-2019 08:30:42    [testng] PASSED: testProcessCdnaMatch_spliced
20-Apr-2019 08:30:42    [testng] PASSED: testParseNameValuePairs
20-Apr-2019 08:30:42    [testng] PASSED: testTrimMapping
20-Apr-2019 08:30:42    [testng] PASSED: testGetHelper
20-Apr-2019 08:30:42    [testng] PASSED: testResolveExonerateGff
20-Apr-2019 08:30:42    [testng] PASSED: testMakeGroupsWithBoth
20-Apr-2019 08:30:42    [testng] PASSED: testFindColour
20-Apr-2019 08:30:42    [testng] PASSED: checkHelpTargets
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testFindRegionForColumn
20-Apr-2019 08:30:42    [testng] PASSED: testFindRegionForColumn_Visible
20-Apr-2019 08:30:42    [testng] PASSED: testAdjustForHiddenColumns
20-Apr-2019 08:30:42    [testng] PASSED: testBoundedIterator
20-Apr-2019 08:30:42    [testng] PASSED: testBoundedStartIterator
20-Apr-2019 08:30:42    [testng] PASSED: testCopyConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testCopyConstructor2
20-Apr-2019 08:30:42    [testng] PASSED: testEquals
20-Apr-2019 08:30:42    [testng] PASSED: testFindColumnPosition
20-Apr-2019 08:30:42    [testng] PASSED: testGetNextHiddenBoundary_Left
20-Apr-2019 08:30:42    [testng] PASSED: testGetNextHiddenBoundary_Right
20-Apr-2019 08:30:42    [testng] PASSED: testGetRegionWithEdgeAtRes
20-Apr-2019 08:30:42    [testng] PASSED: testGetSize
20-Apr-2019 08:30:42    [testng] PASSED: testGetVisibleColsIterator
20-Apr-2019 08:30:42    [testng] PASSED: testGetVisibleStartAndEndIndex
20-Apr-2019 08:30:42    [testng] PASSED: testHasHiddenColumns
20-Apr-2019 08:30:42    [testng] PASSED: testHasManyHiddenColumns
20-Apr-2019 08:30:42    [testng] PASSED: testHashCode
20-Apr-2019 08:30:42    [testng] PASSED: testHideColumns
20-Apr-2019 08:30:42    [testng] PASSED: testHideColumns_BitSet
20-Apr-2019 08:30:42    [testng] PASSED: testHideColumns_BitSet_range
20-Apr-2019 08:30:42    [testng] PASSED: testHideColumns_subsumingHidden
20-Apr-2019 08:30:42    [testng] PASSED: testHideInsertionsFor
20-Apr-2019 08:30:42    [testng] PASSED: testIsVisible
20-Apr-2019 08:30:42    [testng] PASSED: testIterator
20-Apr-2019 08:30:42    [testng] PASSED: testOffsetByVisibleColumns
20-Apr-2019 08:30:42    [testng] PASSED: testRegionsToString
20-Apr-2019 08:30:42    [testng] PASSED: testRevealAllHiddenColumns
20-Apr-2019 08:30:42    [testng] PASSED: testRevealHiddenColumns
20-Apr-2019 08:30:42    [testng] PASSED: testVisibleBlocksVisBoundsIterator
20-Apr-2019 08:30:42    [testng] PASSED: testVisibleContigsIterator
20-Apr-2019 08:30:42    [testng] PASSED: testAdjustForHiddenSeqs
20-Apr-2019 08:30:42    [testng] PASSED: testAdjustHeightSequenceAdded
20-Apr-2019 08:30:42    [testng] PASSED: testAdjustHeightSequenceDeleted
20-Apr-2019 08:30:42    [testng] PASSED: testFindIndexNFromRow
20-Apr-2019 08:30:42    [testng] PASSED: testFindIndexWithoutHiddenSeqs
20-Apr-2019 08:30:42    [testng] PASSED: testGetFullAlignment
20-Apr-2019 08:30:42    [testng] PASSED: testGetHiddenSequence
20-Apr-2019 08:30:42    [testng] PASSED: testGetSize
20-Apr-2019 08:30:42    [testng] PASSED: testGetWidth
20-Apr-2019 08:30:42    [testng] PASSED: testHideShowLastSequences
20-Apr-2019 08:30:42    [testng] PASSED: testHideShowSequence
20-Apr-2019 08:30:42    [testng] PASSED: testHideShowSequence_withHiddenRepSequence
20-Apr-2019 08:30:42    [testng] PASSED: testIsHidden
20-Apr-2019 08:30:42    [testng] PASSED: testFindColour
20-Apr-2019 08:30:42    [testng] PASSED: testDefaultUrl
20-Apr-2019 08:30:42    [testng] PASSED: testUrlLinks
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/example.json", Json)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/plantfdx.fa", Fasta)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/dna_interleaved.phy", Phylip)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/2GIS.pdb", PDB)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/RF00031_folded.stk", Stockholm)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/test.rnaml", Rnaml)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/test.aln", Clustal)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/test.pfam", Pfam)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/test.msf", MSF)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/test.pir", PIR)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/test.html", Html)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/test.pileup", Pileup)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/test.blc", BLC)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/exampleFeatures.txt", Features)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/simpleGff3.gff", Features)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/test.jvp", Jalview)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/test.cif", MMCif)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("examples/testdata/cullpdb_pc25_res3.0_R0.3_d150729_chains9361.fasta.15316", Fasta)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("resources/scoreModel/pam250.scm", ScoreMatrix)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify("resources/scoreModel/blosum80.scm", ScoreMatrix)
20-Apr-2019 08:30:42    [testng] PASSED: testIdentify_featureFile
20-Apr-2019 08:30:42    [testng] PASSED: testLooksLikeFeatureData
20-Apr-2019 08:30:42    [testng] PASSED: testProcessProteinMatch
20-Apr-2019 08:30:42    [testng] PASSED: colorSchemeTest
20-Apr-2019 08:30:42    [testng] PASSED: hiddenColsTest
20-Apr-2019 08:30:42    [testng] PASSED: hiddenSeqsTest
20-Apr-2019 08:30:42    [testng] PASSED: isShowSeqFeaturesSet
20-Apr-2019 08:30:42    [testng] PASSED: roundTripTest
20-Apr-2019 08:30:42    [testng] PASSED: testAnnotationParsed
20-Apr-2019 08:30:42    [testng] PASSED: testBioJSONRoundTripWithColourSchemeNone
20-Apr-2019 08:30:42    [testng] PASSED: testGrpParsed
20-Apr-2019 08:30:42    [testng] PASSED: testGrpParsed_colourNone
20-Apr-2019 08:30:42    [testng] PASSED: testSeqParsed
20-Apr-2019 08:30:42    [testng] PASSED: testArrayToList
20-Apr-2019 08:30:42    [testng] PASSED: gatherViewsHere
20-Apr-2019 08:30:42    [testng] PASSED: noDuplicatePdbMappingsMade
20-Apr-2019 08:30:42    [testng] PASSED: testColourByAnnotScores
20-Apr-2019 08:30:42    [testng] PASSED: testCopyViewSettings
20-Apr-2019 08:30:42    [testng] PASSED: testIsVersionStringLaterThan
20-Apr-2019 08:30:42    [testng] PASSED: testMergeDatasetsforManyViews
20-Apr-2019 08:30:42    [testng] PASSED: testMergeDatasetsforViews
20-Apr-2019 08:30:42    [testng] PASSED: testPcaViewAssociation
20-Apr-2019 08:30:42    [testng] PASSED: testRNAStructureRecovery
20-Apr-2019 08:30:42    [testng] PASSED: testSaveLoadFeatureColoursAndFilters
20-Apr-2019 08:30:42    [testng] PASSED: testStoreAndRecoverColourThresholds
20-Apr-2019 08:30:42    [testng] PASSED: testStoreAndRecoverExpandedviews
20-Apr-2019 08:30:42    [testng] PASSED: testStoreAndRecoverGroupRepSeqs
20-Apr-2019 08:30:42    [testng] PASSED: testStoreAndRecoverPDBEntry
20-Apr-2019 08:30:42    [testng] PASSED: testStoreAndRecoverReferenceSeqSettings
20-Apr-2019 08:30:42    [testng] PASSED: testTCoffeeScores
20-Apr-2019 08:30:42    [testng] PASSED: viewRefPdbAnnotation
20-Apr-2019 08:30:42    [testng] PASSED: testGetSchemeClass
20-Apr-2019 08:30:42    [testng] PASSED: testToString
20-Apr-2019 08:30:42    [testng] PASSED: testImportExportPeriodGaps
20-Apr-2019 08:30:42    [testng] PASSED: testGetExtension
20-Apr-2019 08:30:42    [testng] PASSED: testGetImageIcon
20-Apr-2019 08:30:42    [testng] PASSED: testGetTypeDescription
20-Apr-2019 08:30:42    [testng] PASSED: testSeparatorListToArray
20-Apr-2019 08:30:42    [testng] PASSED: testGetColourBySequenceCommand_noFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testGetColourBySequenceCommands_hiddenColumns
20-Apr-2019 08:30:42    [testng] PASSED: testAlignmentLoader
20-Apr-2019 08:30:42    [testng] PASSED: testFileParser
20-Apr-2019 08:30:42    [testng] PASSED: testLocalPDBId
20-Apr-2019 08:30:42    [testng] PASSED: testParse_alternativeResidues
20-Apr-2019 08:30:42    [testng] PASSED: testParse_missingResidues
20-Apr-2019 08:30:42    [testng] PASSED: testSetSecondaryStructure
20-Apr-2019 08:30:42    [testng] PASSED: testAddStrToSingleSeqViewJMol
20-Apr-2019 08:30:42    [testng] PASSED: testSingleSeqViewJMol
20-Apr-2019 08:30:42    [testng] PASSED: getUserInputTest
20-Apr-2019 08:30:42    [testng] PASSED: updateCacheTest
20-Apr-2019 08:30:42    [testng] PASSED: showConfirmDialogFamilyTest
20-Apr-2019 08:30:42    [testng] PASSED: showInputDialogFamilyTest
20-Apr-2019 08:30:42    [testng] PASSED: showInternalConfirmDialogFamilyTest
20-Apr-2019 08:30:42    [testng] PASSED: showInternalMessageDialogFamilyTest
20-Apr-2019 08:30:42    [testng] PASSED: showMessageDialogFamilyTest
20-Apr-2019 08:30:42    [testng] PASSED: testGetScrollBarProportion
20-Apr-2019 08:30:42    [testng] PASSED: testGetScrollValueForProportion
20-Apr-2019 08:30:42    [testng] PASSED: testWrapTooltip_longText
20-Apr-2019 08:30:42    [testng] PASSED: testWrapTooltip_multilineShortText
20-Apr-2019 08:30:42    [testng] PASSED: testWrapTooltip_shortText
20-Apr-2019 08:30:42    [testng] PASSED: testAddMapList
20-Apr-2019 08:30:42    [testng] PASSED: testAddMapList_contiguous
20-Apr-2019 08:30:42    [testng] PASSED: testAddMapList_sameMap
20-Apr-2019 08:30:42    [testng] PASSED: testAddRange
20-Apr-2019 08:30:42    [testng] PASSED: testCoalesceRanges
20-Apr-2019 08:30:42    [testng] PASSED: testCoalesceRanges_withOverlap
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_mergeRanges
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_withLists
20-Apr-2019 08:30:42    [testng] PASSED: testEquals
20-Apr-2019 08:30:42    [testng] PASSED: testGetInverse
20-Apr-2019 08:30:42    [testng] PASSED: testGetRanges
20-Apr-2019 08:30:42    [testng] PASSED: testIsFromForwardStrand
20-Apr-2019 08:30:42    [testng] PASSED: testIsToForwardsStrand
20-Apr-2019 08:30:42    [testng] PASSED: testLocateInFrom_noIntrons
20-Apr-2019 08:30:42    [testng] PASSED: testLocateInFrom_withIntrons
20-Apr-2019 08:30:42    [testng] PASSED: testLocateInTo_noIntrons
20-Apr-2019 08:30:42    [testng] PASSED: testLocateInTo_withIntrons
20-Apr-2019 08:30:42    [testng] PASSED: testSomething
20-Apr-2019 08:30:42    [testng] PASSED: testToString
20-Apr-2019 08:30:42    [testng] PASSED: testTraverse
20-Apr-2019 08:30:42    [testng] PASSED: compareTransferredToRefPDBAnnot
20-Apr-2019 08:30:42    [testng] PASSED: mapFer1From3W5V
20-Apr-2019 08:30:42    [testng] PASSED: testCopyConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testIntersectVisContigs
20-Apr-2019 08:30:42    [testng] PASSED: testToString
20-Apr-2019 08:30:42    [testng] PASSED: testGetFromRatio
20-Apr-2019 08:30:42    [testng] PASSED: testGetInverse
20-Apr-2019 08:30:42    [testng] PASSED: testGetToRatio
20-Apr-2019 08:30:42    [testng] PASSED: testBuildSearchResults
20-Apr-2019 08:30:42    [testng] PASSED: testBuildSearchResults_withIntron
20-Apr-2019 08:30:42    [testng] PASSED: testContains
20-Apr-2019 08:30:42    [testng] PASSED: testFindMappingsForSequence
20-Apr-2019 08:30:42    [testng] PASSED: testFindMappingsForSequenceAndOthers
20-Apr-2019 08:30:42    [testng] PASSED: testFlattenRanges
20-Apr-2019 08:30:42    [testng] PASSED: testFlattenRanges_reverseStrand
20-Apr-2019 08:30:42    [testng] PASSED: testGetLength
20-Apr-2019 08:30:42    [testng] PASSED: testMapColumnSelection_dnaToProtein
20-Apr-2019 08:30:42    [testng] PASSED: testMapColumnSelection_hiddenColumns
20-Apr-2019 08:30:42    [testng] PASSED: testMapColumnSelection_null
20-Apr-2019 08:30:42    [testng] PASSED: testMapColumnSelection_proteinToDna
20-Apr-2019 08:30:42    [testng] PASSED: testMapEditCommand
20-Apr-2019 08:30:42    [testng] PASSED: testMapSequenceGroup_columns
20-Apr-2019 08:30:42    [testng] PASSED: testMapSequenceGroup_region
20-Apr-2019 08:30:42    [testng] PASSED: testMapSequenceGroup_sequences
20-Apr-2019 08:30:42    [testng] PASSED: testRangeContains
20-Apr-2019 08:30:42    [testng] PASSED: testRemoveEndPositions
20-Apr-2019 08:30:42    [testng] PASSED: testRemoveStartPositions
20-Apr-2019 08:30:42    [testng] PASSED: testRemoveStartPositions_reverseStrand
20-Apr-2019 08:30:42    [testng] PASSED: testEquals
20-Apr-2019 08:30:42    [testng] PASSED: testToString
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testEquals
20-Apr-2019 08:30:42    [testng] PASSED: testHashCode
20-Apr-2019 08:30:42    [testng] PASSED: testMatches_float
20-Apr-2019 08:30:42    [testng] PASSED: testMatches_floatNullOrInvalid
20-Apr-2019 08:30:42    [testng] PASSED: testMatches_floatWithStringCondition
20-Apr-2019 08:30:42    [testng] PASSED: testMatches_pattern
20-Apr-2019 08:30:42    [testng] PASSED: testToString
20-Apr-2019 08:30:42    [testng] PASSED: testGcd
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testCopy
20-Apr-2019 08:30:42    [testng] PASSED: testEquals
20-Apr-2019 08:30:42    [testng] PASSED: testFindMinMax
20-Apr-2019 08:30:42    [testng] PASSED: testFindMinMax_timing
20-Apr-2019 08:30:42    [testng] PASSED: testMultiply
20-Apr-2019 08:30:42    [testng] PASSED: testPostMultiply
20-Apr-2019 08:30:42    [testng] PASSED: testPreMultiply
20-Apr-2019 08:30:42    [testng] PASSED: testPreMultiply_tooFewColumns
20-Apr-2019 08:30:42    [testng] PASSED: testPreMultiply_tooManyColumns
20-Apr-2019 08:30:42    [testng] PASSED: testReverseRange_maxToZero
20-Apr-2019 08:30:42    [testng] PASSED: testReverseRange_swapMinMax
20-Apr-2019 08:30:42    [testng] PASSED: testTred_reproducible
20-Apr-2019 08:30:42    [testng] PASSED: testTreeIO
20-Apr-2019 08:30:42    [testng] PASSED: testTreeIO
20-Apr-2019 08:30:42    [testng] PASSED: testTreeIO
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testDragging
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenColsAtEnd
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenColsAtStart
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenColsInMiddle
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenRowsAtEnd
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenRowsAtStart
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenRowsInMiddle
20-Apr-2019 08:30:42    [testng] PASSED: testPositionInBox
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromMouseClick
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewport
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenColsAtEnd
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenColsAtStart
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenColsInMiddle
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenRowsAtEnd
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenRowsAtStart
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenRowsInMiddle
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testDragging
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenColsAtEnd
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenColsAtStart
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenColsInMiddle
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenRowsAtEnd
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenRowsAtStart
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenRowsAtStartWrapped
20-Apr-2019 08:30:42    [testng] PASSED: testFromMouseWithHiddenRowsInMiddle
20-Apr-2019 08:30:42    [testng] PASSED: testPositionInBox
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromMouseClick
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewport
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenColsAtEnd
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenColsAtStart
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenColsInMiddle
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenRowsAtEnd
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenRowsAtStart
20-Apr-2019 08:30:42    [testng] PASSED: testSetBoxFromViewportHiddenRowsInMiddle
20-Apr-2019 08:30:42    [testng] PASSED: testGetResidueBoxColour_none
20-Apr-2019 08:30:42    [testng] PASSED: testGetResidueBoxColour_userdef
20-Apr-2019 08:30:42    [testng] PASSED: testGetResidueBoxColour_zappo
20-Apr-2019 08:30:42    [testng] PASSED: testGetChargeColour
20-Apr-2019 08:30:42    [testng] PASSED: testGetNewlineString
20-Apr-2019 08:30:42    [testng] PASSED: testMakeBond
20-Apr-2019 08:30:42    [testng] PASSED: testMakeCaBondList
20-Apr-2019 08:30:42    [testng] PASSED: testMakeCaBondList_nucleotide
20-Apr-2019 08:30:42    [testng] PASSED: testMakeExactMapping
20-Apr-2019 08:30:42    [testng] PASSED: testMakeResidueList_noAnnotation
20-Apr-2019 08:30:42    [testng] PASSED: testMakeResidueList_withTempFactor
20-Apr-2019 08:30:42    [testng] PASSED: testPrint
20-Apr-2019 08:30:42    [testng] PASSED: testSetChainColours_colour
20-Apr-2019 08:30:42    [testng] PASSED: testSetChainColours_colourScheme
20-Apr-2019 08:30:42    [testng] PASSED: testSetChargeColours
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_fromDbref
20-Apr-2019 08:30:42    [testng] PASSED: testEquals
20-Apr-2019 08:30:42    [testng] PASSED: testGetType
20-Apr-2019 08:30:42    [testng] PASSED: testSetChainCode
20-Apr-2019 08:30:42    [testng] PASSED: testTypeMatches
20-Apr-2019 08:30:42    [testng] PASSED: testUpdateFrom
20-Apr-2019 08:30:42    [testng] PASSED: populateCmbSearchTargetOptionsTest
20-Apr-2019 08:30:42    [testng] PASSED: testDecodeSearchTerm
20-Apr-2019 08:30:42    [testng] PASSED: testgetPDBIdwithSpecifiedChain
20-Apr-2019 08:30:42    [testng] PASSED: getPDBDocFieldsAsCommaDelimitedStringTest
20-Apr-2019 08:30:42    [testng] PASSED: getPDBIdColumIndexTest
20-Apr-2019 08:30:42    [testng] PASSED: testIsRna
20-Apr-2019 08:30:42    [testng] PASSED: testParse
20-Apr-2019 08:30:42    [testng] PASSED: testParse_withAnnotations_noSS
20-Apr-2019 08:30:42    [testng] PASSED: testParse_withJmolAddAlignmentAnnotations
20-Apr-2019 08:30:42    [testng] PASSED: testParse_withJmol_noAnnotations
20-Apr-2019 08:30:42    [testng] PASSED: testFindColour
20-Apr-2019 08:30:42    [testng] PASSED: testFindColour_ignoreGaps
20-Apr-2019 08:30:42    [testng] PASSED: testComputePID_matchLongestSequence
20-Apr-2019 08:30:42    [testng] PASSED: testComputePID_matchShortestSequence
20-Apr-2019 08:30:42    [testng] PASSED: testComputePID_matchesComparisonPID
20-Apr-2019 08:30:42    [testng] PASSED: testGetPairwiseScore
20-Apr-2019 08:30:42    [testng] PASSED: testGetAssociatedPanels
20-Apr-2019 08:30:42    [testng] PASSED: testRegister
20-Apr-2019 08:30:42    [testng] PASSED: testRemoveComponent
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_noSelectionGroup
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_withSelectionGroup
20-Apr-2019 08:30:42    [testng] PASSED: testParseHtml_noLinks
20-Apr-2019 08:30:42    [testng] PASSED: testParseHtml_withLinks
20-Apr-2019 08:30:42    [testng] PASSED: testParseHtml_withLinksWithEncoding
20-Apr-2019 08:30:42    [testng] PASSED: testParseHtml_withLinksWithParameters
20-Apr-2019 08:30:42    [testng] PASSED: testGetScoresFromDescription
20-Apr-2019 08:30:42    [testng] PASSED: testGetScoresFromDescription_twoScores
20-Apr-2019 08:30:42    [testng] PASSED: testGetScoresFromDescription_wordBoundaries
20-Apr-2019 08:30:42    [testng] PASSED: testPfamFormatNoLimits
20-Apr-2019 08:30:42    [testng] PASSED: testPfamFormatValidLimits
20-Apr-2019 08:30:42    [testng] PASSED: testGetURL
20-Apr-2019 08:30:42    [testng] PASSED: testGetURL
20-Apr-2019 08:30:42    [testng] PASSED: testInterleavedDataExtraction
20-Apr-2019 08:30:42    [testng] PASSED: testInterleavedIO
20-Apr-2019 08:30:42    [testng] PASSED: testSequentialDataExtraction
20-Apr-2019 08:30:42    [testng] PASSED: testSequentialIO
20-Apr-2019 08:30:42    [testng] PASSED: testIsControlDown_mac
20-Apr-2019 08:30:42    [testng] PASSED: testIsControlDown_notMac
20-Apr-2019 08:30:42    [testng] PASSED: testBuildAnnotationTypesMenus
20-Apr-2019 08:30:42    [testng] PASSED: testBuildAnnotationTypesMenus_hideDisabled
20-Apr-2019 08:30:42    [testng] PASSED: testBuildAnnotationTypesMenus_showDisabled
20-Apr-2019 08:30:42    [testng] PASSED: testBuildLinkMenu
20-Apr-2019 08:30:42    [testng] PASSED: testConfigureReferenceAnnotationsMenu
20-Apr-2019 08:30:42    [testng] PASSED: testConfigureReferenceAnnotationsMenu_alreadyAdded
20-Apr-2019 08:30:42    [testng] PASSED: testConfigureReferenceAnnotationsMenu_noReferenceAnnotations
20-Apr-2019 08:30:42    [testng] PASSED: testConfigureReferenceAnnotationsMenu_noSequenceSelected
20-Apr-2019 08:30:42    [testng] PASSED: testConfigureReferenceAnnotationsMenu_notOnAlignment
20-Apr-2019 08:30:42    [testng] PASSED: testConfigureReferenceAnnotationsMenu_twoViews
20-Apr-2019 08:30:42    [testng] PASSED: testHideInsertions
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_prematureInstantiation
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_wrongLayout
20-Apr-2019 08:30:42    [testng] PASSED: testSetProgressBar
20-Apr-2019 08:30:42    [testng] PASSED: testCharSortByFloat
20-Apr-2019 08:30:42    [testng] PASSED: testCharSortByInt
20-Apr-2019 08:30:42    [testng] PASSED: testSortByInt
20-Apr-2019 08:30:42    [testng] PASSED: testSortByString
20-Apr-2019 08:30:42    [testng] PASSED: testSort_byDoubleValues
20-Apr-2019 08:30:42    [testng] PASSED: testSort_byFloatValues
20-Apr-2019 08:30:42    [testng] PASSED: testSort_byIntValues
20-Apr-2019 08:30:42    [testng] PASSED: testSort_byStringValues
20-Apr-2019 08:30:42    [testng] PASSED: testSort_charSortByFloat_mostlyZeroValues
20-Apr-2019 08:30:42    [testng] PASSED: testSort_charSortByInt_mostlyZeroValues
20-Apr-2019 08:30:42    [testng] PASSED: testRnamlToStockholmIO
20-Apr-2019 08:30:42    [testng] PASSED: testHasNextAndNextEndHidden
20-Apr-2019 08:30:42    [testng] PASSED: testHasNextAndNextNoHidden
20-Apr-2019 08:30:42    [testng] PASSED: testHasNextAndNextStartHidden
20-Apr-2019 08:30:42    [testng] PASSED: testHasNextAndNextWithHidden
20-Apr-2019 08:30:42    [testng] PASSED: testLastNextEndHidden
20-Apr-2019 08:30:42    [testng] PASSED: testLastNextNoHidden
20-Apr-2019 08:30:42    [testng] PASSED: testLastNextStartHidden
20-Apr-2019 08:30:42    [testng] PASSED: testLastNextWithHidden
20-Apr-2019 08:30:42    [testng] PASSED: testRemove
20-Apr-2019 08:30:42    [testng] PASSED: testGetResidueColour_none
20-Apr-2019 08:30:42    [testng] PASSED: testGetResidueColour_userdef
20-Apr-2019 08:30:42    [testng] PASSED: testGetResidueColour_zappo
20-Apr-2019 08:30:42    [testng] PASSED: testGetName
20-Apr-2019 08:30:42    [testng] PASSED: testIsApplicableTo
20-Apr-2019 08:30:42    [testng] PASSED: testIsApplicableTo_dynamicColourScheme
20-Apr-2019 08:30:42    [testng] PASSED: testAddGap
20-Apr-2019 08:30:42    [testng] PASSED: testGetModalCount
20-Apr-2019 08:30:42    [testng] PASSED: testGetResiduesForCount
20-Apr-2019 08:30:42    [testng] PASSED: testGetSymbolCounts_nucleotide
20-Apr-2019 08:30:42    [testng] PASSED: testGetSymbolCounts_peptide
20-Apr-2019 08:30:42    [testng] PASSED: testGetTooltip
20-Apr-2019 08:30:42    [testng] PASSED: testOverflow
20-Apr-2019 08:30:42    [testng] PASSED: testPut
20-Apr-2019 08:30:42    [testng] PASSED: testToString
20-Apr-2019 08:30:42    [testng] PASSED: test_countNucleotide
20-Apr-2019 08:30:42    [testng] PASSED: test_countPeptide
20-Apr-2019 08:30:42    [testng] PASSED: test_unexpectedNucleotide
20-Apr-2019 08:30:42    [testng] PASSED: test_unexpectedPeptide
20-Apr-2019 08:30:42    [testng] PASSED: testCodonTranslate
20-Apr-2019 08:30:42    [testng] PASSED: testCodonTranslate_ambiguityCodes
20-Apr-2019 08:30:42    [testng] PASSED: testGetCanonicalAminoAcid
20-Apr-2019 08:30:42    [testng] PASSED: testGetDssp3State
20-Apr-2019 08:30:42    [testng] PASSED: testGetResidues_nucleotide
20-Apr-2019 08:30:42    [testng] PASSED: testGetResidues_peptide
20-Apr-2019 08:30:42    [testng] PASSED: testGetSingleCharacterCode
20-Apr-2019 08:30:42    [testng] PASSED: testPhysicoChemicalProperties
20-Apr-2019 08:30:42    [testng] PASSED: testAboveThreshold
20-Apr-2019 08:30:42    [testng] PASSED: testApplyConservation
20-Apr-2019 08:30:42    [testng] PASSED: testFindColour_gapColour
20-Apr-2019 08:30:42    [testng] PASSED: testFindAtom
20-Apr-2019 08:30:42    [testng] PASSED: testGetRestClient
20-Apr-2019 08:30:42    [testng] PASSED: testGetURL
20-Apr-2019 08:30:42    [testng] PASSED: testGetURL
20-Apr-2019 08:30:42    [testng] PASSED: testGetHelixMap_oneHelix
20-Apr-2019 08:30:42    [testng] PASSED: testGetHelixMap_twoHelices
20-Apr-2019 08:30:42    [testng] PASSED: testGetMatchingOpeningParenthesis
20-Apr-2019 08:30:42    [testng] PASSED: testGetRNASecStrucState
20-Apr-2019 08:30:42    [testng] PASSED: testGetSimpleBPs
20-Apr-2019 08:30:42    [testng] PASSED: testGetSimpleBPs_unmatchedCloser
20-Apr-2019 08:30:42    [testng] PASSED: testGetSimpleBPs_unmatchedOpener
20-Apr-2019 08:30:42    [testng] PASSED: testIsCanonicalOrWobblePair
20-Apr-2019 08:30:42    [testng] PASSED: testIsCanonicalPair
20-Apr-2019 08:30:42    [testng] PASSED: testIsClosingParenthesis
20-Apr-2019 08:30:42    [testng] PASSED: testIsOpeningParenthesis
20-Apr-2019 08:30:42    [testng] PASSED: testIsRnaSecondaryStructureSymbol
20-Apr-2019 08:30:42    [testng] PASSED: testGetRotation
20-Apr-2019 08:30:42    [testng] PASSED: testPreMultiply
20-Apr-2019 08:30:42    [testng] PASSED: testVectorMultiply
20-Apr-2019 08:30:42    [testng] PASSED: testBuildPopupMenu
20-Apr-2019 08:30:42    [testng] PASSED: testPreventNegativeStartColumn
20-Apr-2019 08:30:42    [testng] PASSED: testSelectColumns_withHidden
20-Apr-2019 08:30:42    [testng] PASSED: testCalculateMarks
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_aaIndexBlosum80
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_aaindexFormat
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_aaindex_extraDataLines
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_aaindex_mMissing
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_aaindex_rowColMismatch
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_aaindex_tooFewColumns
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_aaindex_tooManyRows
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_headerMissing
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_ncbiBadDelimiter
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_ncbiBadFloat
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_ncbiBadGuideCharacter
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_ncbiFormat
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_ncbiHeaderRepeated
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_ncbiMixedDelimiters
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_ncbiNameMissing
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_ncbiNotEnoughColumns
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_ncbiNotEnoughRows
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_ncbiTooManyColumns
20-Apr-2019 08:30:42    [testng] PASSED: testParseMatrix_ncbiTooManyRows
20-Apr-2019 08:30:42    [testng] PASSED: testParse_ncbiFormat
20-Apr-2019 08:30:42    [testng] PASSED: testBlosum62_values
20-Apr-2019 08:30:42    [testng] PASSED: testBuildSymbolIndex
20-Apr-2019 08:30:42    [testng] PASSED: testBuildSymbolIndex_nonAscii
20-Apr-2019 08:30:42    [testng] PASSED: testComputePairwiseScores
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_gapDash
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_matrixNotSquare
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_matrixTooBig
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_matrixTooSmall
20-Apr-2019 08:30:42    [testng] PASSED: testEqualsAndHashCode
20-Apr-2019 08:30:42    [testng] PASSED: testGetMatrix
20-Apr-2019 08:30:42    [testng] PASSED: testGetMatrixIndex
20-Apr-2019 08:30:42    [testng] PASSED: testGetMaximumScore
20-Apr-2019 08:30:42    [testng] PASSED: testGetMinimumScore
20-Apr-2019 08:30:42    [testng] PASSED: testGetPairwiseScore
20-Apr-2019 08:30:42    [testng] PASSED: testGetSize
20-Apr-2019 08:30:42    [testng] PASSED: testIsSymmetric
20-Apr-2019 08:30:42    [testng] PASSED: testOutputMatrix_html
20-Apr-2019 08:30:42    [testng] PASSED: testOutputMatrix_roundTrip
20-Apr-2019 08:30:42    [testng] PASSED: testSymmetric
20-Apr-2019 08:30:42    [testng] PASSED: testcomputeSimilarity_matchLongestSequence
20-Apr-2019 08:30:42    [testng] PASSED: testcomputeSimilarity_matchShortestSequence
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testAddResult
20-Apr-2019 08:30:42    [testng] PASSED: testEquals
20-Apr-2019 08:30:42    [testng] PASSED: testEquals_distinctSequences
20-Apr-2019 08:30:42    [testng] PASSED: testEquals_orderDiffers
20-Apr-2019 08:30:42    [testng] PASSED: testHashcode
20-Apr-2019 08:30:42    [testng] PASSED: testMarkColumns
20-Apr-2019 08:30:42    [testng] PASSED: testMatchConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testMatchContains
20-Apr-2019 08:30:42    [testng] PASSED: testToString
20-Apr-2019 08:30:42    [testng] PASSED: testCalculateWrappedGeometry_fromScrolled
20-Apr-2019 08:30:42    [testng] PASSED: testCalculateWrappedGeometry_noAnnotations
20-Apr-2019 08:30:42    [testng] PASSED: testCalculateWrappedGeometry_withAnnotations
20-Apr-2019 08:30:42    [testng] PASSED: testFindPosition
20-Apr-2019 08:30:42    [testng] PASSED: testSomething
20-Apr-2019 08:30:42    [testng] PASSED: testAmbiguousAminoAcidGetsStatusMessage
20-Apr-2019 08:30:42    [testng] PASSED: testFindColumn_unwrapped
20-Apr-2019 08:30:42    [testng] PASSED: testFindColumn_wrapped
20-Apr-2019 08:30:42    [testng] PASSED: testFindMousePosition_wrapped_annotations
20-Apr-2019 08:30:42    [testng] PASSED: testFindMousePosition_wrapped_noAnnotations
20-Apr-2019 08:30:42    [testng] PASSED: testFindMousePosition_wrapped_scaleAbove
20-Apr-2019 08:30:42    [testng] PASSED: testGetEditStatusMessage
20-Apr-2019 08:30:42    [testng] PASSED: testGetEditStatusMessage_lockedEditing
20-Apr-2019 08:30:42    [testng] PASSED: testSetStatusReturnsNearestResiduePosition
20-Apr-2019 08:30:42    [testng] PASSED: testSeqFeatureAddition
20-Apr-2019 08:30:42    [testng] PASSED: testAppendFeature_DescEqualsType
20-Apr-2019 08:30:42    [testng] PASSED: testAppendFeature_colouredByAttribute
20-Apr-2019 08:30:42    [testng] PASSED: testAppendFeature_disulfideBond
20-Apr-2019 08:30:42    [testng] PASSED: testAppendFeature_noScore
20-Apr-2019 08:30:42    [testng] PASSED: testAppendFeature_status
20-Apr-2019 08:30:42    [testng] PASSED: testAppendFeature_stripHtml
20-Apr-2019 08:30:42    [testng] PASSED: testAppendFeature_withScore
20-Apr-2019 08:30:42    [testng] PASSED: testAppendFeature_withScoreStatusAttribute
20-Apr-2019 08:30:42    [testng] PASSED: testCreateSequenceAnnotationReport
20-Apr-2019 08:30:42    [testng] PASSED: testCreateSequenceAnnotationReport_withEllipsis
20-Apr-2019 08:30:42    [testng] PASSED: testBecome
20-Apr-2019 08:30:42    [testng] PASSED: testCopyConstructors
20-Apr-2019 08:30:42    [testng] PASSED: testEqualsAndHashCode
20-Apr-2019 08:30:42    [testng] PASSED: testGetDetailsReport
20-Apr-2019 08:30:42    [testng] PASSED: testGetStrand
20-Apr-2019 08:30:42    [testng] PASSED: testGetValue
20-Apr-2019 08:30:42    [testng] PASSED: testIsContactFeature
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testDelete
20-Apr-2019 08:30:42    [testng] PASSED: testDeleteAll
20-Apr-2019 08:30:42    [testng] PASSED: testFindFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testGetAllFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testGetContactFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testGetFeatureCount
20-Apr-2019 08:30:42    [testng] PASSED: testGetFeatureGroups
20-Apr-2019 08:30:42    [testng] PASSED: testGetFeatureTypes
20-Apr-2019 08:30:42    [testng] PASSED: testGetFeatureTypesForGroups
20-Apr-2019 08:30:42    [testng] PASSED: testGetFeatureTypes_byOntology
20-Apr-2019 08:30:42    [testng] PASSED: testGetFeaturesByOntology
20-Apr-2019 08:30:42    [testng] PASSED: testGetFeaturesForGroup
20-Apr-2019 08:30:42    [testng] PASSED: testGetMinimumScore_getMaximumScore
20-Apr-2019 08:30:42    [testng] PASSED: testGetNonPositionalFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testGetPositionalFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testGetTotalFeatureLength
20-Apr-2019 08:30:42    [testng] PASSED: testHasFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testIsOntologyTerm
20-Apr-2019 08:30:42    [testng] PASSED: testShiftFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testSortFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testVarargsToTypes
20-Apr-2019 08:30:42    [testng] PASSED: testAddOrRemove
20-Apr-2019 08:30:42    [testng] PASSED: testAddSequence
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_list
20-Apr-2019 08:30:42    [testng] PASSED: testContains
20-Apr-2019 08:30:42    [testng] PASSED: testCopyConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testGetColourScheme
20-Apr-2019 08:30:42    [testng] PASSED: testSetContext
20-Apr-2019 08:30:42    [testng] PASSED: test_seqIdNameEquals
20-Apr-2019 08:30:42    [testng] PASSED: testIsA_sequenceVariant
20-Apr-2019 08:30:42    [testng] PASSED: testIsA
20-Apr-2019 08:30:42    [testng] PASSED: testIsCDS
20-Apr-2019 08:30:42    [testng] PASSED: testIsSequenceVariant
20-Apr-2019 08:30:42    [testng] PASSED: testGetResidueColour_WithGroup
20-Apr-2019 08:30:42    [testng] PASSED: testAddAlignmentAnnotation
20-Apr-2019 08:30:42    [testng] PASSED: testAddDBRef
20-Apr-2019 08:30:42    [testng] PASSED: testAddPDBId
20-Apr-2019 08:30:42    [testng] PASSED: testAddSequenceFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testCheckValidRange
20-Apr-2019 08:30:42    [testng] PASSED: testCopyConstructor_noDataset
20-Apr-2019 08:30:42    [testng] PASSED: testCopyConstructor_withDataset
20-Apr-2019 08:30:42    [testng] PASSED: testCreateDatasetSequence
20-Apr-2019 08:30:42    [testng] PASSED: testDeleteChars
20-Apr-2019 08:30:42    [testng] PASSED: testDeleteChars_withDbRefsAndFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testDeleteChars_withGaps
20-Apr-2019 08:30:42    [testng] PASSED: testDeriveSequence_existingDataset
20-Apr-2019 08:30:42    [testng] PASSED: testDeriveSequence_noDatasetGapped
20-Apr-2019 08:30:42    [testng] PASSED: testDeriveSequence_noDatasetUngapped
20-Apr-2019 08:30:42    [testng] PASSED: testFindFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testFindIndex
20-Apr-2019 08:30:42    [testng] PASSED: testFindIndex_withCursor
20-Apr-2019 08:30:42    [testng] PASSED: testFindPosition
20-Apr-2019 08:30:42    [testng] PASSED: testFindPositionMap
20-Apr-2019 08:30:42    [testng] PASSED: testFindPosition_withCursor
20-Apr-2019 08:30:42    [testng] PASSED: testFindPosition_withCursorAndEdits
20-Apr-2019 08:30:42    [testng] PASSED: testFindPositions
20-Apr-2019 08:30:42    [testng] PASSED: testGapBitset
20-Apr-2019 08:30:42    [testng] PASSED: testGapMap
20-Apr-2019 08:30:42    [testng] PASSED: testGetAlignmentAnnotations_forCalcIdAndLabel
20-Apr-2019 08:30:42    [testng] PASSED: testGetAnnotation
20-Apr-2019 08:30:42    [testng] PASSED: testGetAnnotation_forLabel
20-Apr-2019 08:30:42    [testng] PASSED: testGetCharAt
20-Apr-2019 08:30:42    [testng] PASSED: testGetPrimaryDBRefs_nucleotide
20-Apr-2019 08:30:42    [testng] PASSED: testGetPrimaryDBRefs_peptide
20-Apr-2019 08:30:42    [testng] PASSED: testGetSequence
20-Apr-2019 08:30:42    [testng] PASSED: testGetSequenceFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testGetStartGetEnd
20-Apr-2019 08:30:42    [testng] PASSED: testGetSubsequence
20-Apr-2019 08:30:42    [testng] PASSED: testInsertCharAt
20-Apr-2019 08:30:42    [testng] PASSED: testInsertGapsAndGapmaps
20-Apr-2019 08:30:42    [testng] PASSED: testIsProtein
20-Apr-2019 08:30:42    [testng] PASSED: testLocateVisibleStartofSequence
20-Apr-2019 08:30:42    [testng] PASSED: testReplace
20-Apr-2019 08:30:42    [testng] PASSED: testSetDatasetSequence_cascading
20-Apr-2019 08:30:42    [testng] PASSED: testSetDatasetSequence_toSelf
20-Apr-2019 08:30:42    [testng] PASSED: testSetName
20-Apr-2019 08:30:42    [testng] PASSED: testUpdatePDBIds
20-Apr-2019 08:30:42    [testng] PASSED: testCountDisjunction
20-Apr-2019 08:30:42    [testng] PASSED: testParseMap
20-Apr-2019 08:30:42    [testng] PASSED: testShmmrService
20-Apr-2019 08:30:42    [testng] PASSED: testShmmrServiceDataprep
20-Apr-2019 08:30:42    [testng] PASSED: testAdd
20-Apr-2019 08:30:42    [testng] PASSED: testKeyAt_ValueAt
20-Apr-2019 08:30:42    [testng] PASSED: testOverflow
20-Apr-2019 08:30:42    [testng] PASSED: testPut
20-Apr-2019 08:30:42    [testng] PASSED: testUnderflow
20-Apr-2019 08:30:42    [testng] PASSED: testAdd
20-Apr-2019 08:30:42    [testng] PASSED: testCheckOverflow
20-Apr-2019 08:30:42    [testng] PASSED: testPut
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testFillRatio
20-Apr-2019 08:30:42    [testng] PASSED: testPostMultiply
20-Apr-2019 08:30:42    [testng] PASSED: testPreMultiply
20-Apr-2019 08:30:42    [testng] PASSED: testPreMultiply_sparseProduct
20-Apr-2019 08:30:42    [testng] PASSED: testPreMultiply_tooFewColumns
20-Apr-2019 08:30:42    [testng] PASSED: testPreMultiply_tooManyColumns
20-Apr-2019 08:30:42    [testng] PASSED: testTqli_matchesMatrix
20-Apr-2019 08:30:42    [testng] PASSED: testTranspose
20-Apr-2019 08:30:42    [testng] PASSED: testTred_matchesMatrix
20-Apr-2019 08:30:42    [testng] PASSED: testTred_reproducible
20-Apr-2019 08:30:42    [testng] PASSED: testAdd
20-Apr-2019 08:30:42    [testng] PASSED: testPut
20-Apr-2019 08:30:42    [testng] PASSED: testBasicBoundsIterator
20-Apr-2019 08:30:42    [testng] PASSED: testBoundsIteratorUsingCursor
20-Apr-2019 08:30:42    [testng] PASSED: testBoundsIteratorUsingNullCursor
20-Apr-2019 08:30:42    [testng] PASSED: curlyWUSSsecondaryStructureForRNASequence
20-Apr-2019 08:30:42    [testng] PASSED: detectWussBrackets
20-Apr-2019 08:30:42    [testng] PASSED: fullWUSSsecondaryStructureForRNASequence
20-Apr-2019 08:30:42    [testng] PASSED: pfamFileDataExtraction
20-Apr-2019 08:30:42    [testng] PASSED: pfamFileIO
20-Apr-2019 08:30:42    [testng] PASSED: rfamFileIO
20-Apr-2019 08:30:42    [testng] PASSED: secondaryStructureForRNASequence
20-Apr-2019 08:30:42    [testng] PASSED: stockholmFileRnaSSAlphaChars
20-Apr-2019 08:30:42    [testng] PASSED: stockholmFileRnaSSSpaceChars
20-Apr-2019 08:30:42    [testng] PASSED: testAnnotationEquivalence
20-Apr-2019 08:30:42    [testng] PASSED: testFindColour
20-Apr-2019 08:30:42    [testng] PASSED: testArrayToSeparatorList
20-Apr-2019 08:30:42    [testng] PASSED: testCompareVersions
20-Apr-2019 08:30:42    [testng] PASSED: testDeleteChars
20-Apr-2019 08:30:42    [testng] PASSED: testGetLastToken
20-Apr-2019 08:30:42    [testng] PASSED: testInsertCharAt
20-Apr-2019 08:30:42    [testng] PASSED: testListToDelimitedString
20-Apr-2019 08:30:42    [testng] PASSED: testParseInt
20-Apr-2019 08:30:42    [testng] PASSED: testSeparatorListToArray
20-Apr-2019 08:30:42    [testng] PASSED: testStripHtmlTags
20-Apr-2019 08:30:42    [testng] PASSED: testToSentenceCase
20-Apr-2019 08:30:42    [testng] PASSED: buildQueryTest
20-Apr-2019 08:30:42    [testng] PASSED: populateFilterComboBoxTest
20-Apr-2019 08:30:42    [testng] PASSED: sanitizeSeqNameTest
20-Apr-2019 08:30:42    [testng] PASSED: testEquals
20-Apr-2019 08:30:42    [testng] PASSED: testGetPDBResNumRanges
20-Apr-2019 08:30:42    [testng] PASSED: testRegisterMapping
20-Apr-2019 08:30:42    [testng] PASSED: testRegisterMappings
20-Apr-2019 08:30:42    [testng] PASSED: testSetMapping_seqFeatures
20-Apr-2019 08:30:42    [testng] PASSED: testGetSequencesForPdbs
20-Apr-2019 08:30:42    [testng] PASSED: testGetAsArray
20-Apr-2019 08:30:42    [testng] PASSED: testGetAsList
20-Apr-2019 08:30:42    [testng] PASSED: testHeightAndWidth
20-Apr-2019 08:30:42    [testng] PASSED: testHeightAndWidthWithResidueNumbers
20-Apr-2019 08:30:42    [testng] PASSED: testParse
20-Apr-2019 08:30:42    [testng] PASSED: testReadBlock
20-Apr-2019 08:30:42    [testng] PASSED: testReadHeader
20-Apr-2019 08:30:42    [testng] PASSED: testWrongFile
20-Apr-2019 08:30:42    [testng] PASSED: testExtractGaps
20-Apr-2019 08:30:42    [testng] PASSED: testGetMappingForS1
20-Apr-2019 08:30:42    [testng] PASSED: testPrintAlignment
20-Apr-2019 08:30:42    [testng] PASSED: testCreateFastaSequenceIndex
20-Apr-2019 08:30:42    [testng] PASSED: testGetSequenceProxy
20-Apr-2019 08:30:42    [testng] PASSED: testGetSequenceProxy_indexed
20-Apr-2019 08:30:42    [testng] PASSED: testTrimLeft_noColumns
20-Apr-2019 08:30:42    [testng] PASSED: testTrimLeft_oneColumn
20-Apr-2019 08:30:42    [testng] PASSED: testTrimLeft_withUndoAndRedo
20-Apr-2019 08:30:42    [testng] PASSED: testTrimRight_noColumns
20-Apr-2019 08:30:42    [testng] PASSED: testTrimRight_oneColumn
20-Apr-2019 08:30:42    [testng] PASSED: testTrimRight_withUndoAndRedo
20-Apr-2019 08:30:42    [testng] PASSED: testFindColour
20-Apr-2019 08:30:42    [testng] PASSED: testGetDescription
20-Apr-2019 08:30:42    [testng] PASSED: testGetUniprotEntries
20-Apr-2019 08:30:42    [testng] PASSED: testGetUniprotEntryDescription
20-Apr-2019 08:30:42    [testng] PASSED: testGetUniprotEntryId
20-Apr-2019 08:30:42    [testng] PASSED: testGetUniprotSequence
20-Apr-2019 08:30:42    [testng] PASSED: getValue
20-Apr-2019 08:30:42    [testng] PASSED: testDescription
20-Apr-2019 08:30:42    [testng] PASSED: testDisplayColumnNames
20-Apr-2019 08:30:42    [testng] PASSED: testGetSetValue
20-Apr-2019 08:30:42    [testng] PASSED: testIsEditable
20-Apr-2019 08:30:42    [testng] PASSED: testName
20-Apr-2019 08:30:42    [testng] PASSED: testUrl
20-Apr-2019 08:30:42    [testng] PASSED: testColumns
20-Apr-2019 08:30:42    [testng] PASSED: testCounts
20-Apr-2019 08:30:42    [testng] PASSED: testDeletable
20-Apr-2019 08:30:42    [testng] PASSED: testEditable
20-Apr-2019 08:30:42    [testng] PASSED: testInitialisation
20-Apr-2019 08:30:42    [testng] PASSED: testRowDelete
20-Apr-2019 08:30:42    [testng] PASSED: testRowEditable
20-Apr-2019 08:30:42    [testng] PASSED: testRowInsert
20-Apr-2019 08:30:42    [testng] PASSED: testValues
20-Apr-2019 08:30:42    [testng] PASSED: testCreateLinksForNonDynamic
20-Apr-2019 08:30:42    [testng] PASSED: testCreateLinksFromNullSequence
20-Apr-2019 08:30:42    [testng] PASSED: testCreateLinksFromSequence
20-Apr-2019 08:30:42    [testng] PASSED: testLinkComparator
20-Apr-2019 08:30:42    [testng] PASSED: testLinksWithTargets
20-Apr-2019 08:30:42    [testng] PASSED: testMakeUrlNoRegex
20-Apr-2019 08:30:42    [testng] PASSED: testMakeUrlWithRegex
20-Apr-2019 08:30:42    [testng] PASSED: testUrlLinkCreationNoRegex
20-Apr-2019 08:30:42    [testng] PASSED: testUrlLinkCreationWithRegex
20-Apr-2019 08:30:42    [testng] PASSED: testInitUrlProvider
20-Apr-2019 08:30:42    [testng] PASSED: testSetDefaultUrl
20-Apr-2019 08:30:42    [testng] PASSED: testSetDefaultUrlWrongly
20-Apr-2019 08:30:42    [testng] PASSED: testConstructor_coloursArray
20-Apr-2019 08:30:42    [testng] PASSED: testParseAppletParameter
20-Apr-2019 08:30:42    [testng] PASSED: testToAppletParameter
20-Apr-2019 08:30:42    [testng] PASSED: testDoLoad
20-Apr-2019 08:30:42    [testng] PASSED: testDoLoad_reverseStrand
20-Apr-2019 08:30:42    [testng] PASSED: testDoLoad_vepCsq
20-Apr-2019 08:30:42    [testng] PASSED: testLoadVCFContig
20-Apr-2019 08:30:42    [testng] PASSED: testQuery_plain
20-Apr-2019 08:30:42    [testng] PASSED: testReadVcf_plain
20-Apr-2019 08:30:42    [testng] PASSED: testCopyConstructor
20-Apr-2019 08:30:42    [testng] PASSED: testEquals
20-Apr-2019 08:30:42    [testng] PASSED: testEventFiring
20-Apr-2019 08:30:42    [testng] PASSED: testGetAbsoluteAlignmentHeight
20-Apr-2019 08:30:42    [testng] PASSED: testGetAbsoluteAlignmentWidth
20-Apr-2019 08:30:42    [testng] PASSED: testGetWrappedMaxScroll
20-Apr-2019 08:30:42    [testng] PASSED: testGetWrappedScrollPosition
20-Apr-2019 08:30:42    [testng] PASSED: testPageUpDown
20-Apr-2019 08:30:42    [testng] PASSED: testPageUpDownWrapped
20-Apr-2019 08:30:42    [testng] PASSED: testScrollRight
20-Apr-2019 08:30:42    [testng] PASSED: testScrollRightWithHidden
20-Apr-2019 08:30:42    [testng] PASSED: testScrollToVisible
20-Apr-2019 08:30:42    [testng] PASSED: testScrollToWrappedVisible
20-Apr-2019 08:30:42    [testng] PASSED: testScrollUp
20-Apr-2019 08:30:42    [testng] PASSED: testScrollUpWithHidden
20-Apr-2019 08:30:42    [testng] PASSED: testScrollUp_wrapped
20-Apr-2019 08:30:42    [testng] PASSED: testSetEndSeq
20-Apr-2019 08:30:42    [testng] PASSED: testSetStartEndRes
20-Apr-2019 08:30:42    [testng] PASSED: testSetStartEndResWrapped
20-Apr-2019 08:30:42    [testng] PASSED: testSetStartEndSeq
20-Apr-2019 08:30:42    [testng] PASSED: testSetStartRes
20-Apr-2019 08:30:42    [testng] PASSED: testSetStartResAndSeq
20-Apr-2019 08:30:42    [testng] PASSED: testSetStartSeq
20-Apr-2019 08:30:42    [testng] PASSED: testSetViewportHeight
20-Apr-2019 08:30:42    [testng] PASSED: testSetViewportLocation
20-Apr-2019 08:30:42    [testng] PASSED: testSetViewportStartAndHeight
20-Apr-2019 08:30:42    [testng] PASSED: testSetViewportStartAndWidth
20-Apr-2019 08:30:42    [testng] PASSED: testSetViewportStartAndWidthWrapped
20-Apr-2019 08:30:42    [testng] PASSED: testSetViewportWidth
20-Apr-2019 08:30:42    [testng] PASSED: testViewportRanges
20-Apr-2019 08:30:42    [testng] PASSED: testMultipleVisibleRegions
20-Apr-2019 08:30:42    [testng] PASSED: testSimpleVisibleRegions
20-Apr-2019 08:30:42    [testng] PASSED: testVisibleRegionsAtHiddenEdges
20-Apr-2019 08:30:42    [testng] PASSED: testHasNextAndNextEndHidden
20-Apr-2019 08:30:42    [testng] PASSED: testHasNextAndNextNoHidden
20-Apr-2019 08:30:42    [testng] PASSED: testHasNextAndNextStartHidden
20-Apr-2019 08:30:42    [testng] PASSED: testHasNextAndNextWithHidden
20-Apr-2019 08:30:42    [testng] PASSED: testLastNextEndHidden
20-Apr-2019 08:30:42    [testng] PASSED: testLastNextNoHidden
20-Apr-2019 08:30:42    [testng] PASSED: testLastNextStartHidden
20-Apr-2019 08:30:42    [testng] PASSED: testLastNextWithHidden
20-Apr-2019 08:30:42    [testng] PASSED: testRemove
20-Apr-2019 08:30:42    [testng] FAILED: testFindXrefSequences_forGeneAndTranscripts
20-Apr-2019 08:30:42    [testng] java.lang.NullPointerException
20-Apr-2019 08:30:42    [testng]         at jalview.analysis.CrossRefTest.__CLR4_2_16yj4942mwj(CrossRefTest.java:535)
20-Apr-2019 08:30:42    [testng]         at jalview.analysis.CrossRefTest.testFindXrefSequences_forGeneAndTranscripts(CrossRefTest.java:469)
20-Apr-2019 08:30:42    [testng]         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
20-Apr-2019 08:30:42    [testng]         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
20-Apr-2019 08:30:42    [testng]         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
20-Apr-2019 08:30:42    [testng]         at java.lang.reflect.Method.invoke(Method.java:498)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestRunner.privateRun(TestRunner.java:771)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestRunner.run(TestRunner.java:621)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.run(SuiteRunner.java:259)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.run(TestNG.java:1009)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.privateMain(TestNG.java:1316)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.main(TestNG.java:1285)
20-Apr-2019 08:30:42    [testng]
20-Apr-2019 08:30:42    [testng] FAILED: testFindXrefSequences_uniprotEmblManyToMany
20-Apr-2019 08:30:42    [testng] java.lang.NullPointerException
20-Apr-2019 08:30:42    [testng]         at jalview.analysis.CrossRefTest.__CLR4_2_1nurnsm2mxa(CrossRefTest.java:711)
20-Apr-2019 08:30:42    [testng]         at jalview.analysis.CrossRefTest.testFindXrefSequences_uniprotEmblManyToMany(CrossRefTest.java:566)
20-Apr-2019 08:30:42    [testng]         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
20-Apr-2019 08:30:42    [testng]         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
20-Apr-2019 08:30:42    [testng]         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
20-Apr-2019 08:30:42    [testng]         at java.lang.reflect.Method.invoke(Method.java:498)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestRunner.privateRun(TestRunner.java:771)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestRunner.run(TestRunner.java:621)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.run(SuiteRunner.java:259)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.run(TestNG.java:1009)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.privateMain(TestNG.java:1316)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.main(TestNG.java:1285)
20-Apr-2019 08:30:42    [testng]
20-Apr-2019 08:30:42    [testng] FAILED: testFindXrefSequences_withFetch
20-Apr-2019 08:30:42    [testng] java.lang.NullPointerException
20-Apr-2019 08:30:42    [testng]         at jalview.analysis.CrossRefTest.__CLR4_2_1ruxmrc2mvx(CrossRefTest.java:452)
20-Apr-2019 08:30:42    [testng]         at jalview.analysis.CrossRefTest.testFindXrefSequences_withFetch(CrossRefTest.java:415)
20-Apr-2019 08:30:42    [testng]         at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
20-Apr-2019 08:30:42    [testng]         at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
20-Apr-2019 08:30:42    [testng]         at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
20-Apr-2019 08:30:42    [testng]         at java.lang.reflect.Method.invoke(Method.java:498)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
20-Apr-2019 08:30:42    [testng]         at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestRunner.privateRun(TestRunner.java:771)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestRunner.run(TestRunner.java:621)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunner.run(SuiteRunner.java:259)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
20-Apr-2019 08:30:42    [testng]         at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.run(TestNG.java:1009)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.privateMain(TestNG.java:1316)
20-Apr-2019 08:30:42    [testng]         at org.testng.TestNG.main(TestNG.java:1285)
20-Apr-2019 08:30:42    [testng]
20-Apr-2019 08:30:42    [testng]
20-Apr-2019 08:30:42    [testng] ===============================================
20-Apr-2019 08:30:42    [testng]     Ant test
20-Apr-2019 08:30:42    [testng]     Tests run: 1286, Failures: 3, Skips: 0
20-Apr-2019 08:30:42    [testng] ===============================================
20-Apr-2019 08:30:42    [testng]
20-Apr-2019 08:30:42    [testng]
20-Apr-2019 08:30:42    [testng] ===============================================
20-Apr-2019 08:30:42    [testng] Ant suite
20-Apr-2019 08:30:42    [testng] Total tests run: 1286, Failures: 3, Skips: 0
20-Apr-2019 08:30:42    [testng] ===============================================
20-Apr-2019 08:30:42    [testng]
20-Apr-2019 08:30:42    [testng] [TestNG] Time taken by [FailedReporter passed=0 failed=0 skipped=0]: 34 ms
20-Apr-2019 08:30:42    [testng] [TestNG] Time taken by org.testng.reporters.jq.Main@2c13da15: 260 ms
20-Apr-2019 08:30:42    [testng] [TestNG] Time taken by org.testng.reporters.EmailableReporter2@71bc1ae4: 23 ms
20-Apr-2019 08:30:42    [testng] [TestNG] Time taken by org.testng.reporters.SuiteHTMLReporter@7960847b: 257 ms
20-Apr-2019 08:30:42    [testng] [TestNG] Time taken by org.testng.reporters.XMLReporter@2aae9190: 92 ms
20-Apr-2019 08:30:42    [testng] [TestNG] Time taken by org.testng.reporters.JUnitReportReporter@e73f9ac: 59 ms
20-Apr-2019 08:30:43    [testng] The tests failed.
20-Apr-2019 08:30:43
20-Apr-2019 08:30:43 clover.save-history:
20-Apr-2019 08:30:43 [clover-historypoint] OpenClover Version 4.2.1, built on November 21 2017 (build-1004)
20-Apr-2019 08:30:43 [clover-historypoint] Loaded from: /home/bamboo/buildtools/clover/lib/clover.jar
20-Apr-2019 08:30:43 [clover-historypoint] Clover free edition.
20-Apr-2019 08:30:46 [clover-historypoint] Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/.cloverhistory/jalviewX/clover-20190420083042.xml.gz'
20-Apr-2019 08:30:47
20-Apr-2019 08:30:47 clover.report:
20-Apr-2019 08:30:47 [clover-report] OpenClover Version 4.2.1, built on November 21 2017 (build-1004)
20-Apr-2019 08:30:47 [clover-report] Loaded from: /home/bamboo/buildtools/clover/lib/clover.jar
20-Apr-2019 08:30:47 [clover-report] Clover free edition.
20-Apr-2019 08:30:47 [clover-report] Loading coverage database from: '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/.clover/clover4_2_1.db'
20-Apr-2019 08:30:47 [clover-report] Loading coverage database from: '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/.clover/clover4_2_1.db'
20-Apr-2019 08:30:47 [clover-report] Loading historical coverage data from: '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/.cloverhistory/jalviewX'
20-Apr-2019 08:30:48 [clover-report] Writing HTML report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/clover/jalviewX'
20-Apr-2019 08:31:10 [clover-report] Done. Processed 89 packages in 21600ms (242ms per package).
20-Apr-2019 08:31:11 [clover-report] Writing report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/clover/jalviewX/clover.xml'
20-Apr-2019 08:31:12 [clover-report] Writing historical report to '/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/clover/jalviewX'
20-Apr-2019 08:31:14 [clover-report] Read 20 history points.
20-Apr-2019 08:31:14 [clover-report] using movers interval of 1 day
20-Apr-2019 08:31:14 [clover-report] using movers interval of 1 day
20-Apr-2019 08:31:15 [clover-report] Writing JSON historical-data to: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/clover/jalviewX/historical-json.js
20-Apr-2019 08:31:15 [clover-report] Done.
20-Apr-2019 08:31:15
20-Apr-2019 08:31:15 BUILD SUCCESSFUL
20-Apr-2019 08:31:15 Total time: 3 minutes 51 seconds
20-Apr-2019 08:31:15 Finished task 'Clover TestNG Suite' with result: Success
20-Apr-2019 08:31:15 Starting task 'Process Jalview TestNG Suite' of type 'com.atlassian.bamboo.plugins.testresultparser:task.testresultparser.testng'
20-Apr-2019 08:31:15 Parsing test results under /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1...
20-Apr-2019 08:31:17 Failing task since 3 failing test cases were found.
20-Apr-2019 08:31:17 Finished task 'Process Jalview TestNG Suite' with result: Failed
20-Apr-2019 08:31:17 Starting task 'build' of type 'com.atlassian.bamboo.plugins.ant:task.builder.ant'
20-Apr-2019 08:31:17
Beginning to execute external process for build 'Jalview Builds - jalview develop build - Default Job #132 (JB-JDB-JOB1-132)'
... running command line:
/usr/share/ant/bin/ant -Djava.io.tmpdir=/home/bamboo/latest/temp/JB-JDB-JOB1 -f build.xml makedist
... in: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1
... using extra environment variables:
bamboo_planRepository_1_branch=develop
bamboo_capability_system_builder_maven_Artifactory_Maven_3=/usr
bamboo_planRepository_1_branchDisplayName=develop
bamboo_repository_revision_number=15c6c6724878a5445e9f5bc6594719dbe81c1735
bamboo_resultsUrl=https://builds.jalview.org/browse/JB-JDB-JOB1-132
bamboo_build_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1
bamboo_planRepository_1_name=Jalview Git
bamboo_buildKey=JB-JDB-JOB1
bamboo_capability_system_jdk_JDK_1_8_0_171=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64
bamboo_shortPlanName=jalview develop build
bamboo_planRepository_name=Jalview Git
bamboo_buildNumber=132
bamboo_capability_system_jdk_OpenJDK_11_JRE_only=/home/bamboo/buildtools/jvm/jre11_x64_linux
bamboo_shortJobName=Default Job
bamboo_buildResultsUrl=https://builds.jalview.org/browse/JB-JDB-JOB1-132
bamboo_repository_720898_git_branch=develop
bamboo_planRepository_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_repository_720898_branch_name=develop
bamboo_repository_720898_name=Jalview Git
bamboo_agentId=196609
bamboo_planName=Jalview Builds - jalview develop build
bamboo_shortPlanKey=JDB
bamboo_shortJobKey=JOB1
bamboo_capability_system_jdk_OpenJDK_11=/home/bamboo/buildtools/jvm/jdk11_x64_linux
bamboo_planRepository_revision=15c6c6724878a5445e9f5bc6594719dbe81c1735
bamboo_buildTimeStamp=2019-04-20T08:27:19.754+01:00
bamboo_repository_previous_revision_number=58ecc1bd5b01acd8f8378980f369003da9db2ee9
bamboo_planRepository_previousRevision=58ecc1bd5b01acd8f8378980f369003da9db2ee9
bamboo_repository_git_branch=develop
bamboo_buildResultKey=JB-JDB-JOB1-132
bamboo_repository_branch_name=develop
bamboo_buildPlanName=Jalview Builds - jalview develop build - Default Job
bamboo_capability_system_builder_ant_j11_Ant=/home/bamboo/buildtools/j11/ant-j11
bamboo_planRepository_1_revision=15c6c6724878a5445e9f5bc6594719dbe81c1735
bamboo_capability_system_builder_ant_x11_Ant=/home/bamboo/buildtools/x11-ant
bamboo_repository_720898_previous_revision_number=58ecc1bd5b01acd8f8378980f369003da9db2ee9
bamboo_repository_name=Jalview Git
JAVA_HOME=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64
bamboo_buildFailed=true
bamboo_build_commandline_com_atlassian_bamboo_plugins_ant_task_builder_ant_3=/home/bamboo/buildtools/x11-ant/bin/ant -Djava.io.tmpdir=/home/bamboo/latest/temp/JB-JDB-JOB1 -f build.xml -Dclover.jar=/home/bamboo/buildtools/clover/lib/clover.jar clean with.clover testng clover.report
ANT_HOME=/usr/share/ant
bamboo_planRepository_branch=develop
bamboo_agentWorkingDirectory=/srv/bamboo/bamboo-home/xml-data/build-dir
bamboo_jobFailed=true
bamboo_capability_system_git_executable=/bin/git
bamboo_repository_720898_git_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_repository_git_username=
bamboo_planRepository_1_previousRevision=58ecc1bd5b01acd8f8378980f369003da9db2ee9
bamboo_planRepository_branchDisplayName=develop
bamboo_planRepository_1_type=gitv2
bamboo_planRepository_branchName=develop
bamboo_capability_system_builder_ant_j11_x11_Ant=/home/bamboo/buildtools/j11/x11-ant-j11
bamboo_capability_system_builderivy_Ivy=/usr
bamboo_capability_system_jdk_JDK=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64
bamboo_plan_storageTag=plan-753665
bamboo_capability_system_builder_gradle_Gradle=/home/bamboo/buildtools/gradle
bamboo_hg_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_hg-repositories-cache
bamboo_planRepository_1_username=
bamboo_planRepository_type=gitv2
bamboo_git_cache_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/_git-repositories-cache
bamboo_repository_git_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_capability_system_builder_ant_Ant=/usr/share/ant
bamboo_capability_system_builder_mvn3_Maven_3=/usr/share/maven
bamboo_tmp_directory=/srv/bamboo/bamboo-home/temp
bamboo_repository_720898_git_username=
bamboo_working_directory=/srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1
bamboo_planKey=JB-JDB
bamboo_planRepository_1_repositoryUrl=http://source.jalview.org/git/jalview.git
bamboo_planRepository_username=
bamboo_capability_system_jdk_JDK_1_8=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64
bamboo_repository_720898_revision_number=15c6c6724878a5445e9f5bc6594719dbe81c1735
bamboo_planRepository_1_branchName=develop
PATH=/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.171-8.b10.el7_5.x86_64/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin
20-Apr-2019 08:31:18 Buildfile: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/build.xml
20-Apr-2019 08:31:18
20-Apr-2019 08:31:18 init:
20-Apr-2019 08:31:18
20-Apr-2019 08:31:18 prepare:
20-Apr-2019 08:31:18      [copy] Copying 2 files to /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/classes
20-Apr-2019 08:31:18
20-Apr-2019 08:31:18 build:
20-Apr-2019 08:31:18     [javac] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/build.xml:279: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
20-Apr-2019 08:31:18     [javac] Compiling 1 source file to /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/classes
20-Apr-2019 08:31:20
20-Apr-2019 08:31:20 buildPropertiesFile:
20-Apr-2019 08:31:21 [properties] write property file /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/classes/.build_properties
20-Apr-2019 08:31:21
20-Apr-2019 08:31:21 linkcheck:
20-Apr-2019 08:31:21     [javac] /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/build.xml:1011: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds
20-Apr-2019 08:31:21      [java] Checking help file links
20-Apr-2019 08:31:22      [java]
20-Apr-2019 08:31:22      [java] Results:
20-Apr-2019 08:31:22      [java] 134 distinct help targets
20-Apr-2019 08:31:22      [java] 134 help mappings
20-Apr-2019 08:31:22      [java] 0 invalid targets
20-Apr-2019 08:31:22      [java] 23 unused targets
20-Apr-2019 08:31:22      [java]     uniprotfetcher: html/features/uniprotsequencefetcher.html
20-Apr-2019 08:31:22      [java]     overviewprefs: html/features/preferences.html#overview
20-Apr-2019 08:31:22      [java]     cdnafeatures: html/features/codingfeatures.html
20-Apr-2019 08:31:22      [java]     ensemblfetch: html/features/ensemblsequencefetcher.html
20-Apr-2019 08:31:22      [java]     io.modellerpir: html/io/modellerpir.html
20-Apr-2019 08:31:22      [java]     pdbmcviewer: html/features/pdbviewer.html
20-Apr-2019 08:31:22      [java]     groovy.colours: html/features/groovy.html#groovyColours
20-Apr-2019 08:31:22      [java]     seqmappings: html/features/seqmappings.html
20-Apr-2019 08:31:22      [java]     uniprotfts: html/features/uniprotsequencefetcher.html#uniprotfts
20-Apr-2019 08:31:22      [java]     splitframe.mirrorfonts: html/features/splitView.html#mirror
20-Apr-2019 08:31:22      [java]     subtMatrices.pam250: html/calculations/scorematrices.html#pam250
20-Apr-2019 08:31:22      [java]     search: html/features/search.html
20-Apr-2019 08:31:22      [java]     viewingpdbs.reps: html/features/viewingpdbs.html#viewreps
20-Apr-2019 08:31:22      [java]     alformats: html/io/fileformats.html
20-Apr-2019 08:31:22      [java]     strucprefs: html/features/preferences.html#structure
20-Apr-2019 08:31:22      [java]     siftsmapping: html/features/siftsmapping.html
20-Apr-2019 08:31:22      [java]     pdbfts: html/features/pdbsequencefetcher.html#pdbfts
20-Apr-2019 08:31:22      [java]     newkeys: html/features/newkeystrokes.html
20-Apr-2019 08:31:22      [java]     seqfeatures.settings.selcols: html/features/featuresettings.html#selectbyfeature
20-Apr-2019 08:31:22      [java]     jalarchive: html/features/jalarchive.html
20-Apr-2019 08:31:22      [java]     newsreader: html/webServices/newsreader.html
20-Apr-2019 08:31:22      [java]     popMenuAddref: html/menus/popupMenu.html#addrefannot
20-Apr-2019 08:31:22      [java]     overview: html/features/overview.html
20-Apr-2019 08:31:22      [java] 0 invalid map urls
20-Apr-2019 08:31:22      [java] 0 invalid image attributes
20-Apr-2019 08:31:22      [java] 356 internal href links (64 with anchors)
20-Apr-2019 08:31:22      [java] 0 invalid internal href links
20-Apr-2019 08:31:22      [java] 0 invalid internal anchor links
20-Apr-2019 08:31:22      [java] 87 external href links
20-Apr-2019 08:31:22      [java] External links not verified as internet not available
20-Apr-2019 08:31:22      [java] *** Success ***
20-Apr-2019 08:31:22
20-Apr-2019 08:31:22 buildindices:
20-Apr-2019 08:31:24
20-Apr-2019 08:31:24 makedist:
20-Apr-2019 08:31:24       [jar] Building jar: /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/dist/jalview.jar
20-Apr-2019 08:31:27      [copy] Copying 51 files to /srv/bamboo/bamboo-home/xml-data/build-dir/JB-JDB-JOB1/dist
20-Apr-2019 08:31:27
20-Apr-2019 08:31:27 BUILD SUCCESSFUL
20-Apr-2019 08:31:27 Total time: 9 seconds
20-Apr-2019 08:31:27 Finished task 'build' with result: Success
20-Apr-2019 08:31:27 Running post build plugin 'NCover Results Collector'
20-Apr-2019 08:31:27 Running post build plugin 'Artifact Copier'
20-Apr-2019 08:31:27 Publishing an artifact: jalview-jars
20-Apr-2019 08:31:27 Finished publishing of artifact Shared artifact: [jalview-jars], pattern: [**/*.*] anchored at: [dist] in 103.7 ms
20-Apr-2019 08:31:27 Publishing an artifact: Clover Report (System)
20-Apr-2019 08:37:09 Finished publishing of artifact Job artifact: [Clover Report (System)], pattern: [**/*.*] anchored at: [clover] in 5.701 min
20-Apr-2019 08:37:09 Running post build plugin 'Artifactory Release Management Staging'
20-Apr-2019 08:37:09 Running post build plugin 'Artifactory Build Info Copier'
20-Apr-2019 08:37:09 Running post build plugin 'Artifactory Gradle Properties Info Copier'
20-Apr-2019 08:37:09 Running post build plugin 'npm Cache Cleanup'
20-Apr-2019 08:37:09 Running post build plugin 'Clover Results Collector'
20-Apr-2019 08:37:09 Running post build plugin 'Docker Container Cleanup'
20-Apr-2019 08:37:09 Finalising the build...
20-Apr-2019 08:37:09 Stopping timer.
20-Apr-2019 08:37:09 Build JB-JDB-JOB1-132 completed.
20-Apr-2019 08:37:09 Running on server: post build plugin 'NCover Results Collector'
20-Apr-2019 08:37:09 Running on server: post build plugin 'Build Hanging Detection Configuration'
20-Apr-2019 08:37:09 Running on server: post build plugin 'Clover Delta Calculator'
20-Apr-2019 08:37:09 Running on server: post build plugin 'Maven Dependencies Postprocessor'
20-Apr-2019 08:37:09 All post build plugins have finished
20-Apr-2019 08:37:09 Generating build results summary...
20-Apr-2019 08:37:09 Saving build results to disk...
20-Apr-2019 08:37:10 Logging substituted variables...
20-Apr-2019 08:37:10 Indexing build results...
20-Apr-2019 08:37:10 Finished building JB-JDB-JOB1-132.