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Test argFilesGlobAndSubstitutionsTest

Test
argFilesGlobAndSubstitutionsTest 1PASS 6 Dec 13:48:07 0.35
 
argFilesGlobAndSubstitutionsTest
jalview.io.DataSourceType   jalview.io.DataSourceType 1.0100%
jalview.ws.WSClient   jalview.ws.WSClient 1.0100%
jalview.urls.IdOrgSettings   jalview.urls.IdOrgSettings 1.0100%
jalview.datamodel.SecondaryStructureCount.SymbolCounts   jalview.datamodel.SecondaryStructureCount.SymbolCounts 1.0100%
jalview.datamodel.ResidueCount.SymbolCounts   jalview.datamodel.ResidueCount.SymbolCounts 1.0100%
jalview.jbgui.GAlignmentPanel   jalview.jbgui.GAlignmentPanel 0.9494%
jalview.io.JalviewFileChooser.RecentlyOpened   jalview.io.JalviewFileChooser.RecentlyOpened 0.990%
jalview.util.UserAgent   jalview.util.UserAgent 0.885714388.6%
jalview.gui.SplashScreen.SplashImage   jalview.gui.SplashScreen.SplashImage 0.8823529588.2%
jalview.util.imagemaker.BitmapImageSizing   jalview.util.imagemaker.BitmapImageSizing 0.8709677587.1%
jalview.io.JalviewFileChooser.recentlyOpenedCellRenderer   jalview.io.JalviewFileChooser.recentlyOpenedCellRenderer 0.869565287%
jalview.util.QuickSort.IntComparator   jalview.util.QuickSort.IntComparator 0.8571428785.7%
jalview.json.binding.biojs.BioJSReleasePojo   jalview.json.binding.biojs.BioJSReleasePojo 0.8461538684.6%
jalview.datamodel.Profiles   jalview.datamodel.Profiles 0.833333383.3%
jalview.util.UrlConstants   jalview.util.UrlConstants 0.880%
jalview.gui.SplashScreen   jalview.gui.SplashScreen 0.792207879.2%
jalview.gui.ItemsRenderer   jalview.gui.ItemsRenderer 0.777777877.8%
jalview.util.LinkedIdentityHashSet   jalview.util.LinkedIdentityHashSet 0.7727272577.3%
jalview.gui.JalviewChangeSupport   jalview.gui.JalviewChangeSupport 0.7575%
jalview.schemes.NucleotideColourScheme   jalview.schemes.NucleotideColourScheme 0.7575%
jalview.workers.SecondaryStructureConsensusThread   jalview.workers.SecondaryStructureConsensusThread 0.7333333573.3%
jalview.gui.FeatureRenderer   jalview.gui.FeatureRenderer 0.7142857371.4%
jalview.util.LinkedIdentityHashSet.IdentityWrapper   jalview.util.LinkedIdentityHashSet.IdentityWrapper 0.7142857371.4%
jalview.io.JalviewFileFilter   jalview.io.JalviewFileFilter 0.707547270.8%
jalview.datamodel.Profile   jalview.datamodel.Profile 0.70491870.5%
jalview.ws.jws2.jabaws2.Jws2InstanceFactory   jalview.ws.jws2.jabaws2.Jws2InstanceFactory 0.770%
jalview.workers.ConsensusThread   jalview.workers.ConsensusThread 0.696969769.7%
jalview.json.binding.biojs.BioJSRepositoryPojo   jalview.json.binding.biojs.BioJSRepositoryPojo 0.687568.8%
jalview.ws.SequenceFetcher   jalview.ws.SequenceFetcher 0.678571467.9%
jalview.log.JalviewAppender   jalview.log.JalviewAppender 0.666666766.7%
jalview.schemes.ResidueColourScheme   jalview.schemes.ResidueColourScheme 0.666666766.7%
jalview.ws.utils.UrlDownloadClient   jalview.ws.utils.UrlDownloadClient 0.657142965.7%
jalview.ws.jws2.jabaws2.Jws2Instance   jalview.ws.jws2.jabaws2.Jws2Instance 0.643678264.4%
jalview.math.AlignmentDimension   jalview.math.AlignmentDimension 0.636363663.6%
jalview.bin.Cache.VersionChecker   jalview.bin.Cache.VersionChecker 0.629629663%
jalview.ws.jws2.JabaWsServerQuery   jalview.ws.jws2.JabaWsServerQuery 0.62562.5%
jalview.util.ParseHtmlBodyAndLinks   jalview.util.ParseHtmlBodyAndLinks 0.594202959.4%
jalview.bin.argparser.BootstrapArgs   jalview.bin.argparser.BootstrapArgs 0.5743801657.4%
jalview.jbgui.GAlignFrame   jalview.jbgui.GAlignFrame 0.57354357.4%
jalview.bin.argparser.ArgValue   jalview.bin.argparser.ArgValue 0.567164256.7%
jalview.jbgui.GDesktop   jalview.jbgui.GDesktop 0.561855756.2%
jalview.io.BioJsHTMLOutput   jalview.io.BioJsHTMLOutput 0.5656%
jalview.workers.AlignCalcManager   jalview.workers.AlignCalcManager 0.559523856%
jalview.ws.sifts.SiftsSettings   jalview.ws.sifts.SiftsSettings 0.555555655.6%
jalview.bin.ArgsParser   jalview.bin.ArgsParser 0.5555%
jalview.viewmodel.ViewportProperties   jalview.viewmodel.ViewportProperties 0.550%
jalview.schemes.TaylorColourScheme   jalview.schemes.TaylorColourScheme 0.550%
jalview.schemes.FlowerColourScheme   jalview.schemes.FlowerColourScheme 0.550%
jalview.schemes.ZappoColourScheme   jalview.schemes.ZappoColourScheme 0.550%
jalview.schemes.NucleotideAmbiguityColourScheme   jalview.schemes.NucleotideAmbiguityColourScheme 0.550%
jalview.schemes.PurinePyrimidineColourScheme   jalview.schemes.PurinePyrimidineColourScheme 0.550%
jalview.schemes.BlossomColourScheme   jalview.schemes.BlossomColourScheme 0.550%
jalview.schemes.SunsetColourScheme   jalview.schemes.SunsetColourScheme 0.550%
jalview.schemes.OceanColourScheme   jalview.schemes.OceanColourScheme 0.550%
jalview.bin.argparser.ArgParser   jalview.bin.argparser.ArgParser 0.4992481249.9%
jalview.io.FileLoader   jalview.io.FileLoader 0.491638849.2%
jalview.gui.BlogReader   jalview.gui.BlogReader 0.483425448.3%
jalview.gui.AlignmentPanel   jalview.gui.AlignmentPanel 0.4723203847.2%
jalview.gui.PromptUserConfig   jalview.gui.PromptUserConfig 0.465909146.6%
jalview.gui.Console   jalview.gui.Console 0.4633027646.3%
jalview.util.FileUtils   jalview.util.FileUtils 0.462365646.2%
jalview.datamodel.ResidueCount   jalview.datamodel.ResidueCount 0.4436363644.4%
jalview.gui.ImageExporter   jalview.gui.ImageExporter 0.4393939443.9%
jalview.gui.APQHandlers   jalview.gui.APQHandlers 0.434782643.5%
jalview.bin.argparser.SubVals   jalview.bin.argparser.SubVals 0.432989743.3%
jalview.gui.ColourMenuHelper   jalview.gui.ColourMenuHelper 0.4322033843.2%
jalview.datamodel.HiddenCursorPosition   jalview.datamodel.HiddenCursorPosition 0.4285714342.9%
jalview.gui.SequenceRenderer   jalview.gui.SequenceRenderer 0.4230769342.3%
jalview.util.ShortcutKeyMaskExWrapper11   jalview.util.ShortcutKeyMaskExWrapper11 0.4166666641.7%
jalview.gui.ProgressBar   jalview.gui.ProgressBar 0.4146341441.5%
jalview.ext.so.SequenceOntology   jalview.ext.so.SequenceOntology 0.412541.2%
jalview.util.HttpUtils   jalview.util.HttpUtils 0.411764741.2%
jalview.ws.jws2.JabaPreset   jalview.ws.jws2.JabaPreset 0.409090940.9%
jalview.bin.Cache   jalview.bin.Cache 0.407713540.8%
jalview.util.MessageManager   jalview.util.MessageManager 0.404761940.5%
jalview.bin.argparser.ArgValuesMap   jalview.bin.argparser.ArgValuesMap 0.40097840.1%
jalview.gui.IdCanvas   jalview.gui.IdCanvas 0.440%
jalview.io.FileFormats   jalview.io.FileFormats 0.440%
jalview.ws.dbsources.EmblSource   jalview.ws.dbsources.EmblSource 0.440%
jalview.schemes.HydrophobicColourScheme   jalview.schemes.HydrophobicColourScheme 0.440%
jalview.schemes.HelixColourScheme   jalview.schemes.HelixColourScheme 0.440%
jalview.schemes.TurnColourScheme   jalview.schemes.TurnColourScheme 0.440%
jalview.schemes.StrandColourScheme   jalview.schemes.StrandColourScheme 0.440%
jalview.schemes.BuriedColourScheme   jalview.schemes.BuriedColourScheme 0.440%
org.json.simple.parser.Yylex   org.json.simple.parser.Yylex 0.3853503238.5%
jalview.gui.PaintRefresher   jalview.gui.PaintRefresher 0.380281738%
jalview.util.ImageMaker   jalview.util.ImageMaker 0.3798449638%
jalview.gui.AlignViewport   jalview.gui.AlignViewport 0.3721461337.2%
jalview.analysis.AAFrequency   jalview.analysis.AAFrequency 0.3683127536.8%
jalview.renderer.ScaleRenderer   jalview.renderer.ScaleRenderer 0.3636%
jalview.io.AlignFile   jalview.io.AlignFile 0.356164435.6%
jalview.gui.UserQuestionnaireCheck   jalview.gui.UserQuestionnaireCheck 0.349397634.9%
jalview.ws.jws2.MsaWSClient   jalview.ws.jws2.MsaWSClient 0.348993334.9%
jalview.ws.jws2.Jws2Discoverer   jalview.ws.jws2.Jws2Discoverer 0.3425742734.3%
jalview.bin.argparser.ArgValues   jalview.bin.argparser.ArgValues 0.3412698534.1%
jalview.ws.jws1.Discoverer   jalview.ws.jws1.Discoverer 0.3397435834%
jalview.viewmodel.styles.ViewStyle   jalview.viewmodel.styles.ViewStyle 0.3369565333.7%
jalview.viewmodel.ViewportRanges   jalview.viewmodel.ViewportRanges 0.33003333%
jalview.gui.IdwidthAdjuster   jalview.gui.IdwidthAdjuster 0.3289473732.9%
jalview.bin.Commands   jalview.bin.Commands 0.3286978632.9%
jalview.io.FastaFile   jalview.io.FastaFile 0.315315331.5%
jalview.ws.rest.RestServiceDescription   jalview.ws.rest.RestServiceDescription 0.31531.5%
jalview.util.Comparison   jalview.util.Comparison 0.3149606331.5%
jalview.gui.Desktop.MyDesktopPane   jalview.gui.Desktop.MyDesktopPane 0.3095238231%
jalview.renderer.AnnotationRenderer   jalview.renderer.AnnotationRenderer 0.295535729.6%
org.json.simple.parser.JSONParser   org.json.simple.parser.JSONParser 0.2945544429.5%
jalview.ws.dbsources.EmblCdsSource   jalview.ws.dbsources.EmblCdsSource 0.285714328.6%
jalview.renderer.ResidueColourFinder   jalview.renderer.ResidueColourFinder 0.285714328.6%
ext.vamsas.ServiceHandle   ext.vamsas.ServiceHandle 0.285714328.6%
jalview.schemes.JalviewColourScheme   jalview.schemes.JalviewColourScheme 0.285714328.6%
jalview.io.IdentifyFile   jalview.io.IdentifyFile 0.279365127.9%
jalview.viewmodel.AlignmentViewport   jalview.viewmodel.AlignmentViewport 0.2747489227.5%
jalview.util.Log4j   jalview.util.Log4j 0.2727272827.3%
jalview.io.JalviewFileChooser   jalview.io.JalviewFileChooser 0.269372726.9%
jalview.bin.Jalview   jalview.bin.Jalview 0.2590252825.9%
jalview.renderer.ResidueShader   jalview.renderer.ResidueShader 0.2560975625.6%
jalview.io.FileParse   jalview.io.FileParse 0.250696425.1%
jalview.gui.Desktop   jalview.gui.Desktop 0.2502837825%
jalview.renderer.AnnotationRendererFactory   jalview.renderer.AnnotationRendererFactory 0.2525%
jalview.io.gff.SequenceOntologyFactory   jalview.io.gff.SequenceOntologyFactory 0.2525%
jalview.ws.rest.params.Alignment   jalview.ws.rest.params.Alignment 0.2435897424.4%
jalview.log.JLogger   jalview.log.JLogger 0.2417582424.2%
jalview.util.ErrorLog   jalview.util.ErrorLog 0.2352941223.5%
jalview.bin.BuildDetails   jalview.bin.BuildDetails 0.2352941223.5%
jalview.gui.JvSwingUtils   jalview.gui.JvSwingUtils 0.2312925223.1%
jalview.gui.AnnotationLabels   jalview.gui.AnnotationLabels 0.2091503320.9%
jalview.gui.BlogReader.LaunchJvBrowserOnItem   jalview.gui.BlogReader.LaunchJvBrowserOnItem 0.2083333320.8%
jalview.ws.rest.InputType   jalview.ws.rest.InputType 0.2056074720.6%
jalview.datamodel.Alignment   jalview.datamodel.Alignment 0.2048417220.5%
jalview.log.JLoggerLog4j   jalview.log.JLoggerLog4j 0.203883520.4%
jalview.bin.Console   jalview.bin.Console 0.2019704420.2%
jalview.gui.Desktop.MyDesktopManager   jalview.gui.Desktop.MyDesktopManager 0.220%
jalview.bin.JalviewTaskbar   jalview.bin.JalviewTaskbar 0.220%
jalview.datamodel.SecondaryStructureCount   jalview.datamodel.SecondaryStructureCount 0.1914062519.1%
jalview.util.QuickSort   jalview.util.QuickSort 0.1844660218.4%
jalview.util.ImageMaker.TYPE   jalview.util.ImageMaker.TYPE 0.1818181918.2%
jalview.schemes.IdColourScheme   jalview.schemes.IdColourScheme 0.1739130517.4%
jalview.util.ChannelProperties   jalview.util.ChannelProperties 0.172413817.2%
jalview.analysis.AnnotationSorter   jalview.analysis.AnnotationSorter 0.1674876816.7%
jalview.gui.ScalePanel   jalview.gui.ScalePanel 0.1601562516%
jalview.ws.jws1.WS1Client   jalview.ws.jws1.WS1Client 0.1616%
jalview.schemes.TCoffeeColourScheme   jalview.schemes.TCoffeeColourScheme 0.1475409914.8%
jalview.ws.jws2.JabaParamStore   jalview.ws.jws2.JabaParamStore 0.1458333314.6%
jalview.io.AppletFormatAdapter   jalview.io.AppletFormatAdapter 0.1428571514.3%
jalview.gui.SeqCanvas   jalview.gui.SeqCanvas 0.1422845714.2%
jalview.gui.AlignFrame   jalview.gui.AlignFrame 0.1417018314.2%
jalview.gui.AnnotationPanel   jalview.gui.AnnotationPanel 0.1402373314%
jalview.util.StringUtils   jalview.util.StringUtils 0.132307713.2%
jalview.ws.rest.params.SeqGroupIndexVector   jalview.ws.rest.params.SeqGroupIndexVector 0.12408759412.4%
jalview.io.FileFormat   jalview.io.FileFormat 0.1240310112.4%
jalview.bin.argparser.Arg   jalview.bin.argparser.Arg 0.1234939812.3%
jalview.util.Platform   jalview.util.Platform 0.1226415112.3%
jalview.io.FormatAdapter   jalview.io.FormatAdapter 0.1212%
jalview.datamodel.Sequence   jalview.datamodel.Sequence 0.1185121111.9%
jalview.schemes.Blosum62ColourScheme   jalview.schemes.Blosum62ColourScheme 0.1176470611.8%
jalview.ws.rest.RestClient   jalview.ws.rest.RestClient 0.11538461611.5%
jalview.datamodel.Annotation   jalview.datamodel.Annotation 0.11428571511.4%
jalview.structure.StructureImportSettings   jalview.structure.StructureImportSettings 0.11428571511.4%
jalview.structure.StructureSelectionManager   jalview.structure.StructureSelectionManager 0.1123882511.2%
jalview.analysis.GeneticCodes   jalview.analysis.GeneticCodes 0.11180124411.2%
jalview.util.ShortcutKeyMaskExWrapper   jalview.util.ShortcutKeyMaskExWrapper 0.1111111111.1%
jalview.schemes.ColourSchemeProperty   jalview.schemes.ColourSchemeProperty 0.1111111111.1%
jalview.ws.rest.params.AnnotationFile   jalview.ws.rest.params.AnnotationFile 0.10256410410.3%
org.json.simple.parser.Yytoken   org.json.simple.parser.Yytoken 0.096774199.7%
jalview.util.ColorUtils   jalview.util.ColorUtils 0.096774199.7%
jalview.workers.AlignCalcWorker   jalview.workers.AlignCalcWorker 0.09523819.5%
jalview.util.JSONUtils   jalview.util.JSONUtils 0.090909099.1%
jalview.ws.dbsources.Xfam   jalview.ws.dbsources.Xfam 0.086956528.7%
jalview.ws.jws2.Jws2Client   jalview.ws.jws2.Jws2Client 0.0843373468.4%
jalview.ext.ensembl.EnsemblSequenceFetcher   jalview.ext.ensembl.EnsemblSequenceFetcher 0.0833333368.3%
jalview.datamodel.features.SequenceFeatures   jalview.datamodel.features.SequenceFeatures 0.082802558.3%
jalview.datamodel.AlignmentAnnotation   jalview.datamodel.AlignmentAnnotation 0.082397018.2%
jalview.schemes.RNAHelicesColour   jalview.schemes.RNAHelicesColour 0.082191788.2%
jalview.analysis.AlignmentUtils   jalview.analysis.AlignmentUtils 0.080801118.1%
jalview.urls.UrlProvider   jalview.urls.UrlProvider 0.079207927.9%
jalview.datamodel.ContactMapHolder   jalview.datamodel.ContactMapHolder 0.076923087.7%
jalview.schemes.ColourSchemes   jalview.schemes.ColourSchemes 0.070175447%
jalview.analysis.CrossRef   jalview.analysis.CrossRef 0.067622956.8%
jalview.gui.IdPanel   jalview.gui.IdPanel 0.067264576.7%
jalview.schemes.PIDColourScheme   jalview.schemes.PIDColourScheme 0.066666676.7%
jalview.util.LaunchUtils   jalview.util.LaunchUtils 0.0661764746.6%
jalview.gui.ViewSelectionMenu   jalview.gui.ViewSelectionMenu 0.059405945.9%
jalview.ws.seqfetcher.ASequenceFetcher   jalview.ws.seqfetcher.ASequenceFetcher 0.0577777775.8%
jalview.urls.CustomUrlProvider   jalview.urls.CustomUrlProvider 0.0569620245.7%
jalview.datamodel.ColumnSelection.IntList   jalview.datamodel.ColumnSelection.IntList 0.0560747655.6%
jalview.ws.seqfetcher.DbSourceProxyImpl   jalview.ws.seqfetcher.DbSourceProxyImpl 0.0540540555.4%
jalview.datamodel.HiddenSequences   jalview.datamodel.HiddenSequences 0.04566214.6%
jalview.util.DBRefUtils   jalview.util.DBRefUtils 0.045317224.5%
jalview.gui.WsParamSetManager   jalview.gui.WsParamSetManager 0.0429447854.3%
jalview.ws.dbsources.Pdb   jalview.ws.dbsources.Pdb 0.042553194.3%
org.json.simple.JSONObject   org.json.simple.JSONObject 0.037735853.8%
jalview.urls.IdentifiersUrlProvider   jalview.urls.IdentifiersUrlProvider 0.0366972463.7%
jalview.util.UrlLink   jalview.util.UrlLink 0.034090913.4%
jalview.ws.jws1.JPredClient   jalview.ws.jws1.JPredClient 0.0310559013.1%
jalview.util.Format   jalview.util.Format 0.0227743282.3%
jalview.datamodel.HiddenColumns   jalview.datamodel.HiddenColumns 0.0188679251.9%
jalview.schemes.ClustalxColourScheme   jalview.schemes.ClustalxColourScheme 0.0169491531.7%
jalview.datamodel.HiddenColumnsCursor   jalview.datamodel.HiddenColumnsCursor 0.0156251.6%
jalview.ws.dbsources.Uniprot   jalview.ws.dbsources.Uniprot 0.0155642021.6%
jalview.controller.AlignViewController   jalview.controller.AlignViewController 0.0135593221.4%
jalview.util.MappingUtils   jalview.util.MappingUtils 0.0129310351.3%
jalview.datamodel.SearchResults   jalview.datamodel.SearchResults 0.0128205131.3%
jalview.analysis.AlignSeq   jalview.analysis.AlignSeq 0.0128205131.3%
jalview.gui.SeqPanel   jalview.gui.SeqPanel 0.0125082291.3%
jalview.io.SequenceAnnotationReport   jalview.io.SequenceAnnotationReport 0.0122699381.2%
jalview.datamodel.ColumnSelection   jalview.datamodel.ColumnSelection 0.0103092781%
jalview.gui.JvOptionPane   jalview.gui.JvOptionPane 0.0091383810.9%
jalview.gui.SequenceFetcher   jalview.gui.SequenceFetcher 0.0089285720.9%
jalview.ext.ensembl.EnsemblGene   jalview.ext.ensembl.EnsemblGene 0.0081632650.8%
org.json.simple.JSONArray   org.json.simple.JSONArray 0.0080645160.8%
jalview.gui.QuitHandler   jalview.gui.QuitHandler 0.0077519380.8%
jalview.renderer.seqfeatures.FeatureRenderer   jalview.renderer.seqfeatures.FeatureRenderer 0.007547170.8%
jalview.schemes.ResidueProperties   jalview.schemes.ResidueProperties 0.00262605050.3%