Test testStoreAndRecoverReferenceSeqSettings

Test	Status	Start time	Time (seconds)	Message
testStoreAndRecoverReferenceSeqSettings	1PASS	4 Dec 16:16:52	24.857

Target Class	Coverage contributed by testStoreAndRecoverReferenceSeqSettings
com.stevesoft.pat.patInf   com.stevesoft.pat.patInf	1.0100%
jalview.io.DataSourceType   jalview.io.DataSourceType	1.0100%
jalview.viewmodel.ViewportProperties   jalview.viewmodel.ViewportProperties	1.0100%
jalview.xml.binding.jalview.AnnotationElement   jalview.xml.binding.jalview.AnnotationElement	1.0100%
jalview.xml.binding.jalview.Property   jalview.xml.binding.jalview.Property	1.0100%
jalview.xml.binding.jalview.SequenceType   jalview.xml.binding.jalview.SequenceType	1.0100%
jalview.xml.binding.jalview.JalviewModel.FeatureSettings   jalview.xml.binding.jalview.JalviewModel.FeatureSettings	1.0100%
jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group   jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group	1.0100%
jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids   jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids	1.0100%
jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns   jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns	1.0100%
jalview.xml.binding.jalview.JalviewModel.Viewport.Overview   jalview.xml.binding.jalview.JalviewModel.Viewport.Overview	1.0100%
jalview.xml.binding.jalview.Pdbentry   jalview.xml.binding.jalview.Pdbentry	1.0100%
jalview.xml.binding.jalview.Pdbentry.Property   jalview.xml.binding.jalview.Pdbentry.Property	1.0100%
jalview.renderer.ScaleRenderer   jalview.renderer.ScaleRenderer	1.0100%
jalview.renderer.ScaleRenderer.ScaleMark   jalview.renderer.ScaleRenderer.ScaleMark	1.0100%
jalview.ws.params.ParamDatastoreI   jalview.ws.params.ParamDatastoreI	1.0100%
jalview.project.Jalview2XML.JvAnnotRow   jalview.project.Jalview2XML.JvAnnotRow	1.0100%
jalview.structures.models.SequenceStructureBindingModel   jalview.structures.models.SequenceStructureBindingModel	1.0100%
jalview.datamodel.VisibleContigsIterator   jalview.datamodel.VisibleContigsIterator	1.0100%
jalview.datamodel.HiddenCursorPosition   jalview.datamodel.HiddenCursorPosition	1.0100%
jalview.datamodel.SecondaryStructureCount.SymbolCounts   jalview.datamodel.SecondaryStructureCount.SymbolCounts	1.0100%
jalview.datamodel.ResidueCount.SymbolCounts   jalview.datamodel.ResidueCount.SymbolCounts	1.0100%
jalview.schemes.ZappoColourScheme   jalview.schemes.ZappoColourScheme	1.0100%
jalview.gui.ProgressPanel   jalview.gui.ProgressPanel	0.975609897.6%
jalview.xml.binding.jalview.Feature   jalview.xml.binding.jalview.Feature	0.941176594.1%
jalview.jbgui.GAlignmentPanel   jalview.jbgui.GAlignmentPanel	0.9494%
jalview.xml.binding.jalview.JalviewModel.JSeq   jalview.xml.binding.jalview.JalviewModel.JSeq	0.923076992.3%
jalview.datamodel.HiddenColumnsCursor   jalview.datamodel.HiddenColumnsCursor	0.92187592.2%
jalview.xml.binding.jalview.SequenceSet   jalview.xml.binding.jalview.SequenceSet	0.894736889.5%
jalview.renderer.OverviewResColourFinder   jalview.renderer.OverviewResColourFinder	0.891891989.2%
jalview.analysis.Conservation   jalview.analysis.Conservation	0.888888988.9%
jalview.xml.binding.jalview.JalviewModel.Viewport   jalview.xml.binding.jalview.JalviewModel.Viewport	0.8709677587.1%
jalview.datamodel.Profiles   jalview.datamodel.Profiles	0.866666786.7%
jalview.viewmodel.styles.ViewStyle   jalview.viewmodel.styles.ViewStyle	0.858695685.9%
jalview.util.QuickSort.IntComparator   jalview.util.QuickSort.IntComparator	0.8571428785.7%
com.stevesoft.pat.OrMark   com.stevesoft.pat.OrMark	0.8585%
com.stevesoft.pat.Rthings   com.stevesoft.pat.Rthings	0.8461538684.6%
mc_view.Residue   mc_view.Residue	0.8461538684.6%
jalview.viewmodel.seqfeatures.FeatureRendererSettings   jalview.viewmodel.seqfeatures.FeatureRendererSettings	0.8444444584.4%
jalview.xml.binding.jalview.Annotation   jalview.xml.binding.jalview.Annotation	0.8421052784.2%
jalview.workers.ConsensusThread   jalview.workers.ConsensusThread	0.837583.7%
jalview.xml.binding.jalview.Feature.OtherData   jalview.xml.binding.jalview.Feature.OtherData	0.833333383.3%
jalview.datamodel.VisibleRowsCollection   jalview.datamodel.VisibleRowsCollection	0.833333383.3%
jalview.xml.binding.jalview.JalviewModel   jalview.xml.binding.jalview.JalviewModel	0.826923182.7%
jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState   jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState	0.821428682.1%
jalview.xml.binding.jalview.Sequence.DBRef   jalview.xml.binding.jalview.Sequence.DBRef	0.812581.2%
jalview.datamodel.RangeIterator   jalview.datamodel.RangeIterator	0.810810881.1%
jalview.xml.binding.jalview.JalviewModel.JGroup   jalview.xml.binding.jalview.JalviewModel.JGroup	0.804347880.4%
com.stevesoft.pat.SubMark   com.stevesoft.pat.SubMark	0.880%
jalview.datamodel.VisibleColsCollection   jalview.datamodel.VisibleColsCollection	0.880%
jalview.datamodel.StructureViewerModel   jalview.datamodel.StructureViewerModel	0.880%
jalview.datamodel.VisibleRowsIterator   jalview.datamodel.VisibleRowsIterator	0.880%
jalview.gui.OverviewCanvas   jalview.gui.OverviewCanvas	0.784482878.4%
jalview.workers.SecondaryStructureConsensusThread   jalview.workers.SecondaryStructureConsensusThread	0.783018978.3%
jalview.util.LinkedIdentityHashSet   jalview.util.LinkedIdentityHashSet	0.7727272577.3%
jalview.gui.AppJmol.RenderPanel   jalview.gui.AppJmol.RenderPanel	0.756756875.7%
jalview.workers.AlignCalcManager2.WorkerManager   jalview.workers.AlignCalcManager2.WorkerManager	0.7575%
com.stevesoft.pat.wrap.StringWrap   com.stevesoft.pat.wrap.StringWrap	0.7575%
jalview.schemes.ResidueColourScheme   jalview.schemes.ResidueColourScheme	0.738095273.8%
jalview.datamodel.Profile   jalview.datamodel.Profile	0.7377049373.8%
jalview.viewmodel.OverviewDimensions   jalview.viewmodel.OverviewDimensions	0.7323943473.2%
jalview.renderer.seqfeatures.FeatureColourFinder   jalview.renderer.seqfeatures.FeatureColourFinder	0.725490272.5%
jalview.datamodel.RangeElementsIterator   jalview.datamodel.RangeElementsIterator	0.7187571.9%
jalview.workers.AlignCalcManager2.SimpleWorkerManager   jalview.workers.AlignCalcManager2.SimpleWorkerManager	0.7142857371.4%
jalview.gui.FeatureRenderer   jalview.gui.FeatureRenderer	0.7142857371.4%
jalview.io.PDBFeatureSettings   jalview.io.PDBFeatureSettings	0.7142857371.4%
jalview.xml.binding.jalview.Sequence   jalview.xml.binding.jalview.Sequence	0.7142857371.4%
jalview.util.LinkedIdentityHashSet.IdentityWrapper   jalview.util.LinkedIdentityHashSet.IdentityWrapper	0.7142857371.4%
jalview.jbgui.GStructureViewer   jalview.jbgui.GStructureViewer	0.7065217570.7%
com.stevesoft.pat.Bracket   com.stevesoft.pat.Bracket	0.770%
jalview.datamodel.StartRegionIterator   jalview.datamodel.StartRegionIterator	0.694444469.4%
com.stevesoft.pat.oneChar   com.stevesoft.pat.oneChar	0.685714368.6%
jalview.renderer.OverviewRenderer   jalview.renderer.OverviewRenderer	0.680722968.1%
jalview.workers.ConservationThread   jalview.workers.ConservationThread	0.666666766.7%
jalview.util.CaseInsensitiveString   jalview.util.CaseInsensitiveString	0.6521739465.2%
jalview.gui.IdCanvas   jalview.gui.IdCanvas	0.6478405664.8%
jalview.ws.api.UIinfo   jalview.ws.api.UIinfo	0.6470588464.7%
jalview.ws.SequenceFetcher   jalview.ws.SequenceFetcher	0.6470588464.7%
com.stevesoft.pat.Range   com.stevesoft.pat.Range	0.636363663.6%
jalview.datamodel.StructureViewerModel.StructureData   jalview.datamodel.StructureViewerModel.StructureData	0.62562.5%
jalview.schemes.FeatureSettingsAdapter   jalview.schemes.FeatureSettingsAdapter	0.62562.5%
com.stevesoft.pat.StrPos   com.stevesoft.pat.StrPos	0.6162790761.6%
jalview.xml.binding.jalview.JalviewModel.Tree   jalview.xml.binding.jalview.JalviewModel.Tree	0.6153846461.5%
jalview.analysis.SequenceIdMatcher.SeqIdName   jalview.analysis.SequenceIdMatcher.SeqIdName	0.605263260.5%
jalview.renderer.ResidueColourFinder   jalview.renderer.ResidueColourFinder	0.595238159.5%
jalview.util.ParseHtmlBodyAndLinks   jalview.util.ParseHtmlBodyAndLinks	0.594202959.4%
jalview.jbgui.GTreePanel   jalview.jbgui.GTreePanel	0.5789473757.9%
jalview.jbgui.GAlignFrame   jalview.jbgui.GAlignFrame	0.5741666657.4%
jalview.ws.jws2.PreferredServiceRegistry   jalview.ws.jws2.PreferredServiceRegistry	0.571428657.1%
jalview.gui.OverviewPanel   jalview.gui.OverviewPanel	0.558823555.9%
jalview.gui.TreePanel.TreeLoader   jalview.gui.TreePanel.TreeLoader	0.553191555.3%
jalview.ws2.gui.WebServicesMenuManager   jalview.ws2.gui.WebServicesMenuManager	0.5428571754.3%
mc_view.PDBChain   mc_view.PDBChain	0.5396825754%
jalview.gui.PaintRefresher   jalview.gui.PaintRefresher	0.539473753.9%
jalview.io.NewickFile   jalview.io.NewickFile	0.538934453.9%
jalview.util.MessageManager   jalview.util.MessageManager	0.5238095552.4%
com.stevesoft.pat.Boundary   com.stevesoft.pat.Boundary	0.518518551.9%
jalview.datamodel.BinaryNode   jalview.datamodel.BinaryNode	0.515151551.5%
jalview.ext.jmol.JmolParser   jalview.ext.jmol.JmolParser	0.514211951.4%
com.stevesoft.pat.Pattern   com.stevesoft.pat.Pattern	0.506944450.7%
jalview.gui.JalviewChangeSupport   jalview.gui.JalviewChangeSupport	0.550%
com.stevesoft.pat.FastChar   com.stevesoft.pat.FastChar	0.550%
com.stevesoft.pat.FastMulti   com.stevesoft.pat.FastMulti	0.550%
jalview.xml.binding.jalview.VAMSAS   jalview.xml.binding.jalview.VAMSAS	0.550%
mc_view.Bond   mc_view.Bond	0.550%
jalview.schemes.TaylorColourScheme   jalview.schemes.TaylorColourScheme	0.550%
jalview.schemes.FlowerColourScheme   jalview.schemes.FlowerColourScheme	0.550%
jalview.schemes.NucleotideAmbiguityColourScheme   jalview.schemes.NucleotideAmbiguityColourScheme	0.550%
jalview.schemes.PurinePyrimidineColourScheme   jalview.schemes.PurinePyrimidineColourScheme	0.550%
jalview.schemes.NucleotideColourScheme   jalview.schemes.NucleotideColourScheme	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.analysis.SequenceIdMatcher   jalview.analysis.SequenceIdMatcher	0.550%
jalview.project.Jalview2XML   jalview.project.Jalview2XML	0.4986601849.9%
jalview.gui.SequenceRenderer   jalview.gui.SequenceRenderer	0.4855769348.6%
jalview.renderer.AnnotationRenderer   jalview.renderer.AnnotationRenderer	0.4697102647%
jalview.ws.jws2.MsaWSClient   jalview.ws.jws2.MsaWSClient	0.4671052746.7%
jalview.gui.ColourMenuHelper   jalview.gui.ColourMenuHelper	0.466101746.6%
jalview.datamodel.features.SequenceFeatures   jalview.datamodel.features.SequenceFeatures	0.4649681446.5%
jalview.renderer.seqfeatures.FeatureRenderer   jalview.renderer.seqfeatures.FeatureRenderer	0.4603773746%
jalview.ws2.gui.WebServicesMenuManager.InteractiveServiceEntryGroup   jalview.ws2.gui.WebServicesMenuManager.InteractiveServiceEntryGroup	0.4579439245.8%
com.stevesoft.pat.parsePerl   com.stevesoft.pat.parsePerl	0.448979644.9%
jalview.datamodel.HiddenSequences   jalview.datamodel.HiddenSequences	0.4474885844.7%
jalview.gui.AlignViewport   jalview.gui.AlignViewport	0.445727544.6%
jalview.datamodel.PDBEntry   jalview.datamodel.PDBEntry	0.4433333344.3%
jalview.util.Format   jalview.util.Format	0.4430641844.3%
jalview.viewmodel.AlignmentViewport   jalview.viewmodel.AlignmentViewport	0.4426229644.3%
jalview.workers.AlignCalcManager2   jalview.workers.AlignCalcManager2	0.4383561643.8%
jalview.gui.SeqCanvas   jalview.gui.SeqCanvas	0.438259143.8%
jalview.viewmodel.seqfeatures.FeaturesDisplayed   jalview.viewmodel.seqfeatures.FeaturesDisplayed	0.437543.8%
jalview.analysis.AlignSeq   jalview.analysis.AlignSeq	0.4336734743.4%
jalview.datamodel.ResidueCount   jalview.datamodel.ResidueCount	0.4320557443.2%
jalview.analysis.AAFrequency   jalview.analysis.AAFrequency	0.4306688343.1%
jalview.ext.jmol.JalviewJmolBinding   jalview.ext.jmol.JalviewJmolBinding	0.427125542.7%
jalview.io.StructureFile   jalview.io.StructureFile	0.4186046441.9%
jalview.gui.AlignmentPanel   jalview.gui.AlignmentPanel	0.4149947241.5%
jalview.analysis.TreeModel   jalview.analysis.TreeModel	0.410852741.1%
jalview.viewmodel.ViewportRanges   jalview.viewmodel.ViewportRanges	0.41059641.1%
com.stevesoft.pat.Or   com.stevesoft.pat.Or	0.4102564241%
jalview.util.Comparison   jalview.util.Comparison	0.4094488340.9%
jalview.ws.dbsources.EmblSource   jalview.ws.dbsources.EmblSource	0.440%
jalview.ws2.actions.BaseAction   jalview.ws2.actions.BaseAction	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%
jalview.datamodel.Sequence   jalview.datamodel.Sequence	0.3924686339.2%
jalview.log.JalviewAppender   jalview.log.JalviewAppender	0.388888938.9%
jalview.datamodel.Range   jalview.datamodel.Range	0.388888938.9%
jalview.datamodel.SequenceFeature   jalview.datamodel.SequenceFeature	0.3812949738.1%
jalview.renderer.ResidueShader   jalview.renderer.ResidueShader	0.3780487837.8%
jalview.structure.StructureSelectionManager   jalview.structure.StructureSelectionManager	0.3765903437.7%
jalview.bin.ApplicationSingletonProvider   jalview.bin.ApplicationSingletonProvider	0.37537.5%
jalview.datamodel.features.FeatureStore   jalview.datamodel.features.FeatureStore	0.3655589236.6%
jalview.datamodel.AlignmentAnnotation   jalview.datamodel.AlignmentAnnotation	0.358733935.9%
jalview.util.QuickSort   jalview.util.QuickSort	0.352750835.3%
jalview.ws.jws2.Jws2Client   jalview.ws.jws2.Jws2Client	0.3333333433.3%
jalview.schemes.ColourSchemeProperty   jalview.schemes.ColourSchemeProperty	0.3333333433.3%
jalview.gui.JvSwingUtils   jalview.gui.JvSwingUtils	0.3310344833.1%
com.stevesoft.pat.Regex   com.stevesoft.pat.Regex	0.330909133.1%
jalview.datamodel.features.FeatureAttributes.AttributeData   jalview.datamodel.features.FeatureAttributes.AttributeData	0.327272732.7%
jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting   jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting	0.3225806432.3%
jalview.ws.rest.RestServiceDescription   jalview.ws.rest.RestServiceDescription	0.3221649532.2%
jalview.datamodel.PDBEntry.Type   jalview.datamodel.PDBEntry.Type	0.312531.2%
jalview.viewmodel.seqfeatures.FeatureRendererModel   jalview.viewmodel.seqfeatures.FeatureRendererModel	0.3098591631%
jalview.structure.StructureImportSettings   jalview.structure.StructureImportSettings	0.3076923230.8%
jalview.gui.IdwidthAdjuster   jalview.gui.IdwidthAdjuster	0.302631630.3%
jalview.io.FileLoader   jalview.io.FileLoader	0.3018292830.2%
jalview.ws2.api.WebService   jalview.ws2.api.WebService	0.330%
jalview.gui.StructureViewerBase   jalview.gui.StructureViewerBase	0.294372329.4%
jalview.ws.dbsources.EmblCdsSource   jalview.ws.dbsources.EmblCdsSource	0.285714328.6%
jalview.datamodel.Annotation   jalview.datamodel.Annotation	0.285714328.6%
jalview.schemes.JalviewColourScheme   jalview.schemes.JalviewColourScheme	0.285714328.6%
jalview.datamodel.annotations.AnnotationRowBuilder   jalview.datamodel.annotations.AnnotationRowBuilder	0.282051328.2%
mc_view.Atom   mc_view.Atom	0.282051328.2%
jalview.datamodel.DBRefEntry   jalview.datamodel.DBRefEntry	0.2808219228.1%
jalview.gui.ScalePanel   jalview.gui.ScalePanel	0.2745098227.5%
jalview.ws.jws2.SequenceAnnotationWSClient   jalview.ws.jws2.SequenceAnnotationWSClient	0.2654867226.5%
jalview.schemes.IdColourScheme   jalview.schemes.IdColourScheme	0.2608695626.1%
com.stevesoft.pat.NullPattern   com.stevesoft.pat.NullPattern	0.2525%
com.stevesoft.pat.StringRule   com.stevesoft.pat.StringRule	0.2525%
jalview.ws.api.ServiceWithParameters   jalview.ws.api.ServiceWithParameters	0.2525%
jalview.ws.jws2.JabaPreset   jalview.ws.jws2.JabaPreset	0.2525%
jalview.renderer.AnnotationRendererFactory   jalview.renderer.AnnotationRendererFactory	0.2525%
jalview.ws.jws2.Jws2ClientFactory   jalview.ws.jws2.Jws2ClientFactory	0.24824.8%
jalview.io.FileParse   jalview.io.FileParse	0.243767324.4%
jalview.ws.rest.params.Alignment   jalview.ws.rest.params.Alignment	0.2435897424.4%
jalview.io.FileFormats   jalview.io.FileFormats	0.2424%
jalview.ws.uimodel.AlignAnalysisUIText   jalview.ws.uimodel.AlignAnalysisUIText	0.2424%
com.stevesoft.pat.RegRes   com.stevesoft.pat.RegRes	0.2391304423.9%
jalview.structures.models.AAStructureBindingModel   jalview.structures.models.AAStructureBindingModel	0.2357723623.6%
jalview.ws.WSClient   jalview.ws.WSClient	0.2352941223.5%
jalview.datamodel.SequenceGroup   jalview.datamodel.SequenceGroup	0.2337349423.4%
jalview.gui.AppJmolBinding   jalview.gui.AppJmolBinding	0.2336448623.4%
jalview.datamodel.SequenceCursor   jalview.datamodel.SequenceCursor	0.2333333323.3%
jalview.datamodel.SequenceNode   jalview.datamodel.SequenceNode	0.2307692323.1%
jalview.datamodel.Alignment   jalview.datamodel.Alignment	0.2301516523%
jalview.gui.AppJmol   jalview.gui.AppJmol	0.226765822.7%
jalview.structure.StructureCommand   jalview.structure.StructureCommand	0.2266666722.7%
jalview.structure.StructureMapping   jalview.structure.StructureMapping	0.2176165721.8%
jalview.ws.rest.InputType   jalview.ws.rest.InputType	0.2056074720.6%
jalview.viewmodel.OverviewDimensionsHideHidden   jalview.viewmodel.OverviewDimensionsHideHidden	0.2054794620.5%
jalview.datamodel.features.FeatureAttributes   jalview.datamodel.features.FeatureAttributes	0.2042253520.4%
jalview.datamodel.HiddenColumns   jalview.datamodel.HiddenColumns	0.202830220.3%
jalview.gui.AnnotationLabels   jalview.gui.AnnotationLabels	0.200787420.1%
com.stevesoft.pat.patInt   com.stevesoft.pat.patInt	0.220%
jalview.gui.TreeCanvas   jalview.gui.TreeCanvas	0.1972656219.7%
jalview.io.AlignFile   jalview.io.AlignFile	0.1959459519.6%
jalview.datamodel.SecondaryStructureCount   jalview.datamodel.SecondaryStructureCount	0.1914062519.1%
jalview.ws.sifts.SiftsSettings   jalview.ws.sifts.SiftsSettings	0.190476219%
jalview.util.StringUtils   jalview.util.StringUtils	0.1892655318.9%
jalview.analysis.scoremodels.ScoreModels   jalview.analysis.scoremodels.ScoreModels	0.187518.8%
jalview.log.JLogger   jalview.log.JLogger	0.1868131918.7%
jalview.bin.Console   jalview.bin.Console	0.1839622718.4%
jalview.schemes.TCoffeeColourScheme   jalview.schemes.TCoffeeColourScheme	0.1803278618%
jalview.schemes.ColourSchemes   jalview.schemes.ColourSchemes	0.1794871817.9%
jalview.schemes.Blosum62ColourScheme   jalview.schemes.Blosum62ColourScheme	0.176470617.6%
jalview.gui.TreePanel   jalview.gui.TreePanel	0.1750972717.5%
jalview.gui.AnnotationPanel   jalview.gui.AnnotationPanel	0.1644260616.4%
jalview.io.IdentifyFile   jalview.io.IdentifyFile	0.1642651316.4%
jalview.ws.jws1.WS1Client   jalview.ws.jws1.WS1Client	0.1616%
jalview.analysis.AnnotationSorter   jalview.analysis.AnnotationSorter	0.1562515.6%
jalview.gui.Desktop.MyDesktopManager   jalview.gui.Desktop.MyDesktopManager	0.1555555615.6%
jalview.gui.AlignFrame   jalview.gui.AlignFrame	0.1493425214.9%
jalview.ws.rest.RestClient   jalview.ws.rest.RestClient	0.1466666614.7%
jalview.gui.Desktop.MyDesktopPane   jalview.gui.Desktop.MyDesktopPane	0.1428571514.3%
com.stevesoft.pat.Branch   com.stevesoft.pat.Branch	0.140939614.1%
jalview.gui.Desktop   jalview.gui.Desktop	0.1371237513.7%
jalview.workers.AlignCalcWorker   jalview.workers.AlignCalcWorker	0.1333333413.3%
jalview.schemes.HmmerGlobalBackground   jalview.schemes.HmmerGlobalBackground	0.1333333413.3%
jalview.schemes.PIDColourScheme   jalview.schemes.PIDColourScheme	0.1333333413.3%
jalview.ws.rest.params.SeqGroupIndexVector   jalview.ws.rest.params.SeqGroupIndexVector	0.12408759412.4%
jalview.analysis.CrossRef   jalview.analysis.CrossRef	0.12320328512.3%
jalview.util.MapList   jalview.util.MapList	0.121612.2%
jalview.util.ColorUtils   jalview.util.ColorUtils	0.116022111.6%
jalview.ws2.client.api.AbstractWebServiceDiscoverer   jalview.ws2.client.api.AbstractWebServiceDiscoverer	0.1132075511.3%
jalview.schemes.RNAHelicesColour   jalview.schemes.RNAHelicesColour	0.1095890411%
jalview.schemes.FeatureColour   jalview.schemes.FeatureColour	0.10736842510.7%
jalview.log.JLoggerLog4j   jalview.log.JLoggerLog4j	0.10679611610.7%
jalview.util.DBRefUtils   jalview.util.DBRefUtils	0.10416666410.4%
jalview.util.Platform   jalview.util.Platform	0.10396039510.4%
jalview.datamodel.Mapping   jalview.datamodel.Mapping	0.10389610410.4%
jalview.analysis.scoremodels.ScoreMatrix   jalview.analysis.scoremodels.ScoreMatrix	0.1028806610.3%
jalview.ws.rest.params.AnnotationFile   jalview.ws.rest.params.AnnotationFile	0.10256410410.3%
jalview.ws2.client.jpred4.JPred4WSDiscoverer   jalview.ws2.client.jpred4.JPred4WSDiscoverer	0.09523819.5%
com.stevesoft.pat.Replacer   com.stevesoft.pat.Replacer	0.091891899.2%
com.stevesoft.pat.ReplaceRule   com.stevesoft.pat.ReplaceRule	0.08771938.8%
jalview.ws.dbsources.Xfam   jalview.ws.dbsources.Xfam	0.086956528.7%
jalview.ws.jws1.Discoverer   jalview.ws.jws1.Discoverer	0.0848484868.5%
jalview.ext.ensembl.EnsemblSequenceFetcher   jalview.ext.ensembl.EnsemblSequenceFetcher	0.0833333368.3%
jalview.ws.dbsources.Pdb   jalview.ws.dbsources.Pdb	0.081632658.2%
jalview.ws2.client.ebi.JobDispatcherWSDiscoverer   jalview.ws2.client.ebi.JobDispatcherWSDiscoverer	0.081632658.2%
jalview.ws.seqfetcher.DbSourceProxyImpl   jalview.ws.seqfetcher.DbSourceProxyImpl	0.081081088.1%
jalview.ws.jws2.jabaws2.Jws2Instance   jalview.ws.jws2.jabaws2.Jws2Instance	0.076923087.7%
jalview.schemes.HmmerLocalBackground   jalview.schemes.HmmerLocalBackground	0.076923087.7%
jalview.schemes.HmmerColourScheme   jalview.schemes.HmmerColourScheme	0.076923087.7%
jalview.analysis.AlignmentAnnotationUtils   jalview.analysis.AlignmentAnnotationUtils	0.0762711847.6%
jalview.datamodel.ColumnSelection.IntList   jalview.datamodel.ColumnSelection.IntList	0.074766357.5%
jalview.gui.ProgressBar   jalview.gui.ProgressBar	0.068965526.9%
jalview.gui.IdPanel   jalview.gui.IdPanel	0.067264576.7%
com.stevesoft.pat.RegOpt   com.stevesoft.pat.RegOpt	0.06474826.5%
jalview.schemes.HMMMatchScoreColourScheme   jalview.schemes.HMMMatchScoreColourScheme	0.063829796.4%
jalview.bin.Cache   jalview.bin.Cache	0.0623306226.2%
ext.vamsas.ServiceHandle   ext.vamsas.ServiceHandle	0.061224496.1%
jalview.gui.ViewSelectionMenu   jalview.gui.ViewSelectionMenu	0.059405945.9%
jalview.ws.seqfetcher.ASequenceFetcher   jalview.ws.seqfetcher.ASequenceFetcher	0.0577777775.8%
jalview.datamodel.ContactMapHolder   jalview.datamodel.ContactMapHolder	0.0576923085.8%
jalview.workers.InformationThread   jalview.workers.InformationThread	0.0555555565.6%
jalview.io.FileFormat   jalview.io.FileFormat	0.0551724145.5%
jalview.ws2.params.SimpleParamDatastore   jalview.ws2.params.SimpleParamDatastore	0.055%
jalview.analysis.GeneticCodes   jalview.analysis.GeneticCodes	0.0496894425%
jalview.io.AppletFormatAdapter   jalview.io.AppletFormatAdapter	0.043478264.3%
jalview.ext.jmol.JmolCommands   jalview.ext.jmol.JmolCommands	0.043307094.3%
jalview.ws.jws2.Jws2Discoverer   jalview.ws.jws2.Jws2Discoverer	0.0416666684.2%
jalview.ws.jws2.JabaParamStore   jalview.ws.jws2.JabaParamStore	0.0416666684.2%
jalview.xml.binding.jalview.ObjectFactory   jalview.xml.binding.jalview.ObjectFactory	0.0413223134.1%
jalview.gui.SliderPanel   jalview.gui.SliderPanel	0.0348837233.5%
jalview.ws.jws1.JPredClient   jalview.ws.jws1.JPredClient	0.0310559013.1%
jalview.ws2.client.slivka.SlivkaWSDiscoverer   jalview.ws2.client.slivka.SlivkaWSDiscoverer	0.0268456382.7%
jalview.util.FileUtils   jalview.util.FileUtils	0.0267857152.7%
jalview.schemes.ClustalxColourScheme   jalview.schemes.ClustalxColourScheme	0.0254237282.5%
jalview.structure.StructureCommandsBase   jalview.structure.StructureCommandsBase	0.0243902432.4%
jalview.controller.AlignViewController   jalview.controller.AlignViewController	0.0237288142.4%
jalview.gui.StructureViewer   jalview.gui.StructureViewer	0.0232558142.3%
jalview.datamodel.ColumnSelection   jalview.datamodel.ColumnSelection	0.017182131.7%
jalview.analysis.AlignmentUtils   jalview.analysis.AlignmentUtils	0.0170268511.7%
jalview.bin.Jalview   jalview.bin.Jalview	0.0153597421.5%
jalview.ws.dbsources.Uniprot   jalview.ws.dbsources.Uniprot	0.015325671.5%
mc_view.PDBfile   mc_view.PDBfile	0.0150375941.5%
jalview.hmmer.HmmerCommand   jalview.hmmer.HmmerCommand	0.0141509441.4%
jalview.gui.SeqPanel   jalview.gui.SeqPanel	0.0129954521.3%
jalview.datamodel.SearchResults   jalview.datamodel.SearchResults	0.0128205131.3%
jalview.io.SequenceAnnotationReport   jalview.io.SequenceAnnotationReport	0.0112359551.1%
jalview.util.HttpUtils   jalview.util.HttpUtils	0.010101011%
jalview.bin.argparser.BootstrapArgs   jalview.bin.argparser.BootstrapArgs	0.0082644620.8%
jalview.ext.ensembl.EnsemblGene   jalview.ext.ensembl.EnsemblGene	0.0081632650.8%
jalview.gui.QuitHandler   jalview.gui.QuitHandler	0.00722021660.7%
com.stevesoft.pat.CaseMgr   com.stevesoft.pat.CaseMgr	0.00278551530.3%
jalview.schemes.ResidueProperties   jalview.schemes.ResidueProperties	0.00103039670.1%