Clover icon

Coverage Report

  1. Project Clover database Thu Nov 7 2024 10:11:34 GMT
  2. Package jalview.project
  3. Class Jalview2xmlTests

Test testAutoShowOverviewForLegacyProjects

Test
testAutoShowOverviewForLegacyProjects 1PASS 7 Nov 10:14:17 0.179
 
testAutoShowOverviewForLegacyProjects
com.stevesoft.pat.patInf   com.stevesoft.pat.patInf 1.0100%
jalview.io.DataSourceType   jalview.io.DataSourceType 1.0100%
jalview.renderer.ScaleRenderer.ScaleMark   jalview.renderer.ScaleRenderer.ScaleMark 1.0100%
jalview.ws.WSClient   jalview.ws.WSClient 1.0100%
jalview.project.Jalview2XML.JvAnnotRow   jalview.project.Jalview2XML.JvAnnotRow 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.jbgui.GAlignmentPanel   jalview.jbgui.GAlignmentPanel 0.9494%
jalview.analysis.Conservation   jalview.analysis.Conservation 0.871921287.2%
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%
jalview.datamodel.VisibleRowsCollection   jalview.datamodel.VisibleRowsCollection 0.833333383.3%
jalview.datamodel.Profiles   jalview.datamodel.Profiles 0.833333383.3%
jalview.schemes.Blosum62ColourScheme   jalview.schemes.Blosum62ColourScheme 0.823529482.4%
com.stevesoft.pat.SubMark   com.stevesoft.pat.SubMark 0.880%
jalview.datamodel.VisibleColsCollection   jalview.datamodel.VisibleColsCollection 0.880%
jalview.schemes.ResidueColourScheme   jalview.schemes.ResidueColourScheme 0.7857142778.6%
jalview.renderer.OverviewResColourFinder   jalview.renderer.OverviewResColourFinder 0.783783878.4%
jalview.viewmodel.OverviewDimensions   jalview.viewmodel.OverviewDimensions 0.7384615573.8%
jalview.datamodel.Profile   jalview.datamodel.Profile 0.7377049373.8%
jalview.xml.binding.jalview.SequenceSet   jalview.xml.binding.jalview.SequenceSet 0.736842173.7%
jalview.workers.SecondaryStructureConsensusThread   jalview.workers.SecondaryStructureConsensusThread 0.7333333573.3%
jalview.datamodel.RangeElementsIterator   jalview.datamodel.RangeElementsIterator 0.7187571.9%
jalview.gui.FeatureRenderer   jalview.gui.FeatureRenderer 0.7142857371.4%
com.stevesoft.pat.Bracket   com.stevesoft.pat.Bracket 0.770%
jalview.datamodel.VisibleRowsIterator   jalview.datamodel.VisibleRowsIterator 0.770%
jalview.workers.ConsensusThread   jalview.workers.ConsensusThread 0.696969769.7%
com.stevesoft.pat.oneChar   com.stevesoft.pat.oneChar 0.685714368.6%
jalview.ws.SequenceFetcher   jalview.ws.SequenceFetcher 0.678571467.9%
jalview.renderer.OverviewRenderer   jalview.renderer.OverviewRenderer 0.6746987767.5%
com.stevesoft.pat.Range   com.stevesoft.pat.Range 0.636363663.6%
com.stevesoft.pat.wrap.StringWrap   com.stevesoft.pat.wrap.StringWrap 0.62562.5%
com.stevesoft.pat.StrPos   com.stevesoft.pat.StrPos 0.6162790761.6%
jalview.xml.binding.jalview.JalviewModel   jalview.xml.binding.jalview.JalviewModel 0.6153846461.5%
jalview.analysis.SequenceIdMatcher.SeqIdName   jalview.analysis.SequenceIdMatcher.SeqIdName 0.605263260.5%
jalview.workers.AlignCalcManager   jalview.workers.AlignCalcManager 0.595238159.5%
jalview.renderer.ResidueColourFinder   jalview.renderer.ResidueColourFinder 0.595238159.5%
jalview.util.ParseHtmlBodyAndLinks   jalview.util.ParseHtmlBodyAndLinks 0.594202959.4%
jalview.gui.TreePanel.TreeLoader   jalview.gui.TreePanel.TreeLoader 0.589743659%
jalview.jbgui.GTreePanel   jalview.jbgui.GTreePanel 0.587301658.7%
jalview.xml.binding.jalview.JalviewModel.JSeq   jalview.xml.binding.jalview.JalviewModel.JSeq 0.583333358.3%
jalview.jbgui.GAlignFrame   jalview.jbgui.GAlignFrame 0.57354357.4%
jalview.workers.ConservationThread   jalview.workers.ConservationThread 0.568965556.9%
jalview.renderer.ScaleRenderer   jalview.renderer.ScaleRenderer 0.5656%
com.stevesoft.pat.Boundary   com.stevesoft.pat.Boundary 0.518518551.9%
jalview.datamodel.BinaryNode   jalview.datamodel.BinaryNode 0.5087719650.9%
jalview.gui.ColourMenuHelper   jalview.gui.ColourMenuHelper 0.550%
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.viewmodel.ViewportProperties   jalview.viewmodel.ViewportProperties 0.550%
jalview.xml.binding.jalview.AnnotationElement   jalview.xml.binding.jalview.AnnotationElement 0.550%
jalview.xml.binding.jalview.SequenceType   jalview.xml.binding.jalview.SequenceType 0.550%
jalview.xml.binding.jalview.Annotation   jalview.xml.binding.jalview.Annotation 0.550%
jalview.xml.binding.jalview.Sequence   jalview.xml.binding.jalview.Sequence 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%
com.stevesoft.pat.Pattern   com.stevesoft.pat.Pattern 0.4930555549.3%
jalview.gui.SequenceRenderer   jalview.gui.SequenceRenderer 0.4855769348.6%
jalview.xml.binding.jalview.JalviewModel.Viewport   jalview.xml.binding.jalview.JalviewModel.Viewport 0.4803921648%
jalview.analysis.AAFrequency   jalview.analysis.AAFrequency 0.4773662747.7%
jalview.xml.binding.jalview.JalviewModel.JGroup   jalview.xml.binding.jalview.JalviewModel.JGroup 0.476562547.7%
jalview.xml.binding.jalview.JalviewModel.Tree   jalview.xml.binding.jalview.JalviewModel.Tree 0.4761904847.6%
jalview.util.MessageManager   jalview.util.MessageManager 0.4761904847.6%
com.stevesoft.pat.parsePerl   com.stevesoft.pat.parsePerl 0.448979644.9%
jalview.ws.jws2.MsaWSClient   jalview.ws.jws2.MsaWSClient 0.4429530244.3%
jalview.gui.OverviewCanvas   jalview.gui.OverviewCanvas 0.4310344843.1%
jalview.datamodel.HiddenCursorPosition   jalview.datamodel.HiddenCursorPosition 0.4285714342.9%
jalview.util.ShortcutKeyMaskExWrapper11   jalview.util.ShortcutKeyMaskExWrapper11 0.4166666641.7%
jalview.analysis.SequenceIdMatcher   jalview.analysis.SequenceIdMatcher 0.412280741.2%
jalview.gui.IdCanvas   jalview.gui.IdCanvas 0.410526341.1%
com.stevesoft.pat.Or   com.stevesoft.pat.Or 0.4102564241%
jalview.ws.dbsources.EmblSource   jalview.ws.dbsources.EmblSource 0.440%
jalview.renderer.AnnotationRenderer   jalview.renderer.AnnotationRenderer 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.viewmodel.AlignmentViewport   jalview.viewmodel.AlignmentViewport 0.3907624839.1%
jalview.log.JalviewAppender   jalview.log.JalviewAppender 0.388888938.9%
jalview.gui.OverviewPanel   jalview.gui.OverviewPanel 0.388235338.8%
jalview.datamodel.ResidueCount   jalview.datamodel.ResidueCount 0.3745454537.5%
jalview.analysis.TreeModel   jalview.analysis.TreeModel 0.3740157537.4%
jalview.io.NewickFile   jalview.io.NewickFile 0.3672055336.7%
jalview.gui.AlignmentPanel   jalview.gui.AlignmentPanel 0.3639575836.4%
jalview.viewmodel.ViewportRanges   jalview.viewmodel.ViewportRanges 0.3531353235.3%
jalview.gui.AlignViewport   jalview.gui.AlignViewport 0.3515981735.2%
jalview.util.Comparison   jalview.util.Comparison 0.350393735%
jalview.renderer.ResidueShader   jalview.renderer.ResidueShader 0.3475609734.8%
jalview.util.QuickSort   jalview.util.QuickSort 0.346278334.6%
jalview.xml.binding.jalview.VAMSAS   jalview.xml.binding.jalview.VAMSAS 0.3333333433.3%
com.stevesoft.pat.Regex   com.stevesoft.pat.Regex 0.3245454432.5%
jalview.ws.rest.RestServiceDescription   jalview.ws.rest.RestServiceDescription 0.31531.5%
jalview.io.FileLoader   jalview.io.FileLoader 0.3143812731.4%
jalview.renderer.seqfeatures.FeatureColourFinder   jalview.renderer.seqfeatures.FeatureColourFinder 0.313725531.4%
jalview.gui.IdwidthAdjuster   jalview.gui.IdwidthAdjuster 0.302631630.3%
jalview.ws.jws2.SequenceAnnotationWSClient   jalview.ws.jws2.SequenceAnnotationWSClient 0.2903225729%
jalview.ws.dbsources.EmblCdsSource   jalview.ws.dbsources.EmblCdsSource 0.285714328.6%
jalview.schemes.JalviewColourScheme   jalview.schemes.JalviewColourScheme 0.285714328.6%
jalview.ws.jws2.JabaPreset   jalview.ws.jws2.JabaPreset 0.2727272827.3%
jalview.gui.JvSwingUtils   jalview.gui.JvSwingUtils 0.258503425.9%
jalview.gui.PaintRefresher   jalview.gui.PaintRefresher 0.253521125.4%
jalview.ws.jws2.jabaws2.Jws2Instance   jalview.ws.jws2.jabaws2.Jws2Instance 0.2528735725.3%
com.stevesoft.pat.NullPattern   com.stevesoft.pat.NullPattern 0.2525%
com.stevesoft.pat.StringRule   com.stevesoft.pat.StringRule 0.2525%
jalview.renderer.AnnotationRendererFactory   jalview.renderer.AnnotationRendererFactory 0.2525%
jalview.schemes.ColourSchemeProperty   jalview.schemes.ColourSchemeProperty 0.2525%
jalview.schemes.ColourSchemes   jalview.schemes.ColourSchemes 0.2456140424.6%
jalview.ws.uimodel.AlignAnalysisUIText   jalview.ws.uimodel.AlignAnalysisUIText 0.2439024424.4%
jalview.ws.rest.params.Alignment   jalview.ws.rest.params.Alignment 0.2435897424.4%
jalview.io.FileFormats   jalview.io.FileFormats 0.2424%
com.stevesoft.pat.RegRes   com.stevesoft.pat.RegRes 0.2391304423.9%
jalview.datamodel.VisibleContigsIterator   jalview.datamodel.VisibleContigsIterator 0.2340425623.4%
jalview.ws.jws2.Jws2Discoverer   jalview.ws.jws2.Jws2Discoverer 0.2336633723.4%
jalview.datamodel.SequenceNode   jalview.datamodel.SequenceNode 0.2307692323.1%
jalview.gui.ScalePanel   jalview.gui.ScalePanel 0.226562522.7%
jalview.ws.jws2.Jws2Client   jalview.ws.jws2.Jws2Client 0.2228915722.3%
jalview.io.FileParse   jalview.io.FileParse 0.2144846821.4%
jalview.viewmodel.OverviewDimensionsHideHidden   jalview.viewmodel.OverviewDimensionsHideHidden 0.211267621.1%
jalview.gui.TreePanel   jalview.gui.TreePanel 0.2099125421%
jalview.ws.rest.InputType   jalview.ws.rest.InputType 0.2056074720.6%
com.stevesoft.pat.patInt   com.stevesoft.pat.patInt 0.220%
jalview.project.Jalview2XML   jalview.project.Jalview2XML 0.1973986219.7%
jalview.gui.AnnotationLabels   jalview.gui.AnnotationLabels 0.1955801119.6%
jalview.gui.SeqCanvas   jalview.gui.SeqCanvas 0.1913827719.1%
jalview.analysis.AnnotationSorter   jalview.analysis.AnnotationSorter 0.1822660118.2%
jalview.datamodel.Alignment   jalview.datamodel.Alignment 0.1815642418.2%
jalview.schemes.IdColourScheme   jalview.schemes.IdColourScheme 0.1739130517.4%
jalview.util.StringUtils   jalview.util.StringUtils 0.1723076917.2%
jalview.io.IdentifyFile   jalview.io.IdentifyFile 0.1650793716.5%
jalview.datamodel.AlignmentAnnotation   jalview.datamodel.AlignmentAnnotation 0.1647940116.5%
jalview.datamodel.SequenceGroup   jalview.datamodel.SequenceGroup 0.163793116.4%
jalview.gui.AnnotationPanel   jalview.gui.AnnotationPanel 0.1628910516.3%
jalview.ws.jws1.WS1Client   jalview.ws.jws1.WS1Client 0.1616%
jalview.gui.Desktop.MyDesktopManager   jalview.gui.Desktop.MyDesktopManager 0.1555555615.6%
jalview.util.Format   jalview.util.Format 0.1490683314.9%
jalview.schemes.TCoffeeColourScheme   jalview.schemes.TCoffeeColourScheme 0.1475409914.8%
jalview.workers.AlignCalcWorker   jalview.workers.AlignCalcWorker 0.1428571514.3%
jalview.log.JLogger   jalview.log.JLogger 0.1428571514.3%
jalview.gui.Desktop.MyDesktopPane   jalview.gui.Desktop.MyDesktopPane 0.1428571514.3%
com.stevesoft.pat.Branch   com.stevesoft.pat.Branch 0.140939614.1%
jalview.gui.AlignFrame   jalview.gui.AlignFrame 0.1375307713.8%
jalview.ws.rest.params.SeqGroupIndexVector   jalview.ws.rest.params.SeqGroupIndexVector 0.12408759412.4%
jalview.structure.StructureSelectionManager   jalview.structure.StructureSelectionManager 0.1174968111.7%
jalview.analysis.scoremodels.ScoreModels   jalview.analysis.scoremodels.ScoreModels 0.11538461611.5%
jalview.ws.rest.RestClient   jalview.ws.rest.RestClient 0.11538461611.5%
jalview.datamodel.Annotation   jalview.datamodel.Annotation 0.11428571511.4%
jalview.util.ShortcutKeyMaskExWrapper   jalview.util.ShortcutKeyMaskExWrapper 0.1111111111.1%
jalview.log.JLoggerLog4j   jalview.log.JLoggerLog4j 0.10679611610.7%
jalview.datamodel.Sequence   jalview.datamodel.Sequence 0.1038062310.4%
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.gui.Desktop   jalview.gui.Desktop 0.10102156510.1%
jalview.util.ColorUtils   jalview.util.ColorUtils 0.096774199.7%
com.stevesoft.pat.ReplaceRule   com.stevesoft.pat.ReplaceRule 0.08771938.8%
jalview.ws.dbsources.Xfam   jalview.ws.dbsources.Xfam 0.086956528.7%
jalview.ext.ensembl.EnsemblSequenceFetcher   jalview.ext.ensembl.EnsemblSequenceFetcher 0.0833333368.3%
jalview.gui.Console   jalview.gui.Console 0.082568818.3%
jalview.datamodel.HiddenSequences   jalview.datamodel.HiddenSequences 0.082191788.2%
jalview.schemes.RNAHelicesColour   jalview.schemes.RNAHelicesColour 0.082191788.2%
jalview.gui.ProgressBar   jalview.gui.ProgressBar 0.081300818.1%
jalview.bin.Console   jalview.bin.Console 0.078817737.9%
jalview.gui.IdPanel   jalview.gui.IdPanel 0.067264576.7%
jalview.schemes.PIDColourScheme   jalview.schemes.PIDColourScheme 0.066666676.7%
jalview.gui.AppJmolBinding   jalview.gui.AppJmolBinding 0.065420566.5%
com.stevesoft.pat.RegOpt   com.stevesoft.pat.RegOpt 0.06474826.5%
jalview.gui.StructureViewerBase   jalview.gui.StructureViewerBase 0.063798226.4%
jalview.analysis.CrossRef   jalview.analysis.CrossRef 0.063524596.4%
jalview.gui.TreeCanvas   jalview.gui.TreeCanvas 0.062721896.3%
jalview.io.FileFormat   jalview.io.FileFormat 0.0620155046.2%
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.util.Platform   jalview.util.Platform 0.0566037745.7%
jalview.datamodel.ColumnSelection.IntList   jalview.datamodel.ColumnSelection.IntList 0.0560747655.6%
jalview.bin.Cache   jalview.bin.Cache 0.0550964185.5%
jalview.ws.seqfetcher.DbSourceProxyImpl   jalview.ws.seqfetcher.DbSourceProxyImpl 0.0540540555.4%
jalview.ws.jws1.Discoverer   jalview.ws.jws1.Discoverer 0.0512820525.1%
jalview.analysis.GeneticCodes   jalview.analysis.GeneticCodes 0.0496894425%
jalview.datamodel.HiddenColumns   jalview.datamodel.HiddenColumns 0.04952835%
jalview.datamodel.SecondaryStructureCount   jalview.datamodel.SecondaryStructureCount 0.0468754.7%
jalview.util.DBRefUtils   jalview.util.DBRefUtils 0.045317224.5%
jalview.ws.dbsources.Pdb   jalview.ws.dbsources.Pdb 0.042553194.3%
jalview.ws.jws2.JabaParamStore   jalview.ws.jws2.JabaParamStore 0.0416666684.2%
jalview.ws.jws1.JPredClient   jalview.ws.jws1.JPredClient 0.0310559013.1%
jalview.ext.jmol.JalviewJmolBinding   jalview.ext.jmol.JalviewJmolBinding 0.0262626262.6%
jalview.structures.models.AAStructureBindingModel   jalview.structures.models.AAStructureBindingModel 0.0257913252.6%
jalview.structure.StructureCommandsBase   jalview.structure.StructureCommandsBase 0.0243902432.4%
jalview.analysis.AlignmentUtils   jalview.analysis.AlignmentUtils 0.024171272.4%
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.gui.AppJmol   jalview.gui.AppJmol 0.0150375941.5%
jalview.controller.AlignViewController   jalview.controller.AlignViewController 0.0136518771.4%
jalview.util.HttpUtils   jalview.util.HttpUtils 0.0130718961.3%
jalview.datamodel.SearchResults   jalview.datamodel.SearchResults 0.0128205131.3%
jalview.analysis.AlignSeq   jalview.analysis.AlignSeq 0.0128205131.3%
jalview.datamodel.features.SequenceFeatures   jalview.datamodel.features.SequenceFeatures 0.0127388541.3%
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.bin.Jalview   jalview.bin.Jalview 0.0099277981%
jalview.gui.SequenceFetcher   jalview.gui.SequenceFetcher 0.0089285720.9%
jalview.ext.ensembl.EnsemblGene   jalview.ext.ensembl.EnsemblGene 0.0081632650.8%
jalview.gui.QuitHandler   jalview.gui.QuitHandler 0.0077519380.8%
jalview.renderer.seqfeatures.FeatureRenderer   jalview.renderer.seqfeatures.FeatureRenderer 0.007547170.8%
jalview.viewmodel.seqfeatures.FeatureRendererModel   jalview.viewmodel.seqfeatures.FeatureRendererModel 0.00312989040.3%
com.stevesoft.pat.CaseMgr   com.stevesoft.pat.CaseMgr 0.00278551530.3%
  • Report generated by OpenClover v 4.4.1 on Thu Nov 7 2024 10:19:08 GMT using coverage data from Thu Nov 7 2024 10:18:53 GMT.
  • OpenClover is free and open-source software.