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Coverage Report

Test allLinkedIdsTest

Test
allLinkedIdsTest 1PASS 2 Sep 17:58:34 1.304
 
allLinkedIdsTest
com.stevesoft.pat.patInf   com.stevesoft.pat.patInf 1.0100%
jalview.io.DataSourceType   jalview.io.DataSourceType 1.0100%
jalview.urls.desktop.DesktopUrlProviderFactory   jalview.urls.desktop.DesktopUrlProviderFactory 1.0100%
jalview.ws.WSClient   jalview.ws.WSClient 1.0100%
jalview.ws.SequenceFetcher   jalview.ws.SequenceFetcher 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.util.UserAgent   jalview.util.UserAgent 0.885714388.6%
jalview.gui.SplashScreen.SplashImage   jalview.gui.SplashScreen.SplashImage 0.8823529588.2%
jalview.json.binding.biojs.BioJSReleasePojo   jalview.json.binding.biojs.BioJSReleasePojo 0.8461538684.6%
com.stevesoft.pat.Rthings   com.stevesoft.pat.Rthings 0.8461538684.6%
jalview.datamodel.Profiles   jalview.datamodel.Profiles 0.833333383.3%
jalview.util.UrlConstants   jalview.util.UrlConstants 0.880%
jalview.analysis.Conservation   jalview.analysis.Conservation 0.783251278.3%
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.ZappoColourScheme   jalview.schemes.ZappoColourScheme 0.7575%
jalview.schemes.NucleotideColourScheme   jalview.schemes.NucleotideColourScheme 0.7575%
jalview.bin.Cache.VersionChecker   jalview.bin.Cache.VersionChecker 0.740740774.1%
jalview.io.JalviewFileFilter   jalview.io.JalviewFileFilter 0.735294173.5%
jalview.io.JalviewFileChooser.RecentlyOpened   jalview.io.JalviewFileChooser.RecentlyOpened 0.7333333573.3%
jalview.gui.FeatureRenderer   jalview.gui.FeatureRenderer 0.7142857371.4%
jalview.util.LinkedIdentityHashSet.IdentityWrapper   jalview.util.LinkedIdentityHashSet.IdentityWrapper 0.7142857371.4%
jalview.gui.SplashScreen   jalview.gui.SplashScreen 0.701298770.1%
jalview.workers.ConsensusThread   jalview.workers.ConsensusThread 0.696969769.7%
jalview.workers.SecondaryStructureConsensusThread   jalview.workers.SecondaryStructureConsensusThread 0.696969769.7%
jalview.json.binding.biojs.BioJSRepositoryPojo   jalview.json.binding.biojs.BioJSRepositoryPojo 0.687568.8%
jalview.datamodel.Profile   jalview.datamodel.Profile 0.678571467.9%
jalview.log.JalviewAppender   jalview.log.JalviewAppender 0.666666766.7%
jalview.bin.argparser.Arg.Type   jalview.bin.argparser.Arg.Type 0.666666766.7%
jalview.schemes.ResidueColourScheme   jalview.schemes.ResidueColourScheme 0.666666766.7%
jalview.io.BackupFilesPresetEntry   jalview.io.BackupFilesPresetEntry 0.661764766.2%
jalview.ws.utils.UrlDownloadClient   jalview.ws.utils.UrlDownloadClient 0.657142965.7%
jalview.ws.dbsources.PfamSeed   jalview.ws.dbsources.PfamSeed 0.636363663.6%
jalview.datamodel.AlignmentExportData   jalview.datamodel.AlignmentExportData 0.62562.5%
com.stevesoft.pat.StrPos   com.stevesoft.pat.StrPos 0.6162790761.6%
jalview.io.IntKeyStringValueEntry   jalview.io.IntKeyStringValueEntry 0.660%
jalview.ws.dbsources.EmblSource   jalview.ws.dbsources.EmblSource 0.660%
jalview.ws.rest.RestServiceDescription   jalview.ws.rest.RestServiceDescription 0.5959%
jalview.jbgui.GAlignFrame   jalview.jbgui.GAlignFrame 0.582542758.3%
jalview.workers.ConservationThread   jalview.workers.ConservationThread 0.568965556.9%
jalview.jbgui.GDesktop   jalview.jbgui.GDesktop 0.567010356.7%
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.ws.dbsources.PfamFull   jalview.ws.dbsources.PfamFull 0.5384615753.8%
jalview.bin.argparser.ArgParser   jalview.bin.argparser.ArgParser 0.5203007552%
ext.vamsas.ServiceHandle   ext.vamsas.ServiceHandle 0.510204151%
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.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.BootstrapArgs   jalview.bin.argparser.BootstrapArgs 0.4917355549.2%
jalview.gui.BlogReader   jalview.gui.BlogReader 0.483425448.3%
jalview.io.FileFormats   jalview.io.FileFormats 0.4646%
com.stevesoft.pat.oneChar   com.stevesoft.pat.oneChar 0.4571428645.7%
jalview.urls.IdentifiersUrlProvider   jalview.urls.IdentifiersUrlProvider 0.4495412745%
jalview.ws.jws2.JabaWsServerQuery   jalview.ws.jws2.JabaWsServerQuery 0.4479166644.8%
jalview.renderer.AnnotationRendererFactory   jalview.renderer.AnnotationRendererFactory 0.437543.8%
jalview.gui.APQHandlers   jalview.gui.APQHandlers 0.434782643.5%
jalview.gui.Console   jalview.gui.Console 0.4334862543.3%
jalview.bin.argparser.SubVals   jalview.bin.argparser.SubVals 0.432989743.3%
jalview.gui.ColourMenuHelper   jalview.gui.ColourMenuHelper 0.4322033843.2%
jalview.ws.dbsources.EmblCdsSource   jalview.ws.dbsources.EmblCdsSource 0.4285714342.9%
jalview.ws.dbsources.RfamSeed   jalview.ws.dbsources.RfamSeed 0.4285714342.9%
jalview.util.QuickSort.IntComparator   jalview.util.QuickSort.IntComparator 0.4285714342.9%
jalview.datamodel.HiddenCursorPosition   jalview.datamodel.HiddenCursorPosition 0.4285714342.9%
jalview.urls.UrlProvider   jalview.urls.UrlProvider 0.4257425742.6%
jalview.util.FileUtils   jalview.util.FileUtils 0.424731242.5%
jalview.io.FileLoader   jalview.io.FileLoader 0.418060241.8%
jalview.bin.argparser.ArgValue   jalview.bin.argparser.ArgValue 0.4179104641.8%
jalview.util.ShortcutKeyMaskExWrapper11   jalview.util.ShortcutKeyMaskExWrapper11 0.4166666641.7%
jalview.gui.SequenceRenderer   jalview.gui.SequenceRenderer 0.4134615441.3%
jalview.ext.so.SequenceOntology   jalview.ext.so.SequenceOntology 0.412541.2%
jalview.util.HttpUtils   jalview.util.HttpUtils 0.411764741.2%
jalview.datamodel.ResidueCount   jalview.datamodel.ResidueCount 0.4072727340.7%
jalview.util.MessageManager   jalview.util.MessageManager 0.404761940.5%
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 0.3949044639.5%
jalview.bin.Cache   jalview.bin.Cache 0.3925619739.3%
jalview.urls.CustomUrlProvider   jalview.urls.CustomUrlProvider 0.3924050639.2%
jalview.ws.jws1.Discoverer   jalview.ws.jws1.Discoverer 0.384615438.5%
jalview.ws.rest.params.Alignment   jalview.ws.rest.params.Alignment 0.384615438.5%
jalview.io.AlignFile   jalview.io.AlignFile 0.3835616438.4%
jalview.analysis.AAFrequency   jalview.analysis.AAFrequency 0.3686440636.9%
jalview.urls.UrlProviderImpl   jalview.urls.UrlProviderImpl 0.3658536736.6%
jalview.renderer.ScaleRenderer   jalview.renderer.ScaleRenderer 0.3636%
jalview.util.ErrorLog   jalview.util.ErrorLog 0.352941235.3%
jalview.gui.UserQuestionnaireCheck   jalview.gui.UserQuestionnaireCheck 0.349397634.9%
jalview.bin.argparser.ArgValues   jalview.bin.argparser.ArgValues 0.3412698534.1%
jalview.bin.argparser.Arg.Opt   jalview.bin.argparser.Arg.Opt 0.3333333433.3%
jalview.gui.IdwidthAdjuster   jalview.gui.IdwidthAdjuster 0.3289473732.9%
jalview.gui.AlignmentPanel   jalview.gui.AlignmentPanel 0.326266232.6%
jalview.viewmodel.styles.ViewStyle   jalview.viewmodel.styles.ViewStyle 0.3242187532.4%
jalview.util.Format   jalview.util.Format 0.3209109632.1%
jalview.viewmodel.ViewportRanges   jalview.viewmodel.ViewportRanges 0.3201320232%
jalview.bin.argparser.ArgValuesMap   jalview.bin.argparser.ArgValuesMap 0.317848431.8%
jalview.io.FastaFile   jalview.io.FastaFile 0.315315331.5%
jalview.util.Comparison   jalview.util.Comparison 0.3149606331.5%
jalview.gui.AlignViewport   jalview.gui.AlignViewport 0.312785431.3%
jalview.bin.Commands   jalview.bin.Commands 0.3097345231%
jalview.gui.Desktop.MyDesktopPane   jalview.gui.Desktop.MyDesktopPane 0.3095238231%
org.json.simple.parser.JSONParser   org.json.simple.parser.JSONParser 0.2995049430%
jalview.gui.JvSwingUtils   jalview.gui.JvSwingUtils 0.299319729.9%
jalview.renderer.AnnotationRenderer   jalview.renderer.AnnotationRenderer 0.2943840629.4%
jalview.viewmodel.AlignmentViewport   jalview.viewmodel.AlignmentViewport 0.2937116629.4%
jalview.io.FileParse   jalview.io.FileParse 0.286908128.7%
jalview.renderer.ResidueColourFinder   jalview.renderer.ResidueColourFinder 0.285714328.6%
jalview.schemes.JalviewColourScheme   jalview.schemes.JalviewColourScheme 0.285714328.6%
jalview.ws.rest.InputType   jalview.ws.rest.InputType 0.2803738428%
jalview.util.UrlLink   jalview.util.UrlLink 0.2803030328%
jalview.io.IdentifyFile   jalview.io.IdentifyFile 0.279365127.9%
jalview.util.Log4j   jalview.util.Log4j 0.2727272827.3%
jalview.renderer.ResidueShader   jalview.renderer.ResidueShader 0.2714285927.1%
jalview.io.JalviewFileChooser   jalview.io.JalviewFileChooser 0.2709923727.1%
jalview.util.ChannelProperties   jalview.util.ChannelProperties 0.268965526.9%
jalview.bin.Jalview   jalview.bin.Jalview 0.2662454826.6%
jalview.log.JLogger   jalview.log.JLogger 0.2637362826.4%
jalview.ws.rest.RestClient   jalview.ws.rest.RestClient 0.2564102725.6%
jalview.ext.ensembl.EnsemblSequenceFetcher   jalview.ext.ensembl.EnsemblSequenceFetcher 0.2525%
jalview.io.gff.SequenceOntologyFactory   jalview.io.gff.SequenceOntologyFactory 0.2525%
jalview.gui.IdCanvas   jalview.gui.IdCanvas 0.2491228124.9%
jalview.gui.PaintRefresher   jalview.gui.PaintRefresher 0.2464788724.6%
com.stevesoft.pat.Regex   com.stevesoft.pat.Regex 0.2454545524.5%
jalview.ws.jws1.WS1Client   jalview.ws.jws1.WS1Client 0.2424%
jalview.io.BackupFiles   jalview.io.BackupFiles 0.23623.6%
jalview.bin.BuildDetails   jalview.bin.BuildDetails 0.2352941223.5%
jalview.datamodel.AlignExportSettingsAdapter   jalview.datamodel.AlignExportSettingsAdapter 0.2307692323.1%
com.stevesoft.pat.Range   com.stevesoft.pat.Range 0.2272727322.7%
com.stevesoft.pat.Bracket   com.stevesoft.pat.Bracket 0.22522.5%
jalview.bin.Console   jalview.bin.Console 0.2216748722.2%
jalview.io.FormatAdapter   jalview.io.FormatAdapter 0.2222%
jalview.gui.Desktop   jalview.gui.Desktop 0.2162315521.6%
jalview.ws.rest.params.SeqGroupIndexVector   jalview.ws.rest.params.SeqGroupIndexVector 0.2116788321.2%
jalview.gui.BlogReader.LaunchJvBrowserOnItem   jalview.gui.BlogReader.LaunchJvBrowserOnItem 0.2083333320.8%
jalview.urls.UrlLinkDisplay   jalview.urls.UrlLinkDisplay 0.2051282120.5%
jalview.log.JLoggerLog4j   jalview.log.JLoggerLog4j 0.203883520.4%
jalview.gui.Desktop.MyDesktopManager   jalview.gui.Desktop.MyDesktopManager 0.220%
jalview.bin.JalviewTaskbar   jalview.bin.JalviewTaskbar 0.220%
jalview.io.AppletFormatAdapter   jalview.io.AppletFormatAdapter 0.1956521719.6%
jalview.gui.AnnotationLabels   jalview.gui.AnnotationLabels 0.1917647119.2%
jalview.datamodel.SecondaryStructureCount   jalview.datamodel.SecondaryStructureCount 0.1914062519.1%
jalview.util.JSONUtils   jalview.util.JSONUtils 0.1818181918.2%
com.stevesoft.pat.patInt   com.stevesoft.pat.patInt 0.17517.5%
jalview.ws.dbsources.Xfam   jalview.ws.dbsources.Xfam 0.1739130517.4%
jalview.schemes.IdColourScheme   jalview.schemes.IdColourScheme 0.1739130517.4%
jalview.util.StringUtils   jalview.util.StringUtils 0.1723076917.2%
jalview.ws.jws2.Jws2Discoverer   jalview.ws.jws2.Jws2Discoverer 0.1722772317.2%
jalview.datamodel.Alignment   jalview.datamodel.Alignment 0.1703910717%
jalview.urls.UrlLinkTableModel   jalview.urls.UrlLinkTableModel 0.1686746916.9%
jalview.analysis.AnnotationSorter   jalview.analysis.AnnotationSorter 0.1674876816.7%
com.stevesoft.pat.Pattern   com.stevesoft.pat.Pattern 0.1666666716.7%
jalview.util.Platform   jalview.util.Platform 0.1650943516.5%
jalview.util.QuickSort   jalview.util.QuickSort 0.1650485416.5%
jalview.bin.argparser.Arg   jalview.bin.argparser.Arg 0.162650616.3%
com.stevesoft.pat.parsePerl   com.stevesoft.pat.parsePerl 0.1598639516%
jalview.gui.AlignFrame   jalview.gui.AlignFrame 0.1571377215.7%
jalview.io.FileFormat   jalview.io.FileFormat 0.1550387615.5%
jalview.ws.seqfetcher.ASequenceFetcher   jalview.ws.seqfetcher.ASequenceFetcher 0.1511111115.1%
jalview.gui.ScalePanel   jalview.gui.ScalePanel 0.148437514.8%
jalview.schemes.TCoffeeColourScheme   jalview.schemes.TCoffeeColourScheme 0.1475409914.8%
jalview.gui.AnnotationPanel   jalview.gui.AnnotationPanel 0.1326860813.3%
jalview.ws.dbsources.Rfam   jalview.ws.dbsources.Rfam 0.12512.5%
jalview.schemes.Blosum62ColourScheme   jalview.schemes.Blosum62ColourScheme 0.1176470611.8%
jalview.datamodel.Annotation   jalview.datamodel.Annotation 0.11428571511.4%
jalview.structure.StructureImportSettings   jalview.structure.StructureImportSettings 0.11428571511.4%
jalview.gui.PromptUserConfig   jalview.gui.PromptUserConfig 0.1136363711.4%
jalview.analysis.scoremodels.ScoreModels   jalview.analysis.scoremodels.ScoreModels 0.1132075511.3%
jalview.util.ShortcutKeyMaskExWrapper   jalview.util.ShortcutKeyMaskExWrapper 0.1111111111.1%
jalview.schemes.ColourSchemeProperty   jalview.schemes.ColourSchemeProperty 0.1111111111.1%
jalview.datamodel.Sequence   jalview.datamodel.Sequence 0.1038062310.4%
jalview.ws.rest.params.AnnotationFile   jalview.ws.rest.params.AnnotationFile 0.10256410410.3%
jalview.io.StockholmFile   jalview.io.StockholmFile 0.098930489.9%
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%
com.stevesoft.pat.Start   com.stevesoft.pat.Start 0.090909099.1%
jalview.util.LaunchUtils   jalview.util.LaunchUtils 0.090686289.1%
com.stevesoft.pat.Or   com.stevesoft.pat.Or 0.089743599%
jalview.structure.StructureSelectionManager   jalview.structure.StructureSelectionManager 0.0888.8%
jalview.ws.dbsources.Pfam   jalview.ws.dbsources.Pfam 0.086956528.7%
jalview.schemes.RNAHelicesColour   jalview.schemes.RNAHelicesColour 0.082191788.2%
jalview.gui.ProgressBar   jalview.gui.ProgressBar 0.081300818.1%
jalview.ws.seqfetcher.DbSourceProxyImpl   jalview.ws.seqfetcher.DbSourceProxyImpl 0.081081088.1%
jalview.datamodel.AlignmentAnnotation   jalview.datamodel.AlignmentAnnotation 0.077791727.8%
jalview.gui.SeqCanvas   jalview.gui.SeqCanvas 0.07515037.5%
com.stevesoft.pat.OrMark   com.stevesoft.pat.OrMark 0.0757.5%
com.stevesoft.pat.FastMulti   com.stevesoft.pat.FastMulti 0.0740740757.4%
jalview.schemes.ColourSchemes   jalview.schemes.ColourSchemes 0.070175447%
jalview.analysis.CrossRef   jalview.analysis.CrossRef 0.069672137%
com.stevesoft.pat.End   com.stevesoft.pat.End 0.068965526.9%
jalview.gui.IdPanel   jalview.gui.IdPanel 0.067264576.7%
jalview.schemes.PIDColourScheme   jalview.schemes.PIDColourScheme 0.066666676.7%
com.stevesoft.pat.RegOpt   com.stevesoft.pat.RegOpt 0.06474826.5%
jalview.ws.dbsources.Pdb   jalview.ws.dbsources.Pdb 0.063829796.4%
jalview.analysis.scoremodels.ScoreMatrix   jalview.analysis.scoremodels.ScoreMatrix 0.0617283966.2%
jalview.gui.ViewSelectionMenu   jalview.gui.ViewSelectionMenu 0.059405945.9%
jalview.datamodel.ColumnSelection.IntList   jalview.datamodel.ColumnSelection.IntList 0.0560747655.6%
jalview.analysis.GeneticCodes   jalview.analysis.GeneticCodes 0.0496894425%
jalview.util.DBRefUtils   jalview.util.DBRefUtils 0.045317224.5%
jalview.ws.jws1.JPredClient   jalview.ws.jws1.JPredClient 0.043478264.3%
jalview.datamodel.HiddenColumns   jalview.datamodel.HiddenColumns 0.040094344%
org.json.simple.JSONObject   org.json.simple.JSONObject 0.037735853.8%
jalview.ws.jws1.SeqSearchWSClient   jalview.ws.jws1.SeqSearchWSClient 0.029629633%
jalview.ext.ensembl.EnsemblRestClient   jalview.ext.ensembl.EnsemblRestClient 0.0283018872.8%
jalview.datamodel.HiddenSequences   jalview.datamodel.HiddenSequences 0.027397262.7%
jalview.gui.AlignExportOptions   jalview.gui.AlignExportOptions 0.026315792.6%
jalview.ws.jws1.MsaWSClient   jalview.ws.jws1.MsaWSClient 0.026315792.6%
jalview.ws.dbsources.Uniprot   jalview.ws.dbsources.Uniprot 0.0233463032.3%
jalview.gui.Preferences   jalview.gui.Preferences 0.0186513631.9%
jalview.schemes.ClustalxColourScheme   jalview.schemes.ClustalxColourScheme 0.0169491531.7%
jalview.ext.ensembl.EnsemblGene   jalview.ext.ensembl.EnsemblGene 0.016326531.6%
jalview.datamodel.HiddenColumnsCursor   jalview.datamodel.HiddenColumnsCursor 0.0156251.6%
jalview.controller.AlignViewController   jalview.controller.AlignViewController 0.0136518771.4%
jalview.gui.SequenceFetcher   jalview.gui.SequenceFetcher 0.0133928571.3%
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 0.0125412541.3%
jalview.io.SequenceAnnotationReport   jalview.io.SequenceAnnotationReport 0.0122699381.2%
jalview.datamodel.ColumnSelection   jalview.datamodel.ColumnSelection 0.0103092781%
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%
com.stevesoft.pat.RegRes   com.stevesoft.pat.RegRes 0.0072463770.7%
jalview.ext.ensembl.EnsemblSeqProxy   jalview.ext.ensembl.EnsemblSeqProxy 0.00584795330.6%
jalview.analysis.AlignmentUtils   jalview.analysis.AlignmentUtils 0.0043859650.4%
com.stevesoft.pat.CaseMgr   com.stevesoft.pat.CaseMgr 0.00278551530.3%