|
jalview.io.DataSourceType
jalview.io.DataSourceType
|
1.0100%
|
|
|
jalview.xml.binding.jalview.SequenceType
jalview.xml.binding.jalview.SequenceType
|
1.0100%
|
|
|
jalview.xml.binding.jalview.MapListType
jalview.xml.binding.jalview.MapListType
|
1.0100%
|
|
|
jalview.xml.binding.jalview.MapListType.MapListFrom
jalview.xml.binding.jalview.MapListType.MapListFrom
|
1.0100%
|
|
|
jalview.xml.binding.jalview.MapListType.MapListTo
jalview.xml.binding.jalview.MapListType.MapListTo
|
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.HiddenCursorPosition
jalview.datamodel.HiddenCursorPosition
|
1.0100%
|
|
|
jalview.datamodel.ResidueCount.SymbolCounts
jalview.datamodel.ResidueCount.SymbolCounts
|
1.0100%
|
|
|
jalview.jbgui.GAlignmentPanel
jalview.jbgui.GAlignmentPanel
|
0.9494%
|
|
|
jalview.xml.binding.jalview.Sequence.DBRef
jalview.xml.binding.jalview.Sequence.DBRef
|
0.937593.8%
|
|
|
jalview.xml.binding.jalview.AnnotationElement
jalview.xml.binding.jalview.AnnotationElement
|
0.916666791.7%
|
|
|
jalview.xml.binding.jalview.SequenceSet
jalview.xml.binding.jalview.SequenceSet
|
0.894736889.5%
|
|
|
jalview.analysis.Conservation
jalview.analysis.Conservation
|
0.874384287.4%
|
|
|
jalview.util.QuickSort.IntComparator
jalview.util.QuickSort.IntComparator
|
0.8571428785.7%
|
|
|
jalview.viewmodel.styles.ViewStyle
jalview.viewmodel.styles.ViewStyle
|
0.8476562584.8%
|
|
|
jalview.xml.binding.jalview.JalviewModel.Viewport
jalview.xml.binding.jalview.JalviewModel.Viewport
|
0.844202984.4%
|
|
|
jalview.datamodel.VisibleContigsIterator
jalview.datamodel.VisibleContigsIterator
|
0.8085106680.9%
|
|
|
jalview.util.LinkedIdentityHashSet
jalview.util.LinkedIdentityHashSet
|
0.7727272577.3%
|
|
|
jalview.xml.binding.jalview.JalviewModel
jalview.xml.binding.jalview.JalviewModel
|
0.769230876.9%
|
|
|
jalview.xml.binding.jalview.Annotation
jalview.xml.binding.jalview.Annotation
|
0.7545454575.5%
|
|
|
jalview.xml.binding.jalview.JalviewModel.JSeq
jalview.xml.binding.jalview.JalviewModel.JSeq
|
0.7575%
|
|
|
jalview.schemes.ZappoColourScheme
jalview.schemes.ZappoColourScheme
|
0.7575%
|
|
|
jalview.datamodel.Profiles
jalview.datamodel.Profiles
|
0.7333333573.3%
|
|
|
jalview.gui.FeatureRenderer
jalview.gui.FeatureRenderer
|
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.workers.ConsensusThread
jalview.workers.ConsensusThread
|
0.696969769.7%
|
|
|
jalview.datamodel.StartRegionIterator
jalview.datamodel.StartRegionIterator
|
0.694444469.4%
|
|
|
jalview.datamodel.HiddenColumnsCursor
jalview.datamodel.HiddenColumnsCursor
|
0.687568.8%
|
|
|
jalview.ws.SequenceFetcher
jalview.ws.SequenceFetcher
|
0.678571467.9%
|
|
|
jalview.schemes.ResidueColourScheme
jalview.schemes.ResidueColourScheme
|
0.666666766.7%
|
|
|
jalview.gui.IdCanvas
jalview.gui.IdCanvas
|
0.607017560.7%
|
|
|
jalview.util.ParseHtmlBodyAndLinks
jalview.util.ParseHtmlBodyAndLinks
|
0.594202959.4%
|
|
|
jalview.jbgui.GAlignFrame
jalview.jbgui.GAlignFrame
|
0.581220758.1%
|
|
|
jalview.workers.ConservationThread
jalview.workers.ConservationThread
|
0.568965556.9%
|
|
|
jalview.renderer.ScaleRenderer
jalview.renderer.ScaleRenderer
|
0.5656%
|
|
|
jalview.workers.AlignCalcManager
jalview.workers.AlignCalcManager
|
0.559523856%
|
|
|
jalview.gui.JalviewChangeSupport
jalview.gui.JalviewChangeSupport
|
0.550%
|
|
|
jalview.viewmodel.ViewportProperties
jalview.viewmodel.ViewportProperties
|
0.550%
|
|
|
jalview.xml.binding.jalview.VAMSAS
jalview.xml.binding.jalview.VAMSAS
|
0.550%
|
|
|
jalview.xml.binding.jalview.Mapping
jalview.xml.binding.jalview.Mapping
|
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.gui.SequenceRenderer
jalview.gui.SequenceRenderer
|
0.4855769348.6%
|
|
|
jalview.util.MessageManager
jalview.util.MessageManager
|
0.4761904847.6%
|
|
|
jalview.renderer.AnnotationRenderer
jalview.renderer.AnnotationRenderer
|
0.4592391345.9%
|
|
|
jalview.renderer.ResidueColourFinder
jalview.renderer.ResidueColourFinder
|
0.4523809645.2%
|
|
|
jalview.datamodel.Profile
jalview.datamodel.Profile
|
0.4464285744.6%
|
|
|
jalview.ws.jws2.MsaWSClient
jalview.ws.jws2.MsaWSClient
|
0.4429530244.3%
|
|
|
jalview.gui.ColourMenuHelper
jalview.gui.ColourMenuHelper
|
0.4322033843.2%
|
|
|
jalview.util.ShortcutKeyMaskExWrapper11
jalview.util.ShortcutKeyMaskExWrapper11
|
0.4166666641.7%
|
|
|
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%
|
|
|
jalview.gui.SeqCanvas
jalview.gui.SeqCanvas
|
0.3917835739.2%
|
|
|
jalview.log.JalviewAppender
jalview.log.JalviewAppender
|
0.388888938.9%
|
|
|
jalview.datamodel.Range
jalview.datamodel.Range
|
0.388888938.9%
|
|
|
jalview.io.FileLoader
jalview.io.FileLoader
|
0.3879598738.8%
|
|
|
jalview.datamodel.GeneLocus
jalview.datamodel.GeneLocus
|
0.37537.5%
|
|
|
jalview.viewmodel.AlignmentViewport
jalview.viewmodel.AlignmentViewport
|
0.3664643536.6%
|
|
|
jalview.io.FastaFile
jalview.io.FastaFile
|
0.3603603536%
|
|
|
jalview.viewmodel.ViewportRanges
jalview.viewmodel.ViewportRanges
|
0.3564356635.6%
|
|
|
jalview.datamodel.ResidueCount
jalview.datamodel.ResidueCount
|
0.3563636235.6%
|
|
|
jalview.io.AlignFile
jalview.io.AlignFile
|
0.356164435.6%
|
|
|
jalview.util.QuickSort
jalview.util.QuickSort
|
0.346278334.6%
|
|
|
jalview.gui.AlignViewport
jalview.gui.AlignViewport
|
0.3447488534.5%
|
|
|
jalview.renderer.ResidueShader
jalview.renderer.ResidueShader
|
0.3428571534.3%
|
|
|
jalview.datamodel.DBRefEntry
jalview.datamodel.DBRefEntry
|
0.3356164433.6%
|
|
|
jalview.ws.rest.RestServiceDescription
jalview.ws.rest.RestServiceDescription
|
0.31531.5%
|
|
|
jalview.gui.AlignmentPanel
jalview.gui.AlignmentPanel
|
0.3144876431.4%
|
|
|
jalview.io.IdentifyFile
jalview.io.IdentifyFile
|
0.3142857331.4%
|
|
|
jalview.project.Jalview2XML
jalview.project.Jalview2XML
|
0.3130949431.3%
|
|
|
jalview.renderer.seqfeatures.FeatureRenderer
jalview.renderer.seqfeatures.FeatureRenderer
|
0.3056603730.6%
|
|
|
jalview.util.Comparison
jalview.util.Comparison
|
0.299212629.9%
|
|
|
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.analysis.AAFrequency
jalview.analysis.AAFrequency
|
0.280590728.1%
|
|
|
jalview.io.FileParse
jalview.io.FileParse
|
0.2785515227.9%
|
|
|
jalview.ws.jws2.JabaPreset
jalview.ws.jws2.JabaPreset
|
0.2727272827.3%
|
|
|
jalview.gui.JvSwingUtils
jalview.gui.JvSwingUtils
|
0.258503425.9%
|
|
|
jalview.datamodel.features.SequenceFeatures
jalview.datamodel.features.SequenceFeatures
|
0.2547770725.5%
|
|
|
jalview.gui.PaintRefresher
jalview.gui.PaintRefresher
|
0.253521125.4%
|
|
|
jalview.ws.jws2.jabaws2.Jws2Instance
jalview.ws.jws2.jabaws2.Jws2Instance
|
0.2528735725.3%
|
|
|
jalview.gui.ScalePanel
jalview.gui.ScalePanel
|
0.2525%
|
|
|
jalview.gui.IdwidthAdjuster
jalview.gui.IdwidthAdjuster
|
0.2525%
|
|
|
jalview.renderer.AnnotationRendererFactory
jalview.renderer.AnnotationRendererFactory
|
0.2525%
|
|
|
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.ws.jws2.Jws2Discoverer
jalview.ws.jws2.Jws2Discoverer
|
0.2336633723.4%
|
|
|
jalview.datamodel.SequenceCursor
jalview.datamodel.SequenceCursor
|
0.2333333323.3%
|
|
|
jalview.datamodel.Sequence
jalview.datamodel.Sequence
|
0.2292387522.9%
|
|
|
jalview.ws.jws2.Jws2Client
jalview.ws.jws2.Jws2Client
|
0.2228915722.3%
|
|
|
jalview.gui.AnnotationLabels
jalview.gui.AnnotationLabels
|
0.2163406221.6%
|
|
|
jalview.datamodel.Alignment
jalview.datamodel.Alignment
|
0.2067039220.7%
|
|
|
jalview.ws.rest.InputType
jalview.ws.rest.InputType
|
0.2056074720.6%
|
|
|
jalview.schemes.ColourSchemeProperty
jalview.schemes.ColourSchemeProperty
|
0.1944444519.4%
|
|
|
jalview.schemes.IdColourScheme
jalview.schemes.IdColourScheme
|
0.1739130517.4%
|
|
|
jalview.analysis.AnnotationSorter
jalview.analysis.AnnotationSorter
|
0.1674876816.7%
|
|
|
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.datamodel.AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation
|
0.1462514.6%
|
|
|
jalview.analysis.CrossRef
jalview.analysis.CrossRef
|
0.1434426214.3%
|
|
|
jalview.log.JLogger
jalview.log.JLogger
|
0.1428571514.3%
|
|
|
jalview.gui.Desktop.MyDesktopPane
jalview.gui.Desktop.MyDesktopPane
|
0.1428571514.3%
|
|
|
jalview.bin.Console
jalview.bin.Console
|
0.1330049213.3%
|
|
|
jalview.gui.AlignFrame
jalview.gui.AlignFrame
|
0.1311357913.1%
|
|
|
jalview.ws.rest.params.SeqGroupIndexVector
jalview.ws.rest.params.SeqGroupIndexVector
|
0.12408759412.4%
|
|
|
jalview.util.DBRefUtils
jalview.util.DBRefUtils
|
0.1208459212.1%
|
|
|
jalview.io.FormatAdapter
jalview.io.FormatAdapter
|
0.1212%
|
|
|
jalview.util.StringUtils
jalview.util.StringUtils
|
0.1212%
|
|
|
jalview.structure.StructureSelectionManager
jalview.structure.StructureSelectionManager
|
0.1212%
|
|
|
jalview.schemes.Blosum62ColourScheme
jalview.schemes.Blosum62ColourScheme
|
0.1176470611.8%
|
|
|
jalview.datamodel.Mapping
jalview.datamodel.Mapping
|
0.11688311411.7%
|
|
|
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.gui.AnnotationPanel
jalview.gui.AnnotationPanel
|
0.1123949611.2%
|
|
|
jalview.util.ShortcutKeyMaskExWrapper
jalview.util.ShortcutKeyMaskExWrapper
|
0.1111111111.1%
|
|
|
jalview.gui.Desktop
jalview.gui.Desktop
|
0.1087699310.9%
|
|
|
jalview.io.FileFormat
jalview.io.FileFormat
|
0.1085271310.9%
|
|
|
jalview.log.JLoggerLog4j
jalview.log.JLoggerLog4j
|
0.10679611610.7%
|
|
|
jalview.ws.rest.params.AnnotationFile
jalview.ws.rest.params.AnnotationFile
|
0.10256410410.3%
|
|
|
jalview.io.AppletFormatAdapter
jalview.io.AppletFormatAdapter
|
0.0993788849.9%
|
|
|
jalview.workers.AlignCalcWorker
jalview.workers.AlignCalcWorker
|
0.09523819.5%
|
|
|
jalview.ws.dbsources.Xfam
jalview.ws.dbsources.Xfam
|
0.086956528.7%
|
|
|
jalview.util.ColorUtils
jalview.util.ColorUtils
|
0.0860215058.6%
|
|
|
jalview.datamodel.HiddenColumns
jalview.datamodel.HiddenColumns
|
0.084905668.5%
|
|
|
jalview.ext.ensembl.EnsemblSequenceFetcher
jalview.ext.ensembl.EnsemblSequenceFetcher
|
0.0833333368.3%
|
|
|
jalview.gui.Console
jalview.gui.Console
|
0.082568818.3%
|
|
|
jalview.schemes.RNAHelicesColour
jalview.schemes.RNAHelicesColour
|
0.082191788.2%
|
|
|
jalview.gui.ProgressBar
jalview.gui.ProgressBar
|
0.081300818.1%
|
|
|
jalview.datamodel.SequenceGroup
jalview.datamodel.SequenceGroup
|
0.07413017.4%
|
|
|
jalview.schemes.ColourSchemes
jalview.schemes.ColourSchemes
|
0.070175447%
|
|
|
jalview.gui.IdPanel
jalview.gui.IdPanel
|
0.067264576.7%
|
|
|
jalview.schemes.PIDColourScheme
jalview.schemes.PIDColourScheme
|
0.066666676.7%
|
|
|
jalview.viewmodel.seqfeatures.FeatureRendererModel
jalview.viewmodel.seqfeatures.FeatureRendererModel
|
0.0657276966.6%
|
|
|
jalview.gui.AppJmolBinding
jalview.gui.AppJmolBinding
|
0.065420566.5%
|
|
|
jalview.datamodel.HiddenSequences
jalview.datamodel.HiddenSequences
|
0.063926946.4%
|
|
|
jalview.gui.StructureViewerBase
jalview.gui.StructureViewerBase
|
0.063798226.4%
|
|
|
jalview.viewmodel.seqfeatures.FeaturesDisplayed
jalview.viewmodel.seqfeatures.FeaturesDisplayed
|
0.06256.2%
|
|
|
jalview.util.MapList
jalview.util.MapList
|
0.0623052986.2%
|
|
|
jalview.analysis.scoremodels.ScoreMatrix
jalview.analysis.scoremodels.ScoreMatrix
|
0.0617283966.2%
|
|
|
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.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.features.FeatureStore
jalview.datamodel.features.FeatureStore
|
0.045317224.5%
|
|
|
jalview.xml.binding.jalview.ObjectFactory
jalview.xml.binding.jalview.ObjectFactory
|
0.0427350444.3%
|
|
|
jalview.ws.dbsources.Pdb
jalview.ws.dbsources.Pdb
|
0.042553194.3%
|
|
|
jalview.ws.jws2.JabaParamStore
jalview.ws.jws2.JabaParamStore
|
0.0416666684.2%
|
|
|
jalview.bin.Cache
jalview.bin.Cache
|
0.0385674953.9%
|
|
|
jalview.gui.TreePanel
jalview.gui.TreePanel
|
0.0319488833.2%
|
|
|
jalview.ws.jws1.JPredClient
jalview.ws.jws1.JPredClient
|
0.0310559013.1%
|
|
|
jalview.schemes.FeatureColour
jalview.schemes.FeatureColour
|
0.0294736852.9%
|
|
|
jalview.datamodel.SequenceFeature
jalview.datamodel.SequenceFeature
|
0.028776982.9%
|
|
|
jalview.ext.jmol.JalviewJmolBinding
jalview.ext.jmol.JalviewJmolBinding
|
0.0268595032.7%
|
|
|
jalview.structures.models.AAStructureBindingModel
jalview.structures.models.AAStructureBindingModel
|
0.0257913252.6%
|
|
|
jalview.structure.StructureCommandsBase
jalview.structure.StructureCommandsBase
|
0.0243902432.4%
|
|
|
jalview.schemes.ClustalxColourScheme
jalview.schemes.ClustalxColourScheme
|
0.0169491531.7%
|
|
|
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.analysis.AlignSeq
jalview.analysis.AlignSeq
|
0.0128205131.3%
|
|
|
jalview.gui.SeqPanel
jalview.gui.SeqPanel
|
0.0125412541.3%
|
|
|
jalview.io.SequenceAnnotationReport
jalview.io.SequenceAnnotationReport
|
0.0122699381.2%
|
|
|
jalview.bin.Jalview
jalview.bin.Jalview
|
0.0117328521.2%
|
|
|
jalview.util.HttpUtils
jalview.util.HttpUtils
|
0.01169590651.2%
|
|
|
jalview.datamodel.ColumnSelection
jalview.datamodel.ColumnSelection
|
0.0103092781%
|
|
|
jalview.gui.SequenceFetcher
jalview.gui.SequenceFetcher
|
0.0089285720.9%
|
|
|
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%
|
|
