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jalview.io.DataSourceType
jalview.io.DataSourceType
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1.0100%
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jalview.ws.WSClient
jalview.ws.WSClient
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1.0100%
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jalview.datamodel.ResidueCount.SymbolCounts
jalview.datamodel.ResidueCount.SymbolCounts
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1.0100%
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jalview.schemes.HydrophobicColourScheme
jalview.schemes.HydrophobicColourScheme
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1.0100%
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jalview.schemes.TaylorColourScheme
jalview.schemes.TaylorColourScheme
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1.0100%
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jalview.schemes.HelixColourScheme
jalview.schemes.HelixColourScheme
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1.0100%
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jalview.schemes.FlowerColourScheme
jalview.schemes.FlowerColourScheme
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1.0100%
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jalview.schemes.ZappoColourScheme
jalview.schemes.ZappoColourScheme
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1.0100%
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jalview.schemes.NucleotideAmbiguityColourScheme
jalview.schemes.NucleotideAmbiguityColourScheme
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1.0100%
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jalview.schemes.TurnColourScheme
jalview.schemes.TurnColourScheme
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1.0100%
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jalview.schemes.StrandColourScheme
jalview.schemes.StrandColourScheme
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1.0100%
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jalview.schemes.PurinePyrimidineColourScheme
jalview.schemes.PurinePyrimidineColourScheme
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1.0100%
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jalview.schemes.NucleotideColourScheme
jalview.schemes.NucleotideColourScheme
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1.0100%
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jalview.schemes.BlossomColourScheme
jalview.schemes.BlossomColourScheme
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1.0100%
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jalview.schemes.SunsetColourScheme
jalview.schemes.SunsetColourScheme
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1.0100%
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jalview.schemes.BuriedColourScheme
jalview.schemes.BuriedColourScheme
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1.0100%
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jalview.schemes.OceanColourScheme
jalview.schemes.OceanColourScheme
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1.0100%
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jalview.schemes.ClustalxColourScheme.ConsensusColour
jalview.schemes.ClustalxColourScheme.ConsensusColour
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1.0100%
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jalview.jbgui.GAlignmentPanel
jalview.jbgui.GAlignmentPanel
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0.9494%
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jalview.json.binding.biojs.BioJSReleasePojo
jalview.json.binding.biojs.BioJSReleasePojo
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0.8461538684.6%
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jalview.io.JalviewFileChooser.RecentlyOpened
jalview.io.JalviewFileChooser.RecentlyOpened
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0.833333383.3%
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jalview.analysis.Conservation
jalview.analysis.Conservation
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0.807881880.8%
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jalview.util.LinkedIdentityHashSet
jalview.util.LinkedIdentityHashSet
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0.7727272577.3%
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jalview.datamodel.Profiles
jalview.datamodel.Profiles
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0.7333333573.3%
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jalview.gui.FeatureRenderer
jalview.gui.FeatureRenderer
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0.7142857371.4%
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jalview.util.LinkedIdentityHashSet.IdentityWrapper
jalview.util.LinkedIdentityHashSet.IdentityWrapper
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0.7142857371.4%
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jalview.workers.ConsensusThread
jalview.workers.ConsensusThread
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0.696969769.7%
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jalview.io.JalviewFileFilter
jalview.io.JalviewFileFilter
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0.694444469.4%
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jalview.json.binding.biojs.BioJSRepositoryPojo
jalview.json.binding.biojs.BioJSRepositoryPojo
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0.687568.8%
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jalview.ws.SequenceFetcher
jalview.ws.SequenceFetcher
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0.678571467.9%
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jalview.schemes.ClustalxColourScheme
jalview.schemes.ClustalxColourScheme
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0.644067864.4%
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jalview.jbgui.GAlignFrame
jalview.jbgui.GAlignFrame
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0.581220758.1%
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jalview.schemes.JalviewColourScheme
jalview.schemes.JalviewColourScheme
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0.571428657.1%
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jalview.workers.ConservationThread
jalview.workers.ConservationThread
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0.568965556.9%
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jalview.schemes.ScoreColourScheme
jalview.schemes.ScoreColourScheme
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0.562556.2%
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jalview.io.BioJsHTMLOutput
jalview.io.BioJsHTMLOutput
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0.53653.6%
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jalview.schemes.ResidueColourScheme
jalview.schemes.ResidueColourScheme
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0.5238095552.4%
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jalview.gui.JalviewChangeSupport
jalview.gui.JalviewChangeSupport
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0.550%
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jalview.viewmodel.ViewportProperties
jalview.viewmodel.ViewportProperties
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0.550%
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jalview.schemes.Consensus
jalview.schemes.Consensus
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0.4545454745.5%
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jalview.ws.jws2.MsaWSClient
jalview.ws.jws2.MsaWSClient
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0.436241643.6%
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jalview.gui.ColourMenuHelper
jalview.gui.ColourMenuHelper
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0.4322033843.2%
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jalview.datamodel.HiddenCursorPosition
jalview.datamodel.HiddenCursorPosition
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0.4285714342.9%
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jalview.util.ShortcutKeyMaskExWrapper11
jalview.util.ShortcutKeyMaskExWrapper11
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0.4166666641.7%
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jalview.io.FileFormats
jalview.io.FileFormats
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0.440%
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jalview.ws.dbsources.EmblSource
jalview.ws.dbsources.EmblSource
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0.440%
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jalview.workers.AlignCalcManager
jalview.workers.AlignCalcManager
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0.3928571339.3%
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org.json.simple.parser.Yylex
org.json.simple.parser.Yylex
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0.3853503238.5%
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jalview.datamodel.Profile
jalview.datamodel.Profile
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0.37537.5%
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jalview.schemes.TCoffeeColourScheme
jalview.schemes.TCoffeeColourScheme
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0.3606557336.1%
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jalview.util.MessageManager
jalview.util.MessageManager
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0.3571428735.7%
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jalview.datamodel.ResidueCount
jalview.datamodel.ResidueCount
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0.3563636235.6%
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jalview.io.AlignFile
jalview.io.AlignFile
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0.356164435.6%
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jalview.io.FileLoader
jalview.io.FileLoader
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0.3511705735.1%
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jalview.schemes.IdColourScheme
jalview.schemes.IdColourScheme
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0.347826134.8%
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jalview.schemes.RNAHelicesColour
jalview.schemes.RNAHelicesColour
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0.3424657634.2%
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jalview.io.FastaFile
jalview.io.FastaFile
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0.315315331.5%
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jalview.ws.rest.RestServiceDescription
jalview.ws.rest.RestServiceDescription
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0.31531.5%
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jalview.util.Comparison
jalview.util.Comparison
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0.3110236231.1%
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org.json.simple.parser.JSONParser
org.json.simple.parser.JSONParser
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0.2945544429.5%
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jalview.viewmodel.styles.ViewStyle
jalview.viewmodel.styles.ViewStyle
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0.2929687529.3%
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jalview.ws.dbsources.EmblCdsSource
jalview.ws.dbsources.EmblCdsSource
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0.285714328.6%
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jalview.gui.AlignViewport
jalview.gui.AlignViewport
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0.2853881428.5%
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jalview.schemes.ColourSchemes
jalview.schemes.ColourSchemes
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0.2807017628.1%
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jalview.io.IdentifyFile
jalview.io.IdentifyFile
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0.279365127.9%
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jalview.ws.jws2.JabaPreset
jalview.ws.jws2.JabaPreset
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0.2727272827.3%
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jalview.gui.JvSwingUtils
jalview.gui.JvSwingUtils
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0.258503425.9%
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jalview.gui.AlignmentPanel
jalview.gui.AlignmentPanel
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0.2579505425.8%
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jalview.ws.jws2.jabaws2.Jws2Instance
jalview.ws.jws2.jabaws2.Jws2Instance
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0.2528735725.3%
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jalview.util.HttpUtils
jalview.util.HttpUtils
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0.2514619825.1%
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jalview.ws.uimodel.AlignAnalysisUIText
jalview.ws.uimodel.AlignAnalysisUIText
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0.2439024424.4%
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jalview.ws.rest.params.Alignment
jalview.ws.rest.params.Alignment
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0.2435897424.4%
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jalview.schemes.Blosum62ColourScheme
jalview.schemes.Blosum62ColourScheme
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0.2352941223.5%
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jalview.gui.PaintRefresher
jalview.gui.PaintRefresher
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0.2323943723.2%
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jalview.ws.jws2.Jws2Client
jalview.ws.jws2.Jws2Client
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0.2228915722.3%
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jalview.viewmodel.AlignmentViewport
jalview.viewmodel.AlignmentViewport
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0.2071320120.7%
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jalview.ws.rest.InputType
jalview.ws.rest.InputType
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0.2056074720.6%
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jalview.ws.jws2.SequenceAnnotationWSClient
jalview.ws.jws2.SequenceAnnotationWSClient
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0.2043010720.4%
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jalview.analysis.AAFrequency
jalview.analysis.AAFrequency
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0.1940928319.4%
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jalview.analysis.AnnotationSorter
jalview.analysis.AnnotationSorter
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0.1674876816.7%
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jalview.schemes.PIDColourScheme
jalview.schemes.PIDColourScheme
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0.1666666716.7%
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jalview.schemes.ColourSchemeProperty
jalview.schemes.ColourSchemeProperty
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0.1666666716.7%
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jalview.io.FileParse
jalview.io.FileParse
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0.164345416.4%
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jalview.ws.jws1.WS1Client
jalview.ws.jws1.WS1Client
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0.1616%
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jalview.gui.Desktop.MyDesktopManager
jalview.gui.Desktop.MyDesktopManager
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0.1555555615.6%
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jalview.util.Format
jalview.util.Format
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0.1490683314.9%
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jalview.io.JalviewFileChooser
jalview.io.JalviewFileChooser
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0.1389645813.9%
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jalview.viewmodel.ViewportRanges
jalview.viewmodel.ViewportRanges
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0.1287128812.9%
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jalview.datamodel.Alignment
jalview.datamodel.Alignment
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0.1275605312.8%
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jalview.ws.rest.params.SeqGroupIndexVector
jalview.ws.rest.params.SeqGroupIndexVector
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0.12408759412.4%
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jalview.gui.AlignFrame
jalview.gui.AlignFrame
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0.1228950212.3%
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jalview.io.FormatAdapter
jalview.io.FormatAdapter
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0.1212%
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jalview.analysis.scoremodels.ScoreModels
jalview.analysis.scoremodels.ScoreModels
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0.11538461611.5%
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jalview.ws.rest.RestClient
jalview.ws.rest.RestClient
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0.11538461611.5%
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jalview.ws.jws2.JabaWsServerQuery
jalview.ws.jws2.JabaWsServerQuery
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0.11458333611.5%
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jalview.datamodel.Annotation
jalview.datamodel.Annotation
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0.11428571511.4%
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jalview.util.StringUtils
jalview.util.StringUtils
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0.11239193411.2%
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jalview.util.ShortcutKeyMaskExWrapper
jalview.util.ShortcutKeyMaskExWrapper
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0.1111111111.1%
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jalview.io.FileFormat
jalview.io.FileFormat
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0.1085271310.9%
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jalview.ws.rest.params.AnnotationFile
jalview.ws.rest.params.AnnotationFile
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0.10256410410.3%
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jalview.io.AppletFormatAdapter
jalview.io.AppletFormatAdapter
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0.0993788849.9%
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org.json.simple.parser.Yytoken
org.json.simple.parser.Yytoken
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0.096774199.7%
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jalview.workers.AlignCalcWorker
jalview.workers.AlignCalcWorker
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0.09523819.5%
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jalview.datamodel.Sequence
jalview.datamodel.Sequence
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0.094290669.4%
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jalview.util.JSONUtils
jalview.util.JSONUtils
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0.090909099.1%
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jalview.ws.jws2.Jws2Discoverer
jalview.ws.jws2.Jws2Discoverer
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0.0871287148.7%
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jalview.ws.dbsources.Xfam
jalview.ws.dbsources.Xfam
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0.086956528.7%
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jalview.ext.ensembl.EnsemblSequenceFetcher
jalview.ext.ensembl.EnsemblSequenceFetcher
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0.0833333368.3%
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jalview.gui.ProgressBar
jalview.gui.ProgressBar
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0.081300818.1%
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jalview.gui.Console
jalview.gui.Console
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0.081081088.1%
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jalview.datamodel.AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation
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0.07757.8%
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jalview.gui.Desktop
jalview.gui.Desktop
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0.071184517.1%
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jalview.util.Platform
jalview.util.Platform
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0.0707547147.1%
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jalview.gui.IdPanel
jalview.gui.IdPanel
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0.067264576.7%
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jalview.log.JLogger
jalview.log.JLogger
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0.065934076.6%
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jalview.gui.IdwidthAdjuster
jalview.gui.IdwidthAdjuster
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0.0657894766.6%
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jalview.renderer.ResidueShader
jalview.renderer.ResidueShader
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0.064285726.4%
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jalview.analysis.CrossRef
jalview.analysis.CrossRef
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0.063524596.4%
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jalview.structure.StructureSelectionManager
jalview.structure.StructureSelectionManager
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0.062666676.3%
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jalview.analysis.scoremodels.ScoreMatrix
jalview.analysis.scoremodels.ScoreMatrix
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0.0617283966.2%
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ext.vamsas.ServiceHandle
ext.vamsas.ServiceHandle
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0.061224496.1%
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jalview.gui.ViewSelectionMenu
jalview.gui.ViewSelectionMenu
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0.059405945.9%
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jalview.ws.seqfetcher.ASequenceFetcher
jalview.ws.seqfetcher.ASequenceFetcher
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0.0577777775.8%
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jalview.ws.seqfetcher.DbSourceProxyImpl
jalview.ws.seqfetcher.DbSourceProxyImpl
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0.0540540555.4%
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jalview.gui.AnnotationPanel
jalview.gui.AnnotationPanel
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0.052521015.3%
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jalview.ws.jws1.Discoverer
jalview.ws.jws1.Discoverer
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0.0512820525.1%
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jalview.analysis.GeneticCodes
jalview.analysis.GeneticCodes
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0.0496894425%
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jalview.bin.Console
jalview.bin.Console
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0.0492610824.9%
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jalview.util.ColorUtils
jalview.util.ColorUtils
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0.0489296654.9%
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jalview.gui.Desktop.MyDesktopPane
jalview.gui.Desktop.MyDesktopPane
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0.047619054.8%
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jalview.util.DBRefUtils
jalview.util.DBRefUtils
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0.045317224.5%
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jalview.ws.dbsources.Pdb
jalview.ws.dbsources.Pdb
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0.042553194.3%
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jalview.ws.jws2.JabaParamStore
jalview.ws.jws2.JabaParamStore
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0.0416666684.2%
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jalview.bin.Cache
jalview.bin.Cache
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0.038461543.8%
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org.json.simple.JSONObject
org.json.simple.JSONObject
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0.037735853.8%
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jalview.datamodel.ColumnSelection.IntList
jalview.datamodel.ColumnSelection.IntList
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0.0373831763.7%
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jalview.ws.jws1.JPredClient
jalview.ws.jws1.JPredClient
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0.0310559013.1%
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jalview.gui.IdCanvas
jalview.gui.IdCanvas
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0.0245614032.5%
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jalview.renderer.ResidueColourFinder
jalview.renderer.ResidueColourFinder
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0.0238095242.4%
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jalview.gui.ScalePanel
jalview.gui.ScalePanel
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0.02343752.3%
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jalview.datamodel.HiddenColumnsCursor
jalview.datamodel.HiddenColumnsCursor
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0.0156251.6%
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jalview.ws.dbsources.Uniprot
jalview.ws.dbsources.Uniprot
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0.0155642021.6%
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jalview.gui.SequenceRenderer
jalview.gui.SequenceRenderer
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0.0144230771.4%
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jalview.controller.AlignViewController
jalview.controller.AlignViewController
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0.0136518771.4%
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jalview.analysis.AlignSeq
jalview.analysis.AlignSeq
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0.0128205131.3%
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jalview.datamodel.features.SequenceFeatures
jalview.datamodel.features.SequenceFeatures
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0.0127388541.3%
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jalview.gui.SeqPanel
jalview.gui.SeqPanel
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0.0125412541.3%
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jalview.io.SequenceAnnotationReport
jalview.io.SequenceAnnotationReport
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0.0122699381.2%
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jalview.renderer.AnnotationRenderer
jalview.renderer.AnnotationRenderer
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0.0117753621.2%
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jalview.gui.AnnotationLabels
jalview.gui.AnnotationLabels
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0.01150747951.2%
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jalview.datamodel.HiddenSequences
jalview.datamodel.HiddenSequences
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0.009132420.9%
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jalview.gui.SequenceFetcher
jalview.gui.SequenceFetcher
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0.0089285720.9%
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jalview.ext.ensembl.EnsemblGene
jalview.ext.ensembl.EnsemblGene
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0.0081632650.8%
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jalview.bin.Jalview
jalview.bin.Jalview
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0.0081227440.8%
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org.json.simple.JSONArray
org.json.simple.JSONArray
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0.0080645160.8%
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jalview.gui.SeqCanvas
jalview.gui.SeqCanvas
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0.0080160320.8%
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jalview.renderer.seqfeatures.FeatureRenderer
jalview.renderer.seqfeatures.FeatureRenderer
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0.007547170.8%
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jalview.gui.QuitHandler
jalview.gui.QuitHandler
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0.00722021660.7%
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jalview.datamodel.HiddenColumns
jalview.datamodel.HiddenColumns
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0.0070754720.7%
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jalview.datamodel.ColumnSelection
jalview.datamodel.ColumnSelection
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0.00343642620.3%
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