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com.stevesoft.pat.patInf
com.stevesoft.pat.patInf
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1.0100%
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com.stevesoft.pat.FastChar
com.stevesoft.pat.FastChar
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1.0100%
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jalview.io.DataSourceType
jalview.io.DataSourceType
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1.0100%
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jalview.xml.binding.jalview.AnnotationElement
jalview.xml.binding.jalview.AnnotationElement
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1.0100%
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jalview.xml.binding.jalview.SequenceType
jalview.xml.binding.jalview.SequenceType
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1.0100%
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jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties
jalview.xml.binding.jalview.SequenceSet.SequenceSetProperties
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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.project.Jalview2XML.JvAnnotRow
jalview.project.Jalview2XML.JvAnnotRow
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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.jbgui.GAlignmentPanel
jalview.jbgui.GAlignmentPanel
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0.9494%
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jalview.io.BackupFilenameFilter
jalview.io.BackupFilenameFilter
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0.928571492.9%
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jalview.xml.binding.jalview.SequenceSet
jalview.xml.binding.jalview.SequenceSet
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0.9210526392.1%
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com.stevesoft.pat.OrMark
com.stevesoft.pat.OrMark
|
0.990%
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jalview.analysis.Conservation
jalview.analysis.Conservation
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0.8620689586.2%
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jalview.datamodel.AlignmentAnnotation.AnnotCharSequence
jalview.datamodel.AlignmentAnnotation.AnnotCharSequence
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0.851851985.2%
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jalview.xml.binding.jalview.JalviewModel.Viewport
jalview.xml.binding.jalview.JalviewModel.Viewport
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0.8514492585.1%
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jalview.viewmodel.styles.ViewStyle
jalview.viewmodel.styles.ViewStyle
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0.8476562584.8%
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com.stevesoft.pat.Rthings
com.stevesoft.pat.Rthings
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0.8461538684.6%
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jalview.xml.binding.jalview.Annotation
jalview.xml.binding.jalview.Annotation
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0.809090980.9%
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com.stevesoft.pat.SubMark
com.stevesoft.pat.SubMark
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0.880%
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com.stevesoft.pat.StrPos
com.stevesoft.pat.StrPos
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0.779069877.9%
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com.stevesoft.pat.Skip2
com.stevesoft.pat.Skip2
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0.777777877.8%
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jalview.util.LinkedIdentityHashSet
jalview.util.LinkedIdentityHashSet
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0.7727272577.3%
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jalview.xml.binding.jalview.JalviewModel
jalview.xml.binding.jalview.JalviewModel
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0.769230876.9%
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com.stevesoft.pat.FastBracket
com.stevesoft.pat.FastBracket
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0.7544910375.4%
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com.stevesoft.pat.Bracket
com.stevesoft.pat.Bracket
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0.7575%
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jalview.xml.binding.jalview.JalviewModel.JSeq
jalview.xml.binding.jalview.JalviewModel.JSeq
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0.7575%
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jalview.xml.binding.jalview.Sequence.DBRef
jalview.xml.binding.jalview.Sequence.DBRef
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0.7575%
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jalview.io.BackupFilesPresetEntry
jalview.io.BackupFilesPresetEntry
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0.735294173.5%
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jalview.datamodel.Profiles
jalview.datamodel.Profiles
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0.7333333573.3%
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jalview.analysis.Rna
jalview.analysis.Rna
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0.7272%
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jalview.gui.FeatureRenderer
jalview.gui.FeatureRenderer
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0.7142857371.4%
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jalview.xml.binding.jalview.Sequence
jalview.xml.binding.jalview.Sequence
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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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com.stevesoft.pat.oneChar
com.stevesoft.pat.oneChar
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0.685714368.6%
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jalview.ws.SequenceFetcher
jalview.ws.SequenceFetcher
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0.678571467.9%
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com.stevesoft.pat.patInt
com.stevesoft.pat.patInt
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0.662566.3%
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jalview.schemes.ColourSchemeProperty
jalview.schemes.ColourSchemeProperty
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0.638888963.9%
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com.stevesoft.pat.Range
com.stevesoft.pat.Range
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0.636363663.6%
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com.stevesoft.pat.wrap.StringWrap
com.stevesoft.pat.wrap.StringWrap
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0.62562.5%
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com.stevesoft.pat.FastMulti
com.stevesoft.pat.FastMulti
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0.620370462%
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jalview.workers.StrucConsensusThread
jalview.workers.StrucConsensusThread
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0.660%
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com.stevesoft.pat.Or
com.stevesoft.pat.Or
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0.589743659%
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com.stevesoft.pat.Pattern
com.stevesoft.pat.Pattern
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0.583333358.3%
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jalview.jbgui.GAlignFrame
jalview.jbgui.GAlignFrame
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0.581220758.1%
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jalview.analysis.StructureFrequency
jalview.analysis.StructureFrequency
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0.580524358.1%
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com.stevesoft.pat.Start
com.stevesoft.pat.Start
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0.5454545654.5%
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jalview.schemes.RNAHelicesColour
jalview.schemes.RNAHelicesColour
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0.5342465653.4%
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com.stevesoft.pat.RegOpt
com.stevesoft.pat.RegOpt
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0.5251798652.5%
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jalview.gui.ColourMenuHelper
jalview.gui.ColourMenuHelper
|
0.550%
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jalview.gui.JalviewChangeSupport
jalview.gui.JalviewChangeSupport
|
0.550%
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com.stevesoft.pat.NullPattern
com.stevesoft.pat.NullPattern
|
0.550%
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jalview.viewmodel.ViewportProperties
jalview.viewmodel.ViewportProperties
|
0.550%
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jalview.xml.binding.jalview.VAMSAS
jalview.xml.binding.jalview.VAMSAS
|
0.550%
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jalview.schemes.TaylorColourScheme
jalview.schemes.TaylorColourScheme
|
0.550%
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jalview.schemes.FlowerColourScheme
jalview.schemes.FlowerColourScheme
|
0.550%
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jalview.schemes.ZappoColourScheme
jalview.schemes.ZappoColourScheme
|
0.550%
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jalview.schemes.NucleotideAmbiguityColourScheme
jalview.schemes.NucleotideAmbiguityColourScheme
|
0.550%
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jalview.schemes.PurinePyrimidineColourScheme
jalview.schemes.PurinePyrimidineColourScheme
|
0.550%
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jalview.schemes.NucleotideColourScheme
jalview.schemes.NucleotideColourScheme
|
0.550%
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jalview.schemes.BlossomColourScheme
jalview.schemes.BlossomColourScheme
|
0.550%
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jalview.schemes.SunsetColourScheme
jalview.schemes.SunsetColourScheme
|
0.550%
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jalview.schemes.OceanColourScheme
jalview.schemes.OceanColourScheme
|
0.550%
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jalview.analysis.SecStrConsensus.SimpleBP
jalview.analysis.SecStrConsensus.SimpleBP
|
0.550%
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jalview.io.AlignFile
jalview.io.AlignFile
|
0.4931506849.3%
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jalview.util.MessageManager
jalview.util.MessageManager
|
0.4761904847.6%
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com.stevesoft.pat.Branch
com.stevesoft.pat.Branch
|
0.4630872646.3%
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jalview.io.FileLoader
jalview.io.FileLoader
|
0.4615384646.2%
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com.stevesoft.pat.Skip
com.stevesoft.pat.Skip
|
0.4594594545.9%
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jalview.workers.ConservationThread
jalview.workers.ConservationThread
|
0.4482758644.8%
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jalview.ws.jws2.MsaWSClient
jalview.ws.jws2.MsaWSClient
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0.4429530244.3%
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jalview.workers.AlignCalcManager
jalview.workers.AlignCalcManager
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0.4404761844%
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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
|
0.4166666641.7%
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jalview.io.StockholmFile
jalview.io.StockholmFile
|
0.406417140.6%
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jalview.schemes.ResidueColourScheme
jalview.schemes.ResidueColourScheme
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0.404761940.5%
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jalview.io.FileFormats
jalview.io.FileFormats
|
0.440%
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jalview.ws.dbsources.EmblSource
jalview.ws.dbsources.EmblSource
|
0.440%
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jalview.schemes.HydrophobicColourScheme
jalview.schemes.HydrophobicColourScheme
|
0.440%
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jalview.schemes.HelixColourScheme
jalview.schemes.HelixColourScheme
|
0.440%
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jalview.schemes.TurnColourScheme
jalview.schemes.TurnColourScheme
|
0.440%
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jalview.schemes.StrandColourScheme
jalview.schemes.StrandColourScheme
|
0.440%
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jalview.schemes.BuriedColourScheme
jalview.schemes.BuriedColourScheme
|
0.440%
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com.stevesoft.pat.Regex
com.stevesoft.pat.Regex
|
0.392727339.3%
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jalview.datamodel.ResidueCount
jalview.datamodel.ResidueCount
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0.3854545438.5%
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jalview.datamodel.Profile
jalview.datamodel.Profile
|
0.37537.5%
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jalview.datamodel.AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation
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0.37537.5%
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jalview.io.BackupFilenameParts
jalview.io.BackupFilenameParts
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0.3648648636.5%
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jalview.gui.AlignViewport
jalview.gui.AlignViewport
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0.3447488534.5%
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jalview.viewmodel.AlignmentViewport
jalview.viewmodel.AlignmentViewport
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0.3406676734.1%
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jalview.io.Jalview2xmlBase
jalview.io.Jalview2xmlBase
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0.3333333433.3%
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jalview.gui.AlignmentPanel
jalview.gui.AlignmentPanel
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0.3309776233.1%
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jalview.util.Format
jalview.util.Format
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0.3209109632.1%
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jalview.ws.rest.RestServiceDescription
jalview.ws.rest.RestServiceDescription
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0.31531.5%
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com.stevesoft.pat.End
com.stevesoft.pat.End
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0.3103448231%
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jalview.project.Jalview2XML
jalview.project.Jalview2XML
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0.3079495730.8%
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com.stevesoft.pat.DotMulti
com.stevesoft.pat.DotMulti
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0.2971014429.7%
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jalview.io.BackupFiles
jalview.io.BackupFiles
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0.29229.2%
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jalview.ws.jws2.SequenceAnnotationWSClient
jalview.ws.jws2.SequenceAnnotationWSClient
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0.2903225729%
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jalview.viewmodel.ViewportRanges
jalview.viewmodel.ViewportRanges
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0.2871287228.7%
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jalview.ws.dbsources.EmblCdsSource
jalview.ws.dbsources.EmblCdsSource
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0.285714328.6%
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jalview.datamodel.Annotation
jalview.datamodel.Annotation
|
0.285714328.6%
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jalview.schemes.JalviewColourScheme
jalview.schemes.JalviewColourScheme
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0.285714328.6%
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jalview.datamodel.Sequence
jalview.datamodel.Sequence
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0.276816627.7%
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jalview.ws.jws2.JabaPreset
jalview.ws.jws2.JabaPreset
|
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.io.IdentifyFile
jalview.io.IdentifyFile
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0.2571428725.7%
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jalview.gui.PaintRefresher
jalview.gui.PaintRefresher
|
0.253521125.4%
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jalview.ws.jws2.jabaws2.Jws2Instance
jalview.ws.jws2.jabaws2.Jws2Instance
|
0.2528735725.3%
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jalview.io.FileParse
jalview.io.FileParse
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0.250696425.1%
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com.stevesoft.pat.StringRule
com.stevesoft.pat.StringRule
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0.2525%
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jalview.datamodel.DBRefEntry
jalview.datamodel.DBRefEntry
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0.2465753424.7%
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jalview.schemes.ColourSchemes
jalview.schemes.ColourSchemes
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0.2456140424.6%
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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.ws.jws2.Jws2Discoverer
jalview.ws.jws2.Jws2Discoverer
|
0.2336633723.4%
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jalview.datamodel.SequenceCursor
jalview.datamodel.SequenceCursor
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0.2333333323.3%
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jalview.ws.jws2.Jws2Client
jalview.ws.jws2.Jws2Client
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0.2228915722.3%
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jalview.util.Comparison
jalview.util.Comparison
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0.2204724422%
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com.stevesoft.pat.RegRes
com.stevesoft.pat.RegRes
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0.217391321.7%
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jalview.ws.rest.InputType
jalview.ws.rest.InputType
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0.2056074720.6%
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jalview.analysis.AAFrequency
jalview.analysis.AAFrequency
|
0.2046413620.5%
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jalview.datamodel.Alignment
jalview.datamodel.Alignment
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0.2001862220%
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jalview.analysis.AnnotationSorter
jalview.analysis.AnnotationSorter
|
0.1970443319.7%
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jalview.util.QuickSort
jalview.util.QuickSort
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0.1877022718.8%
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jalview.schemes.IdColourScheme
jalview.schemes.IdColourScheme
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0.1739130517.4%
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jalview.renderer.ResidueShader
jalview.renderer.ResidueShader
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0.1714285817.1%
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jalview.ws.jws1.WS1Client
jalview.ws.jws1.WS1Client
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0.1616%
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com.stevesoft.pat.parsePerl
com.stevesoft.pat.parsePerl
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0.1598639516%
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jalview.gui.Desktop.MyDesktopManager
jalview.gui.Desktop.MyDesktopManager
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0.1555555615.6%
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jalview.schemes.TCoffeeColourScheme
jalview.schemes.TCoffeeColourScheme
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0.1475409914.8%
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jalview.gui.AlignFrame
jalview.gui.AlignFrame
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0.1461841614.6%
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jalview.gui.Desktop.MyDesktopPane
jalview.gui.Desktop.MyDesktopPane
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0.1428571514.3%
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jalview.util.DBRefUtils
jalview.util.DBRefUtils
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0.1419939514.2%
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jalview.bin.Console
jalview.bin.Console
|
0.1330049213.3%
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jalview.analysis.CrossRef
jalview.analysis.CrossRef
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0.1270491812.7%
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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.datamodel.features.SequenceFeatures
jalview.datamodel.features.SequenceFeatures
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0.1210191112.1%
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jalview.io.FormatAdapter
jalview.io.FormatAdapter
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0.1212%
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jalview.schemes.Blosum62ColourScheme
jalview.schemes.Blosum62ColourScheme
|
0.1176470611.8%
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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
|
0.11538461611.5%
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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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jalview.gui.Desktop
jalview.gui.Desktop
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0.099088849.9%
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jalview.workers.AlignCalcWorker
jalview.workers.AlignCalcWorker
|
0.09523819.5%
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jalview.util.StringUtils
jalview.util.StringUtils
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0.092219029.2%
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jalview.log.JLogger
jalview.log.JLogger
|
0.087912098.8%
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com.stevesoft.pat.ReplaceRule
com.stevesoft.pat.ReplaceRule
|
0.08771938.8%
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jalview.ws.dbsources.Xfam
jalview.ws.dbsources.Xfam
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0.086956528.7%
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jalview.util.ColorUtils
jalview.util.ColorUtils
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0.085626918.6%
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jalview.ext.ensembl.EnsemblSequenceFetcher
jalview.ext.ensembl.EnsemblSequenceFetcher
|
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
|
0.081081088.1%
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jalview.gui.IdPanel
jalview.gui.IdPanel
|
0.067264576.7%
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jalview.schemes.PIDColourScheme
jalview.schemes.PIDColourScheme
|
0.066666676.7%
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jalview.gui.IdwidthAdjuster
jalview.gui.IdwidthAdjuster
|
0.0657894766.6%
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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
|
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.AnnotationPanel
jalview.gui.AnnotationPanel
|
0.060924376.1%
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jalview.gui.IdCanvas
jalview.gui.IdCanvas
|
0.059649126%
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jalview.gui.ViewSelectionMenu
jalview.gui.ViewSelectionMenu
|
0.059405945.9%
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jalview.ws.seqfetcher.ASequenceFetcher
jalview.ws.seqfetcher.ASequenceFetcher
|
0.0577777775.8%
|
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jalview.datamodel.SequenceFeature
jalview.datamodel.SequenceFeature
|
0.057553965.8%
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jalview.util.Platform
jalview.util.Platform
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0.0566037745.7%
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jalview.ws.seqfetcher.DbSourceProxyImpl
jalview.ws.seqfetcher.DbSourceProxyImpl
|
0.0540540555.4%
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jalview.ws.jws1.Discoverer
jalview.ws.jws1.Discoverer
|
0.0512820525.1%
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jalview.analysis.GeneticCodes
jalview.analysis.GeneticCodes
|
0.0496894425%
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jalview.bin.Cache
jalview.bin.Cache
|
0.0480769244.8%
|
|
|
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.datamodel.ColumnSelection.IntList
jalview.datamodel.ColumnSelection.IntList
|
0.0373831763.7%
|
|
|
jalview.gui.ScalePanel
jalview.gui.ScalePanel
|
0.035156253.5%
|
|
|
jalview.ws.jws1.JPredClient
jalview.ws.jws1.JPredClient
|
0.0310559013.1%
|
|
|
jalview.datamodel.HiddenSequences
jalview.datamodel.HiddenSequences
|
0.027397262.7%
|
|
|
jalview.gui.SeqCanvas
jalview.gui.SeqCanvas
|
0.0270541092.7%
|
|
|
jalview.renderer.ResidueColourFinder
jalview.renderer.ResidueColourFinder
|
0.0238095242.4%
|
|
|
jalview.datamodel.HiddenColumns
jalview.datamodel.HiddenColumns
|
0.0188679251.9%
|
|
|
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.SequenceRenderer
jalview.gui.SequenceRenderer
|
0.0144230771.4%
|
|
|
jalview.controller.AlignViewController
jalview.controller.AlignViewController
|
0.0136518771.4%
|
|
|
jalview.datamodel.SearchResults
jalview.datamodel.SearchResults
|
0.0128205131.3%
|
|
|
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.renderer.AnnotationRenderer
jalview.renderer.AnnotationRenderer
|
0.0117753621.2%
|
|
|
jalview.bin.Jalview
jalview.bin.Jalview
|
0.0117328521.2%
|
|
|
jalview.util.HttpUtils
jalview.util.HttpUtils
|
0.01169590651.2%
|
|
|
jalview.gui.AnnotationLabels
jalview.gui.AnnotationLabels
|
0.01150747951.2%
|
|
|
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.analysis.AlignmentUtils
jalview.analysis.AlignmentUtils
|
0.0080409360.8%
|
|
|
jalview.gui.PCAPanel
jalview.gui.PCAPanel
|
0.0080321280.8%
|
|
|
jalview.schemes.ResidueProperties
jalview.schemes.ResidueProperties
|
0.0078781520.8%
|
|
|
jalview.renderer.seqfeatures.FeatureRenderer
jalview.renderer.seqfeatures.FeatureRenderer
|
0.007547170.8%
|
|
|
jalview.gui.QuitHandler
jalview.gui.QuitHandler
|
0.00722021660.7%
|
|
|
jalview.datamodel.ColumnSelection
jalview.datamodel.ColumnSelection
|
0.00343642620.3%
|
|
|
com.stevesoft.pat.CaseMgr
com.stevesoft.pat.CaseMgr
|
0.00278551530.3%
|
|
