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com.stevesoft.pat.patInf
com.stevesoft.pat.patInf
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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.renderer.ScaleRenderer.ScaleMark
jalview.renderer.ScaleRenderer.ScaleMark
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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
|
1.0100%
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jalview.structure.StructureImportSettings.TFType
jalview.structure.StructureImportSettings.TFType
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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.analysis.Conservation
jalview.analysis.Conservation
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0.8793103787.9%
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com.stevesoft.pat.Rthings
com.stevesoft.pat.Rthings
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0.8461538684.6%
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mc_view.Residue
mc_view.Residue
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0.8461538684.6%
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jalview.datamodel.Profiles
jalview.datamodel.Profiles
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0.833333383.3%
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jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder
jalview.datamodel.annotations.AlphaFoldAnnotationRowBuilder
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0.8260869482.6%
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jalview.util.LinkedIdentityHashSet
jalview.util.LinkedIdentityHashSet
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0.7727272577.3%
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jalview.schemes.ZappoColourScheme
jalview.schemes.ZappoColourScheme
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0.7575%
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jalview.fts.core.FTSDataColumnPreferences
jalview.fts.core.FTSDataColumnPreferences
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0.745762774.6%
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jalview.workers.SecondaryStructureConsensusThread
jalview.workers.SecondaryStructureConsensusThread
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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.util.MapUtils
jalview.util.MapUtils
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0.695652269.6%
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jalview.ws.SequenceFetcher
jalview.ws.SequenceFetcher
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0.678571467.9%
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jalview.datamodel.Profile
jalview.datamodel.Profile
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0.672131167.2%
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jalview.util.ParseHtmlBodyAndLinks
jalview.util.ParseHtmlBodyAndLinks
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0.594202959.4%
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jalview.jbgui.GAlignFrame
jalview.jbgui.GAlignFrame
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0.57354357.4%
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jalview.workers.ConservationThread
jalview.workers.ConservationThread
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0.568965556.9%
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jalview.renderer.ScaleRenderer
jalview.renderer.ScaleRenderer
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0.5656%
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jalview.gui.AssociatePdbFileWithSeq
jalview.gui.AssociatePdbFileWithSeq
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0.5555%
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mc_view.PDBChain
mc_view.PDBChain
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0.5357142753.6%
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jalview.ext.jmol.JmolParser
jalview.ext.jmol.JmolParser
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0.5253333452.5%
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com.stevesoft.pat.StrPos
com.stevesoft.pat.StrPos
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0.523255852.3%
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jalview.workers.AlignCalcManager
jalview.workers.AlignCalcManager
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0.511904851.2%
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jalview.jbgui.GStructureChooser
jalview.jbgui.GStructureChooser
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0.5024752650.2%
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jalview.viewmodel.ViewportProperties
jalview.viewmodel.ViewportProperties
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0.550%
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mc_view.Bond
mc_view.Bond
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0.550%
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jalview.datamodel.ContactMapHolder
jalview.datamodel.ContactMapHolder
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0.550%
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jalview.schemes.TaylorColourScheme
jalview.schemes.TaylorColourScheme
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0.550%
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jalview.schemes.FlowerColourScheme
jalview.schemes.FlowerColourScheme
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0.550%
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jalview.schemes.NucleotideAmbiguityColourScheme
jalview.schemes.NucleotideAmbiguityColourScheme
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0.550%
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jalview.schemes.PurinePyrimidineColourScheme
jalview.schemes.PurinePyrimidineColourScheme
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0.550%
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jalview.schemes.NucleotideColourScheme
jalview.schemes.NucleotideColourScheme
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0.550%
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jalview.schemes.BlossomColourScheme
jalview.schemes.BlossomColourScheme
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0.550%
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jalview.schemes.SunsetColourScheme
jalview.schemes.SunsetColourScheme
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0.550%
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jalview.schemes.OceanColourScheme
jalview.schemes.OceanColourScheme
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0.550%
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jalview.io.AlignFile
jalview.io.AlignFile
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0.4589041245.9%
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jalview.ws.jws2.MsaWSClient
jalview.ws.jws2.MsaWSClient
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0.4429530244.3%
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jalview.io.FileLoader
jalview.io.FileLoader
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0.438127143.8%
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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.schemes.ResidueColourScheme
jalview.schemes.ResidueColourScheme
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0.4285714342.9%
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jalview.io.StructureFile
jalview.io.StructureFile
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0.42790742.8%
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jalview.analysis.AlignSeq
jalview.analysis.AlignSeq
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0.4256410342.6%
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jalview.util.ShortcutKeyMaskExWrapper11
jalview.util.ShortcutKeyMaskExWrapper11
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0.4166666641.7%
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jalview.datamodel.annotations.AnnotationRowBuilder
jalview.datamodel.annotations.AnnotationRowBuilder
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0.4102564241%
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jalview.gui.SequenceRenderer
jalview.gui.SequenceRenderer
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0.4086538640.9%
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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.schemes.HydrophobicColourScheme
jalview.schemes.HydrophobicColourScheme
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0.440%
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jalview.schemes.HelixColourScheme
jalview.schemes.HelixColourScheme
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0.440%
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jalview.schemes.TurnColourScheme
jalview.schemes.TurnColourScheme
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0.440%
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jalview.schemes.StrandColourScheme
jalview.schemes.StrandColourScheme
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0.440%
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jalview.schemes.BuriedColourScheme
jalview.schemes.BuriedColourScheme
|
0.440%
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org.json.simple.parser.Yylex
org.json.simple.parser.Yylex
|
0.3980891739.8%
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jalview.datamodel.ResidueCount
jalview.datamodel.ResidueCount
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0.389090938.9%
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jalview.datamodel.FloatContactMatrix
jalview.datamodel.FloatContactMatrix
|
0.3838%
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jalview.util.Format
jalview.util.Format
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0.3685300436.9%
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jalview.datamodel.AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation
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0.367041236.7%
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jalview.datamodel.PDBEntry
jalview.datamodel.PDBEntry
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0.365217436.5%
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jalview.ws.datamodel.alphafold.PAEContactMatrix
jalview.ws.datamodel.alphafold.PAEContactMatrix
|
0.3628318636.3%
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jalview.io.FastaFile
jalview.io.FastaFile
|
0.3603603536%
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jalview.util.MessageManager
jalview.util.MessageManager
|
0.3571428735.7%
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jalview.jbgui.GStructureChooser.AssociateSeqPanel
jalview.jbgui.GStructureChooser.AssociateSeqPanel
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0.352941235.3%
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jalview.util.Comparison
jalview.util.Comparison
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0.350393735%
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jalview.datamodel.Annotation
jalview.datamodel.Annotation
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0.3428571534.3%
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jalview.analysis.AAFrequency
jalview.analysis.AAFrequency
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0.3395061834%
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jalview.viewmodel.styles.ViewStyle
jalview.viewmodel.styles.ViewStyle
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0.3369565333.7%
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jalview.gui.IdwidthAdjuster
jalview.gui.IdwidthAdjuster
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0.3289473732.9%
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jalview.datamodel.Sequence
jalview.datamodel.Sequence
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0.325259532.5%
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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.oneChar
com.stevesoft.pat.oneChar
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0.3142857331.4%
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jalview.viewmodel.ViewportRanges
jalview.viewmodel.ViewportRanges
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0.3135313431.4%
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jalview.gui.AlignViewport
jalview.gui.AlignViewport
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0.3036529730.4%
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jalview.gui.AlignmentPanel
jalview.gui.AlignmentPanel
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0.3027090730.3%
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jalview.ws.jws2.SequenceAnnotationWSClient
jalview.ws.jws2.SequenceAnnotationWSClient
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0.2903225729%
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jalview.ws.dbsources.EmblCdsSource
jalview.ws.dbsources.EmblCdsSource
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0.285714328.6%
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jalview.renderer.ResidueColourFinder
jalview.renderer.ResidueColourFinder
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0.285714328.6%
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jalview.schemes.JalviewColourScheme
jalview.schemes.JalviewColourScheme
|
0.285714328.6%
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org.json.simple.parser.JSONParser
org.json.simple.parser.JSONParser
|
0.2846534628.5%
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mc_view.Atom
mc_view.Atom
|
0.282051328.2%
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jalview.gui.IdCanvas
jalview.gui.IdCanvas
|
0.2807017628.1%
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jalview.gui.structurechooser.StructureChooserQuerySource
jalview.gui.structurechooser.StructureChooserQuerySource
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0.2828%
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jalview.io.IdentifyFile
jalview.io.IdentifyFile
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0.279365127.9%
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jalview.io.FileParse
jalview.io.FileParse
|
0.2785515227.9%
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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.structure.StructureSelectionManager
jalview.structure.StructureSelectionManager
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0.254150725.4%
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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.gui.JalviewChangeSupport
jalview.gui.JalviewChangeSupport
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0.2525%
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jalview.renderer.AnnotationRendererFactory
jalview.renderer.AnnotationRendererFactory
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0.2525%
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jalview.viewmodel.AlignmentViewport
jalview.viewmodel.AlignmentViewport
|
0.2460545224.6%
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jalview.ws.uimodel.AlignAnalysisUIText
jalview.ws.uimodel.AlignAnalysisUIText
|
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.gui.PaintRefresher
jalview.gui.PaintRefresher
|
0.2323943723.2%
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com.stevesoft.pat.Range
com.stevesoft.pat.Range
|
0.2272727322.7%
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com.stevesoft.pat.Bracket
com.stevesoft.pat.Bracket
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0.22522.5%
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jalview.datamodel.features.FeatureAttributes
jalview.datamodel.features.FeatureAttributes
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0.224806222.5%
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jalview.ws.jws2.Jws2Client
jalview.ws.jws2.Jws2Client
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0.2228915722.3%
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jalview.log.JalviewAppender
jalview.log.JalviewAppender
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0.2222222222.2%
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jalview.renderer.AnnotationRenderer
jalview.renderer.AnnotationRenderer
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0.2214285722.1%
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jalview.datamodel.features.FeatureStore
jalview.datamodel.features.FeatureStore
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0.220543822.1%
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jalview.util.MapList
jalview.util.MapList
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0.2149532721.5%
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jalview.gui.ScalePanel
jalview.gui.ScalePanel
|
0.2148437521.5%
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jalview.datamodel.features.FeatureAttributes.AttributeData
jalview.datamodel.features.FeatureAttributes.AttributeData
|
0.2127659621.3%
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jalview.analysis.scoremodels.ScoreModels
jalview.analysis.scoremodels.ScoreModels
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0.2115384621.2%
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com.stevesoft.pat.Regex
com.stevesoft.pat.Regex
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0.2072727220.7%
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jalview.ws.rest.InputType
jalview.ws.rest.InputType
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0.2056074720.6%
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jalview.datamodel.SequenceFeature
jalview.datamodel.SequenceFeature
|
0.2014388420.1%
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jalview.gui.AnnotationLabels
jalview.gui.AnnotationLabels
|
0.1993464119.9%
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jalview.analysis.AnnotationSorter
jalview.analysis.AnnotationSorter
|
0.1970443319.7%
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jalview.ws.datamodel.alphafold.MappableContactMatrix
jalview.ws.datamodel.alphafold.MappableContactMatrix
|
0.1924686119.2%
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jalview.datamodel.features.SequenceFeatures
jalview.datamodel.features.SequenceFeatures
|
0.191082819.1%
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jalview.fts.core.FTSDataColumnPreferences.FTSDataColumnPrefsTableModel
jalview.fts.core.FTSDataColumnPreferences.FTSDataColumnPrefsTableModel
|
0.1857142918.6%
|
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com.stevesoft.pat.Pattern
com.stevesoft.pat.Pattern
|
0.1805555518.1%
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com.stevesoft.pat.patInt
com.stevesoft.pat.patInt
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0.17517.5%
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jalview.schemes.IdColourScheme
jalview.schemes.IdColourScheme
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0.1739130517.4%
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jalview.jbgui.GStructureChooser.CustomComboSeparatorsRenderer
jalview.jbgui.GStructureChooser.CustomComboSeparatorsRenderer
|
0.1666666716.7%
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jalview.ws.jws1.WS1Client
jalview.ws.jws1.WS1Client
|
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.schemes.TCoffeeColourScheme
jalview.schemes.TCoffeeColourScheme
|
0.1475409914.8%
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jalview.fts.core.FTSRestClient
jalview.fts.core.FTSRestClient
|
0.1467181414.7%
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jalview.datamodel.Alignment
jalview.datamodel.Alignment
|
0.145251414.5%
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jalview.gui.Desktop.MyDesktopPane
jalview.gui.Desktop.MyDesktopPane
|
0.1428571514.3%
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jalview.io.AppletFormatAdapter
jalview.io.AppletFormatAdapter
|
0.1428571514.3%
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jalview.ws.dbsources.EBIAlfaFold
jalview.ws.dbsources.EBIAlfaFold
|
0.1417910514.2%
|
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jalview.gui.AnnotationPanel
jalview.gui.AnnotationPanel
|
0.1305285813.1%
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jalview.ws.rest.params.SeqGroupIndexVector
jalview.ws.rest.params.SeqGroupIndexVector
|
0.12408759412.4%
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jalview.io.FormatAdapter
jalview.io.FormatAdapter
|
0.1212%
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jalview.util.StringUtils
jalview.util.StringUtils
|
0.1212%
|
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jalview.gui.AlignFrame
jalview.gui.AlignFrame
|
0.11919831511.9%
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jalview.schemes.Blosum62ColourScheme
jalview.schemes.Blosum62ColourScheme
|
0.1176470611.8%
|
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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
|
0.1111111111.1%
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jalview.ws.sifts.SiftsSettings
jalview.ws.sifts.SiftsSettings
|
0.1111111111.1%
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jalview.schemes.ColourSchemeProperty
jalview.schemes.ColourSchemeProperty
|
0.1111111111.1%
|
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jalview.io.FileFormat
jalview.io.FileFormat
|
0.1085271310.9%
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jalview.util.Platform
jalview.util.Platform
|
0.10849056410.8%
|
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jalview.util.QuickSort
jalview.util.QuickSort
|
0.10679611610.7%
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jalview.datamodel.Mapping
jalview.datamodel.Mapping
|
0.10389610410.4%
|
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jalview.analysis.scoremodels.ScoreMatrix
jalview.analysis.scoremodels.ScoreMatrix
|
0.1028806610.3%
|
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jalview.ws.rest.params.AnnotationFile
jalview.ws.rest.params.AnnotationFile
|
0.10256410410.3%
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com.stevesoft.pat.parsePerl
com.stevesoft.pat.parsePerl
|
0.098639469.9%
|
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org.json.simple.parser.Yytoken
org.json.simple.parser.Yytoken
|
0.096774199.7%
|
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jalview.util.ColorUtils
jalview.util.ColorUtils
|
0.096774199.7%
|
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jalview.workers.AlignCalcWorker
jalview.workers.AlignCalcWorker
|
0.09523819.5%
|
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jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient
jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient
|
0.093759.4%
|
|
|
jalview.gui.SeqCanvas
jalview.gui.SeqCanvas
|
0.093186379.3%
|
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com.stevesoft.pat.Or
com.stevesoft.pat.Or
|
0.089743599%
|
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jalview.ws.dbsources.Xfam
jalview.ws.dbsources.Xfam
|
0.086956528.7%
|
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jalview.util.CaseInsensitiveString
jalview.util.CaseInsensitiveString
|
0.086956528.7%
|
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jalview.ext.ensembl.EnsemblSequenceFetcher
jalview.ext.ensembl.EnsemblSequenceFetcher
|
0.0833333368.3%
|
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jalview.gui.Console
jalview.gui.Console
|
0.082568818.3%
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jalview.schemes.RNAHelicesColour
jalview.schemes.RNAHelicesColour
|
0.082191788.2%
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jalview.gui.ProgressBar
jalview.gui.ProgressBar
|
0.081300818.1%
|
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com.stevesoft.pat.OrMark
com.stevesoft.pat.OrMark
|
0.0757.5%
|
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com.stevesoft.pat.FastMulti
com.stevesoft.pat.FastMulti
|
0.0740740757.4%
|
|
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jalview.gui.Desktop
jalview.gui.Desktop
|
0.0726447257.3%
|
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jalview.schemes.ColourSchemes
jalview.schemes.ColourSchemes
|
0.070175447%
|
|
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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.log.JLogger
jalview.log.JLogger
|
0.065934076.6%
|
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|
jalview.fts.service.pdb.PDBFTSRestClient
jalview.fts.service.pdb.PDBFTSRestClient
|
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com.stevesoft.pat.RegOpt
com.stevesoft.pat.RegOpt
|
0.06474826.5%
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jalview.analysis.CrossRef
jalview.analysis.CrossRef
|
0.063524596.4%
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jalview.gui.StructureChooser
jalview.gui.StructureChooser
|
0.063291146.3%
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jalview.datamodel.DBRefEntry
jalview.datamodel.DBRefEntry
|
0.0616438356.2%
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ext.vamsas.ServiceHandle
ext.vamsas.ServiceHandle
|
0.061224496.1%
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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.structure.StructureImportSettings
jalview.structure.StructureImportSettings
|
0.0571428575.7%
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jalview.analysis.AlignmentUtils
jalview.analysis.AlignmentUtils
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0.0566298335.7%
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jalview.datamodel.ColumnSelection.IntList
jalview.datamodel.ColumnSelection.IntList
|
0.0560747655.6%
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jalview.renderer.ResidueShader
jalview.renderer.ResidueShader
|
0.054878055.5%
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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.Console
jalview.bin.Console
|
0.0492610824.9%
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jalview.bin.Cache
jalview.bin.Cache
|
0.0482093654.8%
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jalview.datamodel.SecondaryStructureCount
jalview.datamodel.SecondaryStructureCount
|
0.0468754.7%
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jalview.structure.StructureMapping
jalview.structure.StructureMapping
|
0.0466321264.7%
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jalview.util.DBRefUtils
jalview.util.DBRefUtils
|
0.045317224.5%
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jalview.ws.dbsources.Pdb
jalview.ws.dbsources.Pdb
|
0.042553194.3%
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|
|
jalview.ws.jws2.JabaParamStore
jalview.ws.jws2.JabaParamStore
|
0.0416666684.2%
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|
|
jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource
jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource
|
0.0390879473.9%
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|
|
org.json.simple.JSONObject
org.json.simple.JSONObject
|
0.037735853.8%
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|
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jalview.datamodel.HiddenColumns
jalview.datamodel.HiddenColumns
|
0.037735853.8%
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|
|
jalview.ws.jws1.JPredClient
jalview.ws.jws1.JPredClient
|
0.0310559013.1%
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|
|
jalview.datamodel.HiddenSequences
jalview.datamodel.HiddenSequences
|
0.027397262.7%
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|
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jalview.util.MappingUtils
jalview.util.MappingUtils
|
0.0237068962.4%
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|
|
jalview.gui.structurechooser.PDBStructureChooserQuerySource
jalview.gui.structurechooser.PDBStructureChooserQuerySource
|
0.017751481.8%
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|
|
jalview.schemes.ClustalxColourScheme
jalview.schemes.ClustalxColourScheme
|
0.0169491531.7%
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|
|
jalview.datamodel.HiddenColumnsCursor
jalview.datamodel.HiddenColumnsCursor
|
0.0156251.6%
|
|
|
jalview.ws.dbsources.Uniprot
jalview.ws.dbsources.Uniprot
|
0.0155642021.6%
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|
|
jalview.gui.StructureViewer
jalview.gui.StructureViewer
|
0.0148514851.5%
|
|
|
jalview.controller.AlignViewController
jalview.controller.AlignViewController
|
0.0135593221.4%
|
|
|
jalview.datamodel.SearchResults
jalview.datamodel.SearchResults
|
0.0128205131.3%
|
|
|
jalview.gui.SeqPanel
jalview.gui.SeqPanel
|
0.0125082291.3%
|
|
|
jalview.io.SequenceAnnotationReport
jalview.io.SequenceAnnotationReport
|
0.0122699381.2%
|
|
|
jalview.datamodel.ColumnSelection
jalview.datamodel.ColumnSelection
|
0.0103092781%
|
|
|
jalview.gui.SequenceFetcher
jalview.gui.SequenceFetcher
|
0.0089285720.9%
|
|
|
jalview.datamodel.GroupSet
jalview.datamodel.GroupSet
|
0.008620690.9%
|
|
|
jalview.ext.ensembl.EnsemblGene
jalview.ext.ensembl.EnsemblGene
|
0.0081632650.8%
|
|
|
jalview.bin.Jalview
jalview.bin.Jalview
|
0.0081227440.8%
|
|
|
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.jmol.JalviewJmolBinding
jalview.ext.jmol.JalviewJmolBinding
|
0.0040404040.4%
|
|
|
com.stevesoft.pat.CaseMgr
com.stevesoft.pat.CaseMgr
|
0.00278551530.3%
|
|
|
jalview.schemes.ResidueProperties
jalview.schemes.ResidueProperties
|
0.00105042020.1%
|
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