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com.stevesoft.pat.patInf
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jalview.io.DataSourceType
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jalview.renderer.ScaleRenderer.ScaleMark
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jalview.ws.WSClient
jalview.ws.WSClient
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jalview.datamodel.ResidueCount.SymbolCounts
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1.0100%
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jalview.structure.StructureImportSettings.TFType
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jalview.jbgui.GAlignmentPanel
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jalview.util.UserAgent
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jalview.gui.StructureViewer.ViewerType
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com.stevesoft.pat.Rthings
com.stevesoft.pat.Rthings
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mc_view.Residue
mc_view.Residue
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jalview.util.LinkedIdentityHashSet
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jalview.schemes.ZappoColourScheme
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jalview.fts.core.FTSDataColumnPreferences
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jalview.datamodel.Profiles
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jalview.gui.FeatureRenderer
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jalview.util.LinkedIdentityHashSet.IdentityWrapper
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jalview.schemes.ResidueColourScheme
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jalview.datamodel.ContactMapHolder
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jalview.jbgui.GStructureViewer
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jalview.renderer.ContactMapRenderer
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jalview.ws.SequenceFetcher
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jalview.ws.sifts.SiftsSettings
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jalview.util.MapUtils
jalview.util.MapUtils
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jalview.util.ParseHtmlBodyAndLinks
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jalview.jbgui.GAlignFrame
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jalview.workers.ConservationThread
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jalview.util.CaseInsensitiveString
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jalview.renderer.ScaleRenderer
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jalview.datamodel.ContactRange
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jalview.ext.jmol.JmolParser
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mc_view.PDBChain
mc_view.PDBChain
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jalview.gui.AssociatePdbFileWithSeq
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com.stevesoft.pat.StrPos
com.stevesoft.pat.StrPos
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jalview.bin.argparser.ArgParser
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jalview.ws.datamodel.alphafold.MappableContactMatrix
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jalview.viewmodel.ViewportProperties
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jalview.urls.IdOrgSettings
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mc_view.Bond
mc_view.Bond
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jalview.datamodel.GroupSetHolder
jalview.datamodel.GroupSetHolder
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0.550%
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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
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0.550%
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jalview.schemes.OceanColourScheme
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0.550%
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jalview.bin.argparser.BootstrapArgs
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jalview.jbgui.GStructureChooser
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jalview.gui.ColourMenuHelper
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jalview.io.StructureFile
jalview.io.StructureFile
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jalview.io.AlignFile
jalview.io.AlignFile
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0.4589041245.9%
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jalview.bin.argparser.ArgValue
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jalview.datamodel.ResidueCount
jalview.datamodel.ResidueCount
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0.4436363644.4%
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jalview.renderer.AnnotationRenderer
jalview.renderer.AnnotationRenderer
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jalview.bin.argparser.SubVals
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jalview.datamodel.HiddenCursorPosition
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0.4285714342.9%
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jalview.gui.SequenceRenderer
jalview.gui.SequenceRenderer
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0.427884642.8%
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jalview.gui.ImageExporter
jalview.gui.ImageExporter
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0.4242424442.4%
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jalview.bin.Commands
jalview.bin.Commands
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0.4235145442.4%
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jalview.datamodel.FloatContactMatrix
jalview.datamodel.FloatContactMatrix
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0.4242%
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jalview.util.ShortcutKeyMaskExWrapper11
jalview.util.ShortcutKeyMaskExWrapper11
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0.4166666641.7%
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jalview.analysis.AlignSeq
jalview.analysis.AlignSeq
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jalview.ext.so.SequenceOntology
jalview.ext.so.SequenceOntology
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jalview.datamodel.Profile
jalview.datamodel.Profile
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0.410714341.1%
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jalview.util.Comparison
jalview.util.Comparison
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jalview.io.FileLoader
jalview.io.FileLoader
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0.4046822840.5%
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org.json.simple.parser.Yylex
org.json.simple.parser.Yylex
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0.4012738840.1%
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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
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0.440%
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jalview.schemes.TurnColourScheme
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0.440%
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jalview.schemes.StrandColourScheme
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0.440%
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jalview.schemes.BuriedColourScheme
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0.440%
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jalview.structure.StructureImportSettings
jalview.structure.StructureImportSettings
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0.440%
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jalview.log.JalviewAppender
jalview.log.JalviewAppender
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0.388888938.9%
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jalview.ext.jmol.JalviewJmolBinding
jalview.ext.jmol.JalviewJmolBinding
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0.3884297638.8%
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jalview.datamodel.PDBEntry
jalview.datamodel.PDBEntry
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0.3832599238.3%
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jalview.gui.AppJmolBinding
jalview.gui.AppJmolBinding
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0.3831775838.3%
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jalview.util.ImageMaker
jalview.util.ImageMaker
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0.3798449638%
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jalview.renderer.ContactGeometry
jalview.renderer.ContactGeometry
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0.37537.5%
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jalview.gui.AlignViewport
jalview.gui.AlignViewport
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0.3744292337.4%
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jalview.datamodel.AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation
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jalview.bin.argparser.ArgValues
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jalview.bin.Cache
jalview.bin.Cache
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jalview.util.Format
jalview.util.Format
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jalview.ws.datamodel.alphafold.PAEContactMatrix
jalview.ws.datamodel.alphafold.PAEContactMatrix
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jalview.bin.argparser.ArgValuesMap
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0.361858236.2%
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jalview.io.FastaFile
jalview.io.FastaFile
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0.3603603536%
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jalview.renderer.ContactGeometry.contactInterval
jalview.renderer.ContactGeometry.contactInterval
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0.3571428735.7%
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jalview.util.MessageManager
jalview.util.MessageManager
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jalview.jbgui.GStructureChooser.AssociateSeqPanel
jalview.jbgui.GStructureChooser.AssociateSeqPanel
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0.352941235.3%
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jalview.gui.AlignmentPanel
jalview.gui.AlignmentPanel
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0.3521790235.2%
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jalview.datamodel.SequenceFeature
jalview.datamodel.SequenceFeature
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0.3489208534.9%
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jalview.datamodel.Annotation
jalview.datamodel.Annotation
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0.3428571534.3%
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jalview.viewmodel.styles.ViewStyle
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0.3320312533.2%
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jalview.structure.StructureSelectionManager
jalview.structure.StructureSelectionManager
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0.3253333332.5%
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jalview.datamodel.features.SequenceFeatures
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jalview.ws.rest.RestServiceDescription
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0.31531.5%
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jalview.datamodel.Sequence
jalview.datamodel.Sequence
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0.3148788831.5%
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org.json.simple.parser.JSONParser
org.json.simple.parser.JSONParser
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com.stevesoft.pat.oneChar
com.stevesoft.pat.oneChar
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0.3142857331.4%
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jalview.renderer.seqfeatures.FeatureColourFinder
jalview.renderer.seqfeatures.FeatureColourFinder
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jalview.gui.AppJmol
jalview.gui.AppJmol
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0.3082706630.8%
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jalview.structures.models.AAStructureBindingModel
jalview.structures.models.AAStructureBindingModel
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0.2895662529%
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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.ResidueShader
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jalview.schemes.JalviewColourScheme
jalview.schemes.JalviewColourScheme
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0.285714328.6%
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jalview.datamodel.annotations.AnnotationRowBuilder
jalview.datamodel.annotations.AnnotationRowBuilder
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0.282051328.2%
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mc_view.Atom
mc_view.Atom
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0.282051328.2%
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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
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0.2674094726.7%
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jalview.viewmodel.AlignmentViewport
jalview.viewmodel.AlignmentViewport
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0.2647951526.5%
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jalview.schemes.IdColourScheme
jalview.schemes.IdColourScheme
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0.2608695626.1%
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jalview.analysis.AAFrequency
jalview.analysis.AAFrequency
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0.2594936825.9%
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jalview.datamodel.features.FeatureStore
jalview.datamodel.features.FeatureStore
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0.2567975825.7%
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jalview.gui.JalviewChangeSupport
jalview.gui.JalviewChangeSupport
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0.2525%
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jalview.io.gff.SequenceOntologyFactory
jalview.io.gff.SequenceOntologyFactory
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0.2525%
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jalview.gui.StructureViewerBase
jalview.gui.StructureViewerBase
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0.2492581624.9%
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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.util.ErrorLog
jalview.util.ErrorLog
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0.2352941223.5%
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jalview.bin.BuildDetails
jalview.bin.BuildDetails
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0.2352941223.5%
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jalview.datamodel.SequenceCursor
jalview.datamodel.SequenceCursor
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0.2333333323.3%
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jalview.structure.StructureCommandsBase
jalview.structure.StructureCommandsBase
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0.2317073223.2%
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jalview.gui.JvSwingUtils
jalview.gui.JvSwingUtils
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0.2312925223.1%
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com.stevesoft.pat.Range
com.stevesoft.pat.Range
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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
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0.224806222.5%
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jalview.util.MapList
jalview.util.MapList
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0.2242990622.4%
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jalview.datamodel.Alignment
jalview.datamodel.Alignment
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0.2216014922.2%
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jalview.viewmodel.seqfeatures.FeaturesDisplayed
jalview.viewmodel.seqfeatures.FeaturesDisplayed
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0.2187521.9%
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jalview.io.PDBFeatureSettings
jalview.io.PDBFeatureSettings
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0.2142857221.4%
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jalview.datamodel.features.FeatureAttributes.AttributeData
jalview.datamodel.features.FeatureAttributes.AttributeData
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0.2127659621.3%
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jalview.analysis.AnnotationSorter
jalview.analysis.AnnotationSorter
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0.2118226621.2%
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jalview.analysis.scoremodels.ScoreModels
jalview.analysis.scoremodels.ScoreModels
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0.2115384621.2%
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jalview.util.HttpUtils
jalview.util.HttpUtils
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0.2105263221.1%
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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.viewmodel.seqfeatures.FeatureRendererModel
jalview.viewmodel.seqfeatures.FeatureRendererModel
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0.2050078220.5%
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jalview.util.FileUtils
jalview.util.FileUtils
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0.2043010720.4%
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jalview.bin.Console
jalview.bin.Console
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0.1921182319.2%
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jalview.gui.ScalePanel
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0.1914062519.1%
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jalview.gui.AnnotationLabels
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0.1910241719.1%
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jalview.log.JLogger
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jalview.fts.core.FTSDataColumnPreferences.FTSDataColumnPrefsTableModel
jalview.fts.core.FTSDataColumnPreferences.FTSDataColumnPrefsTableModel
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0.1857142918.6%
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jalview.util.ColorUtils
jalview.util.ColorUtils
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0.182795718.3%
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jalview.util.ImageMaker.TYPE
jalview.util.ImageMaker.TYPE
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0.1818181918.2%
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com.stevesoft.pat.Pattern
com.stevesoft.pat.Pattern
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0.1805555518.1%
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jalview.schemes.TCoffeeColourScheme
jalview.schemes.TCoffeeColourScheme
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0.1803278618%
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jalview.gui.IdCanvas
jalview.gui.IdCanvas
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0.1789473717.9%
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jalview.schemes.Blosum62ColourScheme
jalview.schemes.Blosum62ColourScheme
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0.176470617.6%
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com.stevesoft.pat.patInt
com.stevesoft.pat.patInt
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0.17517.5%
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jalview.util.Platform
jalview.util.Platform
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0.174528317.5%
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jalview.gui.IdwidthAdjuster
jalview.gui.IdwidthAdjuster
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0.1710526317.1%
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jalview.jbgui.GStructureChooser.CustomComboSeparatorsRenderer
jalview.jbgui.GStructureChooser.CustomComboSeparatorsRenderer
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0.1666666716.7%
|
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jalview.ws.dbsources.EBIAlfaFold
jalview.ws.dbsources.EBIAlfaFold
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0.1604477616%
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jalview.ws.jws1.WS1Client
jalview.ws.jws1.WS1Client
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0.1616%
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jalview.util.QuickSort
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jalview.gui.PaintRefresher
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0.1549295815.5%
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jalview.bin.Jalview
jalview.bin.Jalview
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jalview.fts.core.FTSRestClient
jalview.fts.core.FTSRestClient
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0.1467181414.7%
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jalview.io.AppletFormatAdapter
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0.1428571514.3%
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jalview.viewmodel.ViewportRanges
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0.1419141914.2%
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jalview.gui.StructureViewer
jalview.gui.StructureViewer
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0.1386138613.9%
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jalview.log.JLoggerLog4j
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0.1359223313.6%
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jalview.util.StringUtils
jalview.util.StringUtils
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jalview.schemes.PIDColourScheme
jalview.schemes.PIDColourScheme
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0.1333333413.3%
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jalview.datamodel.GroupSet
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0.1293103412.9%
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jalview.gui.AlignFrame
jalview.gui.AlignFrame
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0.1257613712.6%
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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.io.FormatAdapter
jalview.io.FormatAdapter
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0.1212%
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jalview.structure.StructureCommand
jalview.structure.StructureCommand
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0.1212%
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jalview.ws.rest.RestClient
jalview.ws.rest.RestClient
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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.schemes.ColourSchemeProperty
jalview.schemes.ColourSchemeProperty
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0.1111111111.1%
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jalview.schemes.RNAHelicesColour
jalview.schemes.RNAHelicesColour
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0.1095890411%
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jalview.io.FileFormat
jalview.io.FileFormat
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0.1085271310.9%
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jalview.datamodel.Mapping
jalview.datamodel.Mapping
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0.10389610410.4%
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jalview.analysis.scoremodels.ScoreMatrix
jalview.analysis.scoremodels.ScoreMatrix
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0.1028806610.3%
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jalview.ext.jmol.JmolCommands
jalview.ext.jmol.JmolCommands
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0.1028037410.3%
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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.bin.argparser.Arg
jalview.bin.argparser.Arg
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com.stevesoft.pat.parsePerl
com.stevesoft.pat.parsePerl
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0.098639469.9%
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jalview.datamodel.ContactMatrixI
jalview.datamodel.ContactMatrixI
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0.0970873769.7%
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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.gui.StructureChooser
jalview.gui.StructureChooser
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0.0955120859.6%
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jalview.workers.AlignCalcWorker
jalview.workers.AlignCalcWorker
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0.09523819.5%
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jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient
jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient
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0.093759.4%
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com.stevesoft.pat.Or
com.stevesoft.pat.Or
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0.089743599%
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jalview.ws.dbsources.Xfam
jalview.ws.dbsources.Xfam
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0.086956528.7%
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jalview.ws.dbsources.Pdb
jalview.ws.dbsources.Pdb
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0.085106388.5%
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jalview.ext.ensembl.EnsemblSequenceFetcher
jalview.ext.ensembl.EnsemblSequenceFetcher
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0.0833333368.3%
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jalview.structure.StructureMapping
jalview.structure.StructureMapping
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0.082901558.3%
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jalview.ws.seqfetcher.DbSourceProxyImpl
jalview.ws.seqfetcher.DbSourceProxyImpl
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0.081081088.1%
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jalview.schemes.FeatureColour
jalview.schemes.FeatureColour
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0.077894747.8%
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jalview.util.ChannelProperties
jalview.util.ChannelProperties
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0.075862077.6%
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com.stevesoft.pat.OrMark
com.stevesoft.pat.OrMark
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0.0757.5%
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jalview.datamodel.ColumnSelection.IntList
jalview.datamodel.ColumnSelection.IntList
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0.074766357.5%
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com.stevesoft.pat.FastMulti
com.stevesoft.pat.FastMulti
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0.0740740757.4%
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jalview.schemes.ColourSchemes
jalview.schemes.ColourSchemes
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0.070175447%
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jalview.gui.IdPanel
jalview.gui.IdPanel
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0.067264576.7%
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jalview.util.LaunchUtils
jalview.util.LaunchUtils
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0.0661764746.6%
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jalview.fts.service.pdb.PDBFTSRestClient
jalview.fts.service.pdb.PDBFTSRestClient
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0.065502186.6%
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com.stevesoft.pat.RegOpt
com.stevesoft.pat.RegOpt
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0.06474826.5%
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jalview.analysis.CrossRef
jalview.analysis.CrossRef
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0.063524596.4%
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jalview.gui.AnnotationPanel
jalview.gui.AnnotationPanel
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0.061974796.2%
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jalview.datamodel.DBRefEntry
jalview.datamodel.DBRefEntry
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0.0616438356.2%
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ext.vamsas.ServiceHandle
ext.vamsas.ServiceHandle
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0.061224496.1%
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jalview.gui.Desktop
jalview.gui.Desktop
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0.059794996%
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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.datamodel.HiddenColumns
jalview.datamodel.HiddenColumns
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0.0542452825.4%
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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.gui.Desktop.MyDesktopPane
jalview.gui.Desktop.MyDesktopPane
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0.047619054.8%
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jalview.gui.SeqCanvas
jalview.gui.SeqCanvas
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0.0460921864.6%
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jalview.util.DBRefUtils
jalview.util.DBRefUtils
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0.045317224.5%
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jalview.datamodel.ColumnSelection
jalview.datamodel.ColumnSelection
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0.044673544.5%
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jalview.analysis.AlignmentUtils
jalview.analysis.AlignmentUtils
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0.0431286544.3%
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jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource
jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource
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0.0390879473.9%
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org.json.simple.JSONObject
org.json.simple.JSONObject
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0.037735853.8%
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jalview.ws.jws1.JPredClient
jalview.ws.jws1.JPredClient
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0.0310559013.1%
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jalview.datamodel.HiddenSequences
jalview.datamodel.HiddenSequences
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0.027397262.7%
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jalview.schemes.ClustalxColourScheme
jalview.schemes.ClustalxColourScheme
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0.0254237282.5%
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jalview.util.MappingUtils
jalview.util.MappingUtils
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0.0237068962.4%
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jalview.gui.Console
jalview.gui.Console
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0.0206422022.1%
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jalview.gui.structurechooser.PDBStructureChooserQuerySource
jalview.gui.structurechooser.PDBStructureChooserQuerySource
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0.017751481.8%
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jalview.ws.jws2.Jws2Discoverer
jalview.ws.jws2.Jws2Discoverer
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0.0158415851.6%
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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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mc_view.PDBfile
mc_view.PDBfile
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0.0150375941.5%
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jalview.controller.AlignViewController
jalview.controller.AlignViewController
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0.0136518771.4%
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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.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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org.json.simple.JSONArray
org.json.simple.JSONArray
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0.0080645160.8%
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jalview.renderer.seqfeatures.FeatureRenderer
jalview.renderer.seqfeatures.FeatureRenderer
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0.007547170.8%
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com.stevesoft.pat.RegRes
com.stevesoft.pat.RegRes
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0.0072463770.7%
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jalview.gui.QuitHandler
jalview.gui.QuitHandler
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0.00722021660.7%
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com.stevesoft.pat.CaseMgr
com.stevesoft.pat.CaseMgr
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0.00278551530.3%
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jalview.schemes.ResidueProperties
jalview.schemes.ResidueProperties
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0.00105042020.1%
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