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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.params.ParamDatastoreI
jalview.ws.params.ParamDatastoreI
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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.analysis.Conservation
jalview.analysis.Conservation
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0.8719806787.2%
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jalview.datamodel.Profiles
jalview.datamodel.Profiles
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0.866666786.7%
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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.workers.ConsensusThread
jalview.workers.ConsensusThread
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0.880%
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jalview.workers.SecondaryStructureConsensusThread
jalview.workers.SecondaryStructureConsensusThread
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0.773584977.4%
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jalview.util.LinkedIdentityHashSet
jalview.util.LinkedIdentityHashSet
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0.7727272577.3%
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jalview.workers.AlignCalcManager2.WorkerManager
jalview.workers.AlignCalcManager2.WorkerManager
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0.7575%
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jalview.schemes.ZappoColourScheme
jalview.schemes.ZappoColourScheme
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0.7575%
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jalview.datamodel.Profile
jalview.datamodel.Profile
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0.7377049373.8%
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jalview.workers.AlignCalcManager2.SimpleWorkerManager
jalview.workers.AlignCalcManager2.SimpleWorkerManager
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0.7142857371.4%
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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.jbgui.GStructureViewer
jalview.jbgui.GStructureViewer
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0.7065217570.7%
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jalview.workers.ConservationThread
jalview.workers.ConservationThread
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0.666666766.7%
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jalview.ws.SequenceFetcher
jalview.ws.SequenceFetcher
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0.6470588464.7%
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jalview.schemes.FeatureSettingsAdapter
jalview.schemes.FeatureSettingsAdapter
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0.62562.5%
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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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0.567556.7%
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jalview.renderer.ScaleRenderer
jalview.renderer.ScaleRenderer
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0.5656%
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jalview.ws2.gui.WebServicesMenuManager
jalview.ws2.gui.WebServicesMenuManager
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0.5428571754.3%
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jalview.util.MessageManager
jalview.util.MessageManager
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0.5238095552.4%
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com.stevesoft.pat.StrPos
com.stevesoft.pat.StrPos
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0.523255852.3%
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jalview.structure.StructureImportSettings
jalview.structure.StructureImportSettings
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0.5128205451.3%
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jalview.gui.SequenceRenderer
jalview.gui.SequenceRenderer
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0.504807750.5%
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jalview.ext.jmol.JmolParser
jalview.ext.jmol.JmolParser
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0.50129250.1%
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com.stevesoft.pat.OrMark
com.stevesoft.pat.OrMark
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0.550%
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jalview.viewmodel.ViewportProperties
jalview.viewmodel.ViewportProperties
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0.550%
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mc_view.Bond
mc_view.Bond
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0.550%
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com.stevesoft.pat.wrap.StringWrap
com.stevesoft.pat.wrap.StringWrap
|
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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com.stevesoft.pat.oneChar
com.stevesoft.pat.oneChar
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0.485714348.6%
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jalview.schemes.ResidueColourScheme
jalview.schemes.ResidueColourScheme
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0.4761904847.6%
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jalview.gui.ColourMenuHelper
jalview.gui.ColourMenuHelper
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0.466101746.6%
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jalview.ws2.gui.WebServicesMenuManager.InteractiveServiceEntryGroup
jalview.ws2.gui.WebServicesMenuManager.InteractiveServiceEntryGroup
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0.4579439245.8%
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jalview.io.StructureFile
jalview.io.StructureFile
|
0.4325581543.3%
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jalview.gui.AppJmol.RenderPanel
jalview.gui.AppJmol.RenderPanel
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0.4324324443.2%
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jalview.datamodel.HiddenCursorPosition
jalview.datamodel.HiddenCursorPosition
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0.4285714342.9%
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jalview.io.FileLoader
jalview.io.FileLoader
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0.420731742.1%
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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.ws2.actions.BaseAction
jalview.ws2.actions.BaseAction
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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
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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.gui.AlignViewport
jalview.gui.AlignViewport
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0.3810623638.1%
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jalview.bin.ApplicationSingletonProvider
jalview.bin.ApplicationSingletonProvider
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0.37537.5%
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jalview.renderer.AnnotationRenderer
jalview.renderer.AnnotationRenderer
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0.364354736.4%
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jalview.workers.AlignCalcManager2
jalview.workers.AlignCalcManager2
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0.3630136836.3%
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jalview.util.Comparison
jalview.util.Comparison
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0.3543307235.4%
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jalview.datamodel.ResidueCount
jalview.datamodel.ResidueCount
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0.3414634234.1%
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jalview.viewmodel.styles.ViewStyle
jalview.viewmodel.styles.ViewStyle
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0.3369565333.7%
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jalview.datamodel.PDBEntry
jalview.datamodel.PDBEntry
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0.3366666733.7%
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jalview.gui.IdwidthAdjuster
jalview.gui.IdwidthAdjuster
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0.3289473732.9%
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jalview.gui.AppJmolBinding
jalview.gui.AppJmolBinding
|
0.327102832.7%
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jalview.analysis.AAFrequency
jalview.analysis.AAFrequency
|
0.3230016232.3%
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jalview.ws.rest.RestServiceDescription
jalview.ws.rest.RestServiceDescription
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0.3221649532.2%
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jalview.util.Format
jalview.util.Format
|
0.3209109632.1%
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jalview.io.AlignFile
jalview.io.AlignFile
|
0.3175675631.8%
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mc_view.PDBChain
mc_view.PDBChain
|
0.314814831.5%
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jalview.ws.api.UIinfo
jalview.ws.api.UIinfo
|
0.313725531.4%
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jalview.viewmodel.seqfeatures.FeaturesDisplayed
jalview.viewmodel.seqfeatures.FeaturesDisplayed
|
0.312531.2%
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jalview.datamodel.AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation
|
0.309495930.9%
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com.stevesoft.pat.Pattern
com.stevesoft.pat.Pattern
|
0.3055555530.6%
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jalview.ws2.api.WebService
jalview.ws2.api.WebService
|
0.330%
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jalview.gui.AlignmentPanel
jalview.gui.AlignmentPanel
|
0.291446729.1%
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jalview.viewmodel.ViewportRanges
jalview.viewmodel.ViewportRanges
|
0.2913907229.1%
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jalview.viewmodel.AlignmentViewport
jalview.viewmodel.AlignmentViewport
|
0.2865573828.7%
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jalview.ws.dbsources.EmblCdsSource
jalview.ws.dbsources.EmblCdsSource
|
0.285714328.6%
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jalview.renderer.ResidueColourFinder
jalview.renderer.ResidueColourFinder
|
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
|
0.285714328.6%
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jalview.gui.JvSwingUtils
jalview.gui.JvSwingUtils
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0.2827586228.3%
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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
|
0.282051328.2%
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jalview.datamodel.Sequence
jalview.datamodel.Sequence
|
0.278661127.9%
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jalview.io.IdentifyFile
jalview.io.IdentifyFile
|
0.2766570727.7%
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jalview.gui.AppJmol
jalview.gui.AppJmol
|
0.2750929327.5%
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com.stevesoft.pat.Or
com.stevesoft.pat.Or
|
0.2692307826.9%
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jalview.schemes.IdColourScheme
jalview.schemes.IdColourScheme
|
0.2608695626.1%
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jalview.gui.IdCanvas
jalview.gui.IdCanvas
|
0.2524916825.2%
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com.stevesoft.pat.Regex
com.stevesoft.pat.Regex
|
0.250909125.1%
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jalview.gui.JalviewChangeSupport
jalview.gui.JalviewChangeSupport
|
0.2525%
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jalview.renderer.AnnotationRendererFactory
jalview.renderer.AnnotationRendererFactory
|
0.2525%
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jalview.ws.rest.params.Alignment
jalview.ws.rest.params.Alignment
|
0.2435897424.4%
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jalview.gui.ScalePanel
jalview.gui.ScalePanel
|
0.2352941223.5%
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jalview.datamodel.SequenceCursor
jalview.datamodel.SequenceCursor
|
0.2333333323.3%
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jalview.datamodel.SecondaryStructureCount
jalview.datamodel.SecondaryStructureCount
|
0.2304687523%
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jalview.datamodel.features.SequenceFeatures
jalview.datamodel.features.SequenceFeatures
|
0.2292993722.9%
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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
|
0.22522.5%
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jalview.datamodel.features.FeatureStore
jalview.datamodel.features.FeatureStore
|
0.2145015221.5%
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jalview.io.PDBFeatureSettings
jalview.io.PDBFeatureSettings
|
0.2142857221.4%
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jalview.viewmodel.seqfeatures.FeatureRendererModel
jalview.viewmodel.seqfeatures.FeatureRendererModel
|
0.2128325621.3%
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jalview.datamodel.SearchResults
jalview.datamodel.SearchResults
|
0.2115384621.2%
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jalview.ws.rest.InputType
jalview.ws.rest.InputType
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0.2056074720.6%
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jalview.io.FileParse
jalview.io.FileParse
|
0.2022160720.2%
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jalview.gui.AnnotationLabels
jalview.gui.AnnotationLabels
|
0.200787420.1%
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jalview.analysis.AlignmentAnnotationUtils
jalview.analysis.AlignmentAnnotationUtils
|
0.1949152519.5%
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jalview.schemes.TCoffeeColourScheme
jalview.schemes.TCoffeeColourScheme
|
0.1803278618%
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jalview.schemes.Blosum62ColourScheme
jalview.schemes.Blosum62ColourScheme
|
0.176470617.6%
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com.stevesoft.pat.patInt
com.stevesoft.pat.patInt
|
0.17517.5%
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jalview.util.CaseInsensitiveString
jalview.util.CaseInsensitiveString
|
0.1739130517.4%
|
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jalview.ext.jmol.JalviewJmolBinding
jalview.ext.jmol.JalviewJmolBinding
|
0.1720647817.2%
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jalview.ws.jws1.WS1Client
jalview.ws.jws1.WS1Client
|
0.1616%
|
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jalview.analysis.AnnotationSorter
jalview.analysis.AnnotationSorter
|
0.1562515.6%
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jalview.gui.Desktop.MyDesktopManager
jalview.gui.Desktop.MyDesktopManager
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0.1555555615.6%
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jalview.datamodel.Alignment
jalview.datamodel.Alignment
|
0.1471914.7%
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jalview.ws.rest.RestClient
jalview.ws.rest.RestClient
|
0.1466666614.7%
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jalview.gui.StructureViewerBase
jalview.gui.StructureViewerBase
|
0.1457431514.6%
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jalview.gui.PaintRefresher
jalview.gui.PaintRefresher
|
0.1447368414.5%
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jalview.log.JLogger
jalview.log.JLogger
|
0.1428571514.3%
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jalview.gui.Desktop.MyDesktopPane
jalview.gui.Desktop.MyDesktopPane
|
0.1428571514.3%
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jalview.workers.AlignCalcWorker
jalview.workers.AlignCalcWorker
|
0.1333333413.3%
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jalview.schemes.HmmerGlobalBackground
jalview.schemes.HmmerGlobalBackground
|
0.1333333413.3%
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jalview.schemes.PIDColourScheme
jalview.schemes.PIDColourScheme
|
0.1333333413.3%
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jalview.gui.AnnotationPanel
jalview.gui.AnnotationPanel
|
0.1313340213.1%
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jalview.structures.models.AAStructureBindingModel
jalview.structures.models.AAStructureBindingModel
|
0.1312427413.1%
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jalview.io.AppletFormatAdapter
jalview.io.AppletFormatAdapter
|
0.12422360512.4%
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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.structure.StructureCommand
jalview.structure.StructureCommand
|
0.1212%
|
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jalview.gui.AlignFrame
jalview.gui.AlignFrame
|
0.1114589911.1%
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jalview.schemes.ColourSchemeProperty
jalview.schemes.ColourSchemeProperty
|
0.1111111111.1%
|
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jalview.schemes.RNAHelicesColour
jalview.schemes.RNAHelicesColour
|
0.1095890411%
|
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jalview.log.JLoggerLog4j
jalview.log.JLoggerLog4j
|
0.10679611610.7%
|
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jalview.datamodel.DBRefEntry
jalview.datamodel.DBRefEntry
|
0.1027397310.3%
|
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jalview.ws.rest.params.AnnotationFile
jalview.ws.rest.params.AnnotationFile
|
0.10256410410.3%
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jalview.gui.SeqCanvas
jalview.gui.SeqCanvas
|
0.1022267210.2%
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jalview.bin.Console
jalview.bin.Console
|
0.09905669.9%
|
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com.stevesoft.pat.parsePerl
com.stevesoft.pat.parsePerl
|
0.098639469.9%
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jalview.ws.WSClient
jalview.ws.WSClient
|
0.098039229.8%
|
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jalview.ws2.client.jpred4.JPred4WSDiscoverer
jalview.ws2.client.jpred4.JPred4WSDiscoverer
|
0.09523819.5%
|
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jalview.ws2.client.api.AbstractWebServiceDiscoverer
jalview.ws2.client.api.AbstractWebServiceDiscoverer
|
0.0943396249.4%
|
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jalview.util.StringUtils
jalview.util.StringUtils
|
0.090395489%
|
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jalview.ws.dbsources.Xfam
jalview.ws.dbsources.Xfam
|
0.086956528.7%
|
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jalview.datamodel.SequenceFeature
jalview.datamodel.SequenceFeature
|
0.0863309358.6%
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jalview.util.DBRefUtils
jalview.util.DBRefUtils
|
0.086309528.6%
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jalview.renderer.ResidueShader
jalview.renderer.ResidueShader
|
0.0853658548.5%
|
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jalview.ws.jws1.Discoverer
jalview.ws.jws1.Discoverer
|
0.0848484868.5%
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jalview.ext.ensembl.EnsemblSequenceFetcher
jalview.ext.ensembl.EnsemblSequenceFetcher
|
0.0833333368.3%
|
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jalview.analysis.scoremodels.ScoreModels
jalview.analysis.scoremodels.ScoreModels
|
0.0833333368.3%
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jalview.io.FileFormat
jalview.io.FileFormat
|
0.082758628.3%
|
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jalview.ws2.client.ebi.JobDispatcherWSDiscoverer
jalview.ws2.client.ebi.JobDispatcherWSDiscoverer
|
0.081632658.2%
|
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|
jalview.util.ColorUtils
jalview.util.ColorUtils
|
0.08011058%
|
|
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jalview.util.Platform
jalview.util.Platform
|
0.0784313757.8%
|
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jalview.schemes.FeatureColour
jalview.schemes.FeatureColour
|
0.077894747.8%
|
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jalview.schemes.HmmerLocalBackground
jalview.schemes.HmmerLocalBackground
|
0.076923087.7%
|
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jalview.schemes.HmmerColourScheme
jalview.schemes.HmmerColourScheme
|
0.076923087.7%
|
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jalview.gui.Desktop
jalview.gui.Desktop
|
0.075808257.6%
|
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com.stevesoft.pat.FastMulti
com.stevesoft.pat.FastMulti
|
0.0740740757.4%
|
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jalview.gui.StructureViewer
jalview.gui.StructureViewer
|
0.0697674457%
|
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jalview.gui.ProgressBar
jalview.gui.ProgressBar
|
0.068965526.9%
|
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jalview.gui.IdPanel
jalview.gui.IdPanel
|
0.067264576.7%
|
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com.stevesoft.pat.RegOpt
com.stevesoft.pat.RegOpt
|
0.06474826.5%
|
|
|
jalview.schemes.HMMMatchScoreColourScheme
jalview.schemes.HMMMatchScoreColourScheme
|
0.063829796.4%
|
|
|
jalview.analysis.CrossRef
jalview.analysis.CrossRef
|
0.063655036.4%
|
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|
jalview.analysis.scoremodels.ScoreMatrix
jalview.analysis.scoremodels.ScoreMatrix
|
0.0617283966.2%
|
|
|
ext.vamsas.ServiceHandle
ext.vamsas.ServiceHandle
|
0.061224496.1%
|
|
|
jalview.gui.ViewSelectionMenu
jalview.gui.ViewSelectionMenu
|
0.059405945.9%
|
|
|
jalview.ws.seqfetcher.ASequenceFetcher
jalview.ws.seqfetcher.ASequenceFetcher
|
0.0577777775.8%
|
|
|
jalview.structure.StructureSelectionManager
jalview.structure.StructureSelectionManager
|
0.0572519085.7%
|
|
|
jalview.datamodel.ColumnSelection.IntList
jalview.datamodel.ColumnSelection.IntList
|
0.0560747655.6%
|
|
|
jalview.workers.InformationThread
jalview.workers.InformationThread
|
0.0555555565.6%
|
|
|
jalview.ws.seqfetcher.DbSourceProxyImpl
jalview.ws.seqfetcher.DbSourceProxyImpl
|
0.0540540555.4%
|
|
|
jalview.schemes.ColourSchemes
jalview.schemes.ColourSchemes
|
0.0512820525.1%
|
|
|
jalview.bin.Cache
jalview.bin.Cache
|
0.05013555%
|
|
|
jalview.ws2.params.SimpleParamDatastore
jalview.ws2.params.SimpleParamDatastore
|
0.055%
|
|
|
jalview.analysis.GeneticCodes
jalview.analysis.GeneticCodes
|
0.0496894425%
|
|
|
jalview.analysis.AlignmentUtils
jalview.analysis.AlignmentUtils
|
0.0419122464.2%
|
|
|
jalview.ws.dbsources.Pdb
jalview.ws.dbsources.Pdb
|
0.0408163264.1%
|
|
|
jalview.datamodel.HiddenColumns
jalview.datamodel.HiddenColumns
|
0.037735853.8%
|
|
|
jalview.ws.jws1.JPredClient
jalview.ws.jws1.JPredClient
|
0.0310559013.1%
|
|
|
com.stevesoft.pat.RegRes
com.stevesoft.pat.RegRes
|
0.0289855082.9%
|
|
|
jalview.ext.jmol.JmolCommands
jalview.ext.jmol.JmolCommands
|
0.0275590552.8%
|
|
|
jalview.datamodel.HiddenSequences
jalview.datamodel.HiddenSequences
|
0.027397262.7%
|
|
|
jalview.ws2.client.slivka.SlivkaWSDiscoverer
jalview.ws2.client.slivka.SlivkaWSDiscoverer
|
0.0268456382.7%
|
|
|
jalview.util.FileUtils
jalview.util.FileUtils
|
0.0267857152.7%
|
|
|
jalview.ws.jws2.Jws2Discoverer
jalview.ws.jws2.Jws2Discoverer
|
0.0256410262.6%
|
|
|
jalview.schemes.ClustalxColourScheme
jalview.schemes.ClustalxColourScheme
|
0.0254237282.5%
|
|
|
jalview.structure.StructureCommandsBase
jalview.structure.StructureCommandsBase
|
0.0243902432.4%
|
|
|
jalview.datamodel.HiddenColumnsCursor
jalview.datamodel.HiddenColumnsCursor
|
0.0156251.6%
|
|
|
jalview.ws.dbsources.Uniprot
jalview.ws.dbsources.Uniprot
|
0.015325671.5%
|
|
|
jalview.hmmer.HmmerCommand
jalview.hmmer.HmmerCommand
|
0.0141509441.4%
|
|
|
jalview.controller.AlignViewController
jalview.controller.AlignViewController
|
0.0135593221.4%
|
|
|
jalview.gui.SeqPanel
jalview.gui.SeqPanel
|
0.0129954521.3%
|
|
|
jalview.analysis.AlignSeq
jalview.analysis.AlignSeq
|
0.01275510251.3%
|
|
|
jalview.bin.Jalview
jalview.bin.Jalview
|
0.0121261111.2%
|
|
|
jalview.io.SequenceAnnotationReport
jalview.io.SequenceAnnotationReport
|
0.0112359551.1%
|
|
|
jalview.datamodel.ColumnSelection
jalview.datamodel.ColumnSelection
|
0.0103092781%
|
|
|
jalview.ext.ensembl.EnsemblGene
jalview.ext.ensembl.EnsemblGene
|
0.0081632650.8%
|
|
|
jalview.renderer.seqfeatures.FeatureRenderer
jalview.renderer.seqfeatures.FeatureRenderer
|
0.007547170.8%
|
|
|
jalview.gui.QuitHandler
jalview.gui.QuitHandler
|
0.00722021660.7%
|
|
|
com.stevesoft.pat.CaseMgr
com.stevesoft.pat.CaseMgr
|
0.00278551530.3%
|
|
|
jalview.schemes.ResidueProperties
jalview.schemes.ResidueProperties
|
0.00103039670.1%
|
|
