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com.stevesoft.pat.patInf
com.stevesoft.pat.patInf
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jalview.io.DataSourceType
jalview.io.DataSourceType
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1.0100%
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jalview.viewmodel.ViewportProperties
jalview.viewmodel.ViewportProperties
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1.0100%
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jalview.xml.binding.jalview.AnnotationElement
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1.0100%
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jalview.xml.binding.jalview.SequenceType
jalview.xml.binding.jalview.SequenceType
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1.0100%
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jalview.xml.binding.jalview.JalviewModel.Viewport.Overview
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1.0100%
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jalview.ws.WSClient
jalview.ws.WSClient
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1.0100%
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jalview.project.Jalview2XML.JvAnnotRow
jalview.project.Jalview2XML.JvAnnotRow
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1.0100%
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jalview.datamodel.ResidueCount.SymbolCounts
jalview.datamodel.ResidueCount.SymbolCounts
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1.0100%
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jalview.schemes.ZappoColourScheme
jalview.schemes.ZappoColourScheme
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1.0100%
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0.975609897.6%
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jalview.renderer.ScaleRenderer
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0.9292%
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jalview.xml.binding.jalview.JalviewModel.Tree
jalview.xml.binding.jalview.JalviewModel.Tree
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jalview.xml.binding.jalview.SequenceSet
jalview.xml.binding.jalview.SequenceSet
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0.894736889.5%
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jalview.xml.binding.jalview.JalviewModel.Viewport
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jalview.analysis.Conservation
jalview.analysis.Conservation
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jalview.util.QuickSort.IntComparator
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com.stevesoft.pat.OrMark
com.stevesoft.pat.OrMark
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0.8585%
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jalview.viewmodel.styles.ViewStyle
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com.stevesoft.pat.Rthings
com.stevesoft.pat.Rthings
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0.8461538684.6%
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jalview.xml.binding.jalview.JalviewModel.JGroup
jalview.xml.binding.jalview.JalviewModel.JGroup
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jalview.xml.binding.jalview.JalviewModel
jalview.xml.binding.jalview.JalviewModel
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com.stevesoft.pat.SubMark
com.stevesoft.pat.SubMark
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0.880%
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jalview.datamodel.VisibleColsCollection
jalview.datamodel.VisibleColsCollection
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0.880%
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jalview.schemes.ResidueColourScheme
jalview.schemes.ResidueColourScheme
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0.7857142778.6%
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jalview.xml.binding.jalview.Annotation
jalview.xml.binding.jalview.Annotation
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0.7727272577.3%
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jalview.xml.binding.jalview.JalviewModel.JSeq
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0.7575%
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com.stevesoft.pat.wrap.StringWrap
com.stevesoft.pat.wrap.StringWrap
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0.7575%
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jalview.viewmodel.OverviewDimensions
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jalview.gui.FeatureRenderer
jalview.gui.FeatureRenderer
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0.7142857371.4%
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jalview.datamodel.Profile
jalview.datamodel.Profile
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com.stevesoft.pat.Bracket
com.stevesoft.pat.Bracket
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0.770%
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jalview.datamodel.VisibleRowsIterator
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0.770%
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jalview.workers.ConsensusThread
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jalview.workers.SecondaryStructureConsensusThread
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0.696969769.7%
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jalview.gui.TreePanel.TreeLoader
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0.687568.8%
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com.stevesoft.pat.oneChar
com.stevesoft.pat.oneChar
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0.685714368.6%
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jalview.ws.SequenceFetcher
jalview.ws.SequenceFetcher
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0.678571467.9%
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jalview.renderer.OverviewRenderer
jalview.renderer.OverviewRenderer
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0.6746987767.5%
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jalview.workers.ConservationThread
jalview.workers.ConservationThread
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0.655172465.5%
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jalview.xml.binding.jalview.Sequence
jalview.xml.binding.jalview.Sequence
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0.6428571364.3%
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com.stevesoft.pat.Range
com.stevesoft.pat.Range
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0.636363663.6%
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jalview.workers.AlignCalcManager
jalview.workers.AlignCalcManager
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0.6190476461.9%
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com.stevesoft.pat.StrPos
com.stevesoft.pat.StrPos
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0.6162790761.6%
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jalview.analysis.SequenceIdMatcher.SeqIdName
jalview.analysis.SequenceIdMatcher.SeqIdName
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0.605263260.5%
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jalview.renderer.ResidueColourFinder
jalview.renderer.ResidueColourFinder
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0.595238159.5%
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jalview.gui.OverviewCanvas
jalview.gui.OverviewCanvas
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0.586206958.6%
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jalview.jbgui.GTreePanel
jalview.jbgui.GTreePanel
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0.584158458.4%
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jalview.datamodel.BinaryNode
jalview.datamodel.BinaryNode
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0.583333358.3%
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jalview.jbgui.GAlignFrame
jalview.jbgui.GAlignFrame
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0.582542758.3%
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jalview.gui.OverviewPanel
jalview.gui.OverviewPanel
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0.558823555.9%
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jalview.io.NewickFile
jalview.io.NewickFile
|
0.531177853.1%
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com.stevesoft.pat.Boundary
com.stevesoft.pat.Boundary
|
0.518518551.9%
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jalview.gui.ColourMenuHelper
jalview.gui.ColourMenuHelper
|
0.550%
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jalview.gui.JalviewChangeSupport
jalview.gui.JalviewChangeSupport
|
0.550%
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com.stevesoft.pat.FastChar
com.stevesoft.pat.FastChar
|
0.550%
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com.stevesoft.pat.FastMulti
com.stevesoft.pat.FastMulti
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0.550%
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jalview.xml.binding.jalview.VAMSAS
jalview.xml.binding.jalview.VAMSAS
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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
|
0.550%
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jalview.schemes.NucleotideAmbiguityColourScheme
jalview.schemes.NucleotideAmbiguityColourScheme
|
0.550%
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jalview.schemes.PurinePyrimidineColourScheme
jalview.schemes.PurinePyrimidineColourScheme
|
0.550%
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jalview.schemes.NucleotideColourScheme
jalview.schemes.NucleotideColourScheme
|
0.550%
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jalview.schemes.BlossomColourScheme
jalview.schemes.BlossomColourScheme
|
0.550%
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jalview.schemes.SunsetColourScheme
jalview.schemes.SunsetColourScheme
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0.550%
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jalview.schemes.OceanColourScheme
jalview.schemes.OceanColourScheme
|
0.550%
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com.stevesoft.pat.Pattern
com.stevesoft.pat.Pattern
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0.4930555549.3%
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jalview.analysis.AAFrequency
jalview.analysis.AAFrequency
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0.4872881548.7%
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jalview.gui.SequenceRenderer
jalview.gui.SequenceRenderer
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0.4855769348.6%
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jalview.util.MessageManager
jalview.util.MessageManager
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0.4761904847.6%
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jalview.datamodel.RangeIterator
jalview.datamodel.RangeIterator
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0.4594594545.9%
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com.stevesoft.pat.parsePerl
com.stevesoft.pat.parsePerl
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0.448979644.9%
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jalview.ws.jws2.MsaWSClient
jalview.ws.jws2.MsaWSClient
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0.4429530244.3%
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jalview.datamodel.HiddenCursorPosition
jalview.datamodel.HiddenCursorPosition
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0.4285714342.9%
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jalview.gui.IdCanvas
jalview.gui.IdCanvas
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0.4175438641.8%
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jalview.util.ShortcutKeyMaskExWrapper11
jalview.util.ShortcutKeyMaskExWrapper11
|
0.4166666641.7%
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jalview.analysis.SequenceIdMatcher
jalview.analysis.SequenceIdMatcher
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0.412280741.2%
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com.stevesoft.pat.Or
com.stevesoft.pat.Or
|
0.4102564241%
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jalview.analysis.TreeModel
jalview.analysis.TreeModel
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0.406374540.6%
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jalview.renderer.AnnotationRenderer
jalview.renderer.AnnotationRenderer
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0.402173940.2%
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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
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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.viewmodel.AlignmentViewport
jalview.viewmodel.AlignmentViewport
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0.3872699438.7%
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jalview.gui.AlignmentPanel
jalview.gui.AlignmentPanel
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0.382803338.3%
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jalview.renderer.ResidueShader
jalview.renderer.ResidueShader
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0.3785714237.9%
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jalview.datamodel.ResidueCount
jalview.datamodel.ResidueCount
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0.3745454537.5%
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jalview.gui.AlignViewport
jalview.gui.AlignViewport
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0.356164435.6%
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jalview.gui.IdwidthAdjuster
jalview.gui.IdwidthAdjuster
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0.3552631435.5%
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jalview.viewmodel.ViewportRanges
jalview.viewmodel.ViewportRanges
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0.3531353235.3%
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jalview.util.Comparison
jalview.util.Comparison
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0.350393735%
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jalview.util.QuickSort
jalview.util.QuickSort
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0.346278334.6%
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jalview.project.Jalview2XML
jalview.project.Jalview2XML
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0.3375353833.8%
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jalview.schemes.ColourSchemeProperty
jalview.schemes.ColourSchemeProperty
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0.3333333433.3%
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com.stevesoft.pat.Regex
com.stevesoft.pat.Regex
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0.3333%
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jalview.io.FileLoader
jalview.io.FileLoader
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0.3244147332.4%
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jalview.ws.rest.RestServiceDescription
jalview.ws.rest.RestServiceDescription
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0.31531.5%
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jalview.renderer.seqfeatures.FeatureColourFinder
jalview.renderer.seqfeatures.FeatureColourFinder
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0.313725531.4%
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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.schemes.JalviewColourScheme
jalview.schemes.JalviewColourScheme
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0.285714328.6%
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jalview.ws.jws2.JabaPreset
jalview.ws.jws2.JabaPreset
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0.2727272827.3%
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jalview.gui.JvSwingUtils
jalview.gui.JvSwingUtils
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0.258503425.9%
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jalview.gui.PaintRefresher
jalview.gui.PaintRefresher
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0.253521125.4%
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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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com.stevesoft.pat.NullPattern
com.stevesoft.pat.NullPattern
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0.2525%
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com.stevesoft.pat.StringRule
com.stevesoft.pat.StringRule
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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.schemes.ColourSchemes
jalview.schemes.ColourSchemes
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0.2456140424.6%
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jalview.ws.uimodel.AlignAnalysisUIText
jalview.ws.uimodel.AlignAnalysisUIText
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0.2439024424.4%
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jalview.ws.rest.params.Alignment
jalview.ws.rest.params.Alignment
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0.2435897424.4%
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jalview.io.FileFormats
jalview.io.FileFormats
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0.2424%
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com.stevesoft.pat.RegRes
com.stevesoft.pat.RegRes
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0.2391304423.9%
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jalview.datamodel.VisibleContigsIterator
jalview.datamodel.VisibleContigsIterator
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0.2340425623.4%
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jalview.ws.jws2.Jws2Discoverer
jalview.ws.jws2.Jws2Discoverer
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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.datamodel.SequenceNode
jalview.datamodel.SequenceNode
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0.2307692323.1%
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jalview.gui.ScalePanel
jalview.gui.ScalePanel
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0.226562522.7%
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jalview.ws.jws2.Jws2Client
jalview.ws.jws2.Jws2Client
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0.2228915722.3%
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jalview.io.FileParse
jalview.io.FileParse
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0.217270221.7%
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jalview.viewmodel.OverviewDimensionsHideHidden
jalview.viewmodel.OverviewDimensionsHideHidden
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0.211267621.1%
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jalview.gui.TreePanel
jalview.gui.TreePanel
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0.2108626221.1%
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jalview.ws.rest.InputType
jalview.ws.rest.InputType
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0.2056074720.6%
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jalview.gui.AnnotationLabels
jalview.gui.AnnotationLabels
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0.2011764620.1%
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com.stevesoft.pat.patInt
com.stevesoft.pat.patInt
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0.220%
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jalview.datamodel.Sequence
jalview.datamodel.Sequence
|
0.1989619419.9%
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jalview.gui.SeqCanvas
jalview.gui.SeqCanvas
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0.1913827719.1%
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jalview.datamodel.Alignment
jalview.datamodel.Alignment
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0.1852886418.5%
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jalview.analysis.AnnotationSorter
jalview.analysis.AnnotationSorter
|
0.1822660118.2%
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jalview.util.ColorUtils
jalview.util.ColorUtils
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0.1774193517.7%
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jalview.schemes.IdColourScheme
jalview.schemes.IdColourScheme
|
0.1739130517.4%
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jalview.util.StringUtils
jalview.util.StringUtils
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0.1723076917.2%
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jalview.io.IdentifyFile
jalview.io.IdentifyFile
|
0.1682539716.8%
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jalview.datamodel.SequenceGroup
jalview.datamodel.SequenceGroup
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0.1679273816.8%
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jalview.datamodel.AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation
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0.1631116716.3%
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jalview.ws.jws1.WS1Client
jalview.ws.jws1.WS1Client
|
0.1616%
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jalview.gui.AnnotationPanel
jalview.gui.AnnotationPanel
|
0.159654816%
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jalview.gui.Desktop.MyDesktopManager
jalview.gui.Desktop.MyDesktopManager
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0.1555555615.6%
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jalview.util.Format
jalview.util.Format
|
0.1490683314.9%
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jalview.schemes.TCoffeeColourScheme
jalview.schemes.TCoffeeColourScheme
|
0.1475409914.8%
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jalview.workers.AlignCalcWorker
jalview.workers.AlignCalcWorker
|
0.1428571514.3%
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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
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0.1428571514.3%
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jalview.gui.AlignFrame
jalview.gui.AlignFrame
|
0.1409564914.1%
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com.stevesoft.pat.Branch
com.stevesoft.pat.Branch
|
0.140939614.1%
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jalview.bin.Console
jalview.bin.Console
|
0.1330049213.3%
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jalview.ws.rest.params.SeqGroupIndexVector
jalview.ws.rest.params.SeqGroupIndexVector
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0.12408759412.4%
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jalview.datamodel.features.SequenceFeatures
jalview.datamodel.features.SequenceFeatures
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0.1210191112.1%
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jalview.structure.StructureSelectionManager
jalview.structure.StructureSelectionManager
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0.1173333311.7%
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jalview.ws.rest.RestClient
jalview.ws.rest.RestClient
|
0.11538461611.5%
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jalview.datamodel.Annotation
jalview.datamodel.Annotation
|
0.11428571511.4%
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jalview.analysis.scoremodels.ScoreModels
jalview.analysis.scoremodels.ScoreModels
|
0.1132075511.3%
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jalview.util.ShortcutKeyMaskExWrapper
jalview.util.ShortcutKeyMaskExWrapper
|
0.1111111111.1%
|
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jalview.log.JLoggerLog4j
jalview.log.JLoggerLog4j
|
0.10679611610.7%
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jalview.gui.Desktop
jalview.gui.Desktop
|
0.1066969310.7%
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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.Replacer
com.stevesoft.pat.Replacer
|
0.091891899.2%
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com.stevesoft.pat.ReplaceRule
com.stevesoft.pat.ReplaceRule
|
0.08771938.8%
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jalview.gui.TreeCanvas
jalview.gui.TreeCanvas
|
0.087407418.7%
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jalview.ws.dbsources.Xfam
jalview.ws.dbsources.Xfam
|
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.datamodel.HiddenSequences
jalview.datamodel.HiddenSequences
|
0.082191788.2%
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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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jalview.datamodel.HiddenColumns
jalview.datamodel.HiddenColumns
|
0.080188688%
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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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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.io.FileFormat
jalview.io.FileFormat
|
0.0620155046.2%
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ext.vamsas.ServiceHandle
ext.vamsas.ServiceHandle
|
0.061224496.1%
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jalview.bin.Cache
jalview.bin.Cache
|
0.0606060626.1%
|
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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.util.Platform
jalview.util.Platform
|
0.0566037745.7%
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jalview.datamodel.ColumnSelection.IntList
jalview.datamodel.ColumnSelection.IntList
|
0.0560747655.6%
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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%
|
|
|
jalview.datamodel.SecondaryStructureCount
jalview.datamodel.SecondaryStructureCount
|
0.0468754.7%
|
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jalview.util.DBRefUtils
jalview.util.DBRefUtils
|
0.045317224.5%
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jalview.xml.binding.jalview.ObjectFactory
jalview.xml.binding.jalview.ObjectFactory
|
0.0427350444.3%
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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.ws.jws1.JPredClient
jalview.ws.jws1.JPredClient
|
0.0310559013.1%
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jalview.gui.StructureViewerBase
jalview.gui.StructureViewerBase
|
0.028189912.8%
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jalview.gui.AppJmolBinding
jalview.gui.AppJmolBinding
|
0.0280373822.8%
|
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jalview.ext.jmol.JalviewJmolBinding
jalview.ext.jmol.JalviewJmolBinding
|
0.0268595032.7%
|
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jalview.structure.StructureCommandsBase
jalview.structure.StructureCommandsBase
|
0.0243902432.4%
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jalview.structures.models.AAStructureBindingModel
jalview.structures.models.AAStructureBindingModel
|
0.0234466592.3%
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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%
|
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jalview.ws.dbsources.Uniprot
jalview.ws.dbsources.Uniprot
|
0.0155642021.6%
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|
jalview.gui.AppJmol
jalview.gui.AppJmol
|
0.0150375941.5%
|
|
|
jalview.controller.AlignViewController
jalview.controller.AlignViewController
|
0.0136518771.4%
|
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|
jalview.util.HttpUtils
jalview.util.HttpUtils
|
0.0130718961.3%
|
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|
jalview.datamodel.SearchResults
jalview.datamodel.SearchResults
|
0.0128205131.3%
|
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jalview.analysis.AlignSeq
jalview.analysis.AlignSeq
|
0.0128205131.3%
|
|
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jalview.gui.SeqPanel
jalview.gui.SeqPanel
|
0.0125412541.3%
|
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jalview.io.SequenceAnnotationReport
jalview.io.SequenceAnnotationReport
|
0.0122699381.2%
|
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jalview.bin.Jalview
jalview.bin.Jalview
|
0.0117328521.2%
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jalview.datamodel.ColumnSelection
jalview.datamodel.ColumnSelection
|
0.0103092781%
|
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jalview.gui.SequenceFetcher
jalview.gui.SequenceFetcher
|
0.0089285720.9%
|
|
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jalview.bin.argparser.BootstrapArgs
jalview.bin.argparser.BootstrapArgs
|
0.0082644620.8%
|
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jalview.ext.ensembl.EnsemblGene
jalview.ext.ensembl.EnsemblGene
|
0.0081632650.8%
|
|
|
jalview.gui.QuitHandler
jalview.gui.QuitHandler
|
0.0077519380.8%
|
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|
jalview.renderer.seqfeatures.FeatureRenderer
jalview.renderer.seqfeatures.FeatureRenderer
|
0.007547170.8%
|
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|
jalview.analysis.AlignmentUtils
jalview.analysis.AlignmentUtils
|
0.0043859650.4%
|
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jalview.viewmodel.seqfeatures.FeatureRendererModel
jalview.viewmodel.seqfeatures.FeatureRendererModel
|
0.00312989040.3%
|
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|
com.stevesoft.pat.CaseMgr
com.stevesoft.pat.CaseMgr
|
0.00278551530.3%
|
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