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com.stevesoft.pat.patInf
com.stevesoft.pat.patInf
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1.0100%
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jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids
jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids
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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.HiddenCursorPosition
jalview.datamodel.HiddenCursorPosition
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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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jalview.jbgui.GAlignmentPanel
jalview.jbgui.GAlignmentPanel
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0.979166797.9%
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jalview.analysis.Conservation
jalview.analysis.Conservation
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0.8916256489.2%
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jalview.viewmodel.styles.ViewStyle
jalview.viewmodel.styles.ViewStyle
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0.89062589.1%
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jalview.util.QuickSort.IntComparator
jalview.util.QuickSort.IntComparator
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0.8571428785.7%
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com.stevesoft.pat.OrMark
com.stevesoft.pat.OrMark
|
0.8585%
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com.stevesoft.pat.Rthings
com.stevesoft.pat.Rthings
|
0.8461538684.6%
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mc_view.Residue
mc_view.Residue
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0.8461538684.6%
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jalview.datamodel.Profiles
jalview.datamodel.Profiles
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0.833333383.3%
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jalview.datamodel.Profile
jalview.datamodel.Profile
|
0.806451680.6%
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com.stevesoft.pat.SubMark
com.stevesoft.pat.SubMark
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0.880%
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jalview.util.LinkedIdentityHashSet
jalview.util.LinkedIdentityHashSet
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0.7727272577.3%
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jalview.datamodel.StructureViewerModel
jalview.datamodel.StructureViewerModel
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0.7272%
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jalview.workers.ConsensusThread
jalview.workers.ConsensusThread
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0.717171771.7%
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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.gui.JalviewAppender
jalview.gui.JalviewAppender
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0.770%
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com.stevesoft.pat.Bracket
com.stevesoft.pat.Bracket
|
0.770%
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jalview.xml.binding.jalview.SequenceSet
jalview.xml.binding.jalview.SequenceSet
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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.xml.binding.jalview.JalviewModel.FeatureSettings
jalview.xml.binding.jalview.JalviewModel.FeatureSettings
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0.666666766.7%
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jalview.xml.binding.jalview.JalviewModel.JSeq
jalview.xml.binding.jalview.JalviewModel.JSeq
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0.666666766.7%
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jalview.gui.TreePanel.TreeLoader
jalview.gui.TreePanel.TreeLoader
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0.6562565.6%
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jalview.workers.ConservationThread
jalview.workers.ConservationThread
|
0.655172465.5%
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com.stevesoft.pat.Range
com.stevesoft.pat.Range
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0.636363663.6%
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com.stevesoft.pat.wrap.StringWrap
com.stevesoft.pat.wrap.StringWrap
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0.62562.5%
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com.stevesoft.pat.StrPos
com.stevesoft.pat.StrPos
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0.6162790761.6%
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jalview.xml.binding.jalview.Pdbentry
jalview.xml.binding.jalview.Pdbentry
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0.611111161.1%
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jalview.analysis.SequenceIdMatcher.SeqIdName
jalview.analysis.SequenceIdMatcher.SeqIdName
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0.605263260.5%
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jalview.xml.binding.jalview.JalviewModel
jalview.xml.binding.jalview.JalviewModel
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0.5961538659.6%
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jalview.analysis.AlignSeq
jalview.analysis.AlignSeq
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0.589648859%
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jalview.xml.binding.jalview.Feature
jalview.xml.binding.jalview.Feature
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0.588235358.8%
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jalview.jbgui.GAlignFrame
jalview.jbgui.GAlignFrame
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0.586826358.7%
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jalview.jbgui.GTreePanel
jalview.jbgui.GTreePanel
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0.5858%
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jalview.util.CaseInsensitiveString
jalview.util.CaseInsensitiveString
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0.565217456.5%
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jalview.datamodel.HiddenColumnsCursor
jalview.datamodel.HiddenColumnsCursor
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0.562556.2%
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jalview.workers.AlignCalcManager
jalview.workers.AlignCalcManager
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0.554838755.5%
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jalview.datamodel.PDBEntry
jalview.datamodel.PDBEntry
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0.5414012754.1%
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mc_view.PDBChain
mc_view.PDBChain
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0.5359281353.6%
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jalview.xml.binding.jalview.Annotation
jalview.xml.binding.jalview.Annotation
|
0.5288461452.9%
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jalview.gui.PaintRefresher
jalview.gui.PaintRefresher
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0.5211267552.1%
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jalview.ext.jmol.JmolParser
jalview.ext.jmol.JmolParser
|
0.519108351.9%
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com.stevesoft.pat.Boundary
com.stevesoft.pat.Boundary
|
0.518518551.9%
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jalview.xml.binding.jalview.JalviewModel.Viewport
jalview.xml.binding.jalview.JalviewModel.Viewport
|
0.507812550.8%
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jalview.datamodel.BinaryNode
jalview.datamodel.BinaryNode
|
0.5066666650.7%
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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
|
0.550%
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jalview.viewmodel.ViewportProperties
jalview.viewmodel.ViewportProperties
|
0.550%
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jalview.xml.binding.jalview.Feature.OtherData
jalview.xml.binding.jalview.Feature.OtherData
|
0.550%
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jalview.xml.binding.jalview.AnnotationElement
jalview.xml.binding.jalview.AnnotationElement
|
0.550%
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jalview.xml.binding.jalview.SequenceType
jalview.xml.binding.jalview.SequenceType
|
0.550%
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jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group
jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group
|
0.550%
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jalview.xml.binding.jalview.JalviewModel.Tree
jalview.xml.binding.jalview.JalviewModel.Tree
|
0.550%
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jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns
jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns
|
0.550%
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jalview.xml.binding.jalview.Sequence.DBRef
jalview.xml.binding.jalview.Sequence.DBRef
|
0.550%
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mc_view.Bond
mc_view.Bond
|
0.550%
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jalview.datamodel.StructureViewerModel.StructureData
jalview.datamodel.StructureViewerModel.StructureData
|
0.550%
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jalview.schemes.TaylorColourScheme
jalview.schemes.TaylorColourScheme
|
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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com.stevesoft.pat.Pattern
com.stevesoft.pat.Pattern
|
0.4930555549.3%
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jalview.analysis.SequenceIdMatcher
jalview.analysis.SequenceIdMatcher
|
0.4912280749.1%
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jalview.xml.binding.jalview.JalviewModel.JGroup
jalview.xml.binding.jalview.JalviewModel.JGroup
|
0.4901960849%
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jalview.gui.SplashScreen.SplashImage
jalview.gui.SplashScreen.SplashImage
|
0.4705882447.1%
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jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState
jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.StructureState
|
0.464285746.4%
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jalview.ws.jws2.MsaWSClient
jalview.ws.jws2.MsaWSClient
|
0.4551724245.5%
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jalview.schemes.ResidueColourScheme
jalview.schemes.ResidueColourScheme
|
0.4523809645.2%
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com.stevesoft.pat.parsePerl
com.stevesoft.pat.parsePerl
|
0.448979644.9%
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jalview.datamodel.ResidueCount
jalview.datamodel.ResidueCount
|
0.4476534444.8%
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jalview.gui.ColourMenuHelper
jalview.gui.ColourMenuHelper
|
0.4322033843.2%
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jalview.xml.binding.jalview.Sequence
jalview.xml.binding.jalview.Sequence
|
0.4285714342.9%
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jalview.util.ShortcutKeyMaskExWrapper11
jalview.util.ShortcutKeyMaskExWrapper11
|
0.4166666641.7%
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com.stevesoft.pat.Or
com.stevesoft.pat.Or
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0.4102564241%
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jalview.schemes.HydrophobicColourScheme
jalview.schemes.HydrophobicColourScheme
|
0.440%
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jalview.schemes.HelixColourScheme
jalview.schemes.HelixColourScheme
|
0.440%
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jalview.schemes.TurnColourScheme
jalview.schemes.TurnColourScheme
|
0.440%
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jalview.schemes.StrandColourScheme
jalview.schemes.StrandColourScheme
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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.viewmodel.ViewportRanges
jalview.viewmodel.ViewportRanges
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0.3993399439.9%
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jalview.io.StructureFile
jalview.io.StructureFile
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0.379487237.9%
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jalview.datamodel.SequenceFeature
jalview.datamodel.SequenceFeature
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0.3763440837.6%
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jalview.gui.AlignmentPanel
jalview.gui.AlignmentPanel
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0.3754838737.5%
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jalview.analysis.AAFrequency
jalview.analysis.AAFrequency
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0.37537.5%
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jalview.analysis.TreeModel
jalview.analysis.TreeModel
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0.3705179437.1%
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jalview.util.Format
jalview.util.Format
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0.3685300436.9%
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jalview.viewmodel.AlignmentViewport
jalview.viewmodel.AlignmentViewport
|
0.3665835636.7%
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jalview.io.NewickFile
jalview.io.NewickFile
|
0.3663594436.6%
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jalview.datamodel.SequenceNode
jalview.datamodel.SequenceNode
|
0.3658536736.6%
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jalview.util.MessageManager
jalview.util.MessageManager
|
0.3571428735.7%
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jalview.util.QuickSort
jalview.util.QuickSort
|
0.352750835.3%
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jalview.gui.AlignViewport
jalview.gui.AlignViewport
|
0.3388625733.9%
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jalview.datamodel.AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation
|
0.3354510733.5%
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jalview.xml.binding.jalview.VAMSAS
jalview.xml.binding.jalview.VAMSAS
|
0.3333333433.3%
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com.stevesoft.pat.Regex
com.stevesoft.pat.Regex
|
0.3245454432.5%
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jalview.ws.rest.RestServiceDescription
jalview.ws.rest.RestServiceDescription
|
0.31531.5%
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jalview.datamodel.Annotation
jalview.datamodel.Annotation
|
0.3142857331.4%
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jalview.datamodel.PDBEntry.Type
jalview.datamodel.PDBEntry.Type
|
0.312531.2%
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jalview.io.FileLoader
jalview.io.FileLoader
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0.2969924829.7%
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jalview.datamodel.Sequence
jalview.datamodel.Sequence
|
0.290441229%
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jalview.ws.jws2.SequenceAnnotationWSClient
jalview.ws.jws2.SequenceAnnotationWSClient
|
0.2903225729%
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jalview.structure.StructureSelectionManager
jalview.structure.StructureSelectionManager
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0.2892690628.9%
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jalview.datamodel.HiddenSequences
jalview.datamodel.HiddenSequences
|
0.2876712428.8%
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jalview.schemes.JalviewColourScheme
jalview.schemes.JalviewColourScheme
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0.285714328.6%
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mc_view.Atom
mc_view.Atom
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0.282051328.2%
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jalview.datamodel.features.FeatureStore
jalview.datamodel.features.FeatureStore
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0.2809667628.1%
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jalview.ws.jws2.JabaPreset
jalview.ws.jws2.JabaPreset
|
0.2727272827.3%
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jalview.project.Jalview2XML
jalview.project.Jalview2XML
|
0.261334126.1%
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jalview.gui.JvSwingUtils
jalview.gui.JvSwingUtils
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0.258503425.9%
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jalview.structure.StructureImportSettings
jalview.structure.StructureImportSettings
|
0.258064525.8%
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jalview.ws.jws2.jabaws2.Jws2Instance
jalview.ws.jws2.jabaws2.Jws2Instance
|
0.2528735725.3%
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com.stevesoft.pat.NullPattern
com.stevesoft.pat.NullPattern
|
0.2525%
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com.stevesoft.pat.StringRule
com.stevesoft.pat.StringRule
|
0.2525%
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jalview.schemes.ColourSchemeProperty
jalview.schemes.ColourSchemeProperty
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0.2525%
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jalview.util.Comparison
jalview.util.Comparison
|
0.2485875624.9%
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jalview.analysis.scoremodels.ScoreModels
jalview.analysis.scoremodels.ScoreModels
|
0.2444444424.4%
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jalview.ws.uimodel.AlignAnalysisUIText
jalview.ws.uimodel.AlignAnalysisUIText
|
0.2439024424.4%
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jalview.ws.rest.params.Alignment
jalview.ws.rest.params.Alignment
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0.2435897424.4%
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jalview.datamodel.DBRefEntry
jalview.datamodel.DBRefEntry
|
0.2403100724%
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jalview.io.FileFormats
jalview.io.FileFormats
|
0.2424%
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com.stevesoft.pat.RegRes
com.stevesoft.pat.RegRes
|
0.2391304423.9%
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jalview.gui.TreePanel
jalview.gui.TreePanel
|
0.2382671523.8%
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jalview.io.FileParse
jalview.io.FileParse
|
0.2351190423.5%
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jalview.ws.jws2.Jws2Discoverer
jalview.ws.jws2.Jws2Discoverer
|
0.2336633723.4%
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jalview.datamodel.SequenceCursor
jalview.datamodel.SequenceCursor
|
0.2333333323.3%
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jalview.structure.StructureMapping
jalview.structure.StructureMapping
|
0.2279792722.8%
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jalview.datamodel.features.FeatureAttributes
jalview.datamodel.features.FeatureAttributes
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0.224806222.5%
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jalview.ws.jws2.Jws2Client
jalview.ws.jws2.Jws2Client
|
0.2202380922%
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jalview.analysis.AnnotationSorter
jalview.analysis.AnnotationSorter
|
0.2139037421.4%
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jalview.datamodel.features.FeatureAttributes.AttributeData
jalview.datamodel.features.FeatureAttributes.AttributeData
|
0.2127659621.3%
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jalview.ws.rest.InputType
jalview.ws.rest.InputType
|
0.2056074720.6%
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jalview.schemes.ColourSchemes
jalview.schemes.ColourSchemes
|
0.2040816420.4%
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com.stevesoft.pat.patInt
com.stevesoft.pat.patInt
|
0.220%
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jalview.renderer.ResidueShader
jalview.renderer.ResidueShader
|
0.220%
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jalview.util.StringUtils
jalview.util.StringUtils
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0.220%
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jalview.datamodel.Alignment
jalview.datamodel.Alignment
|
0.198623419.9%
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jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting
jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting
|
0.1935483819.4%
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jalview.datamodel.features.SequenceFeatures
jalview.datamodel.features.SequenceFeatures
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0.191082819.1%
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jalview.datamodel.SequenceGroup
jalview.datamodel.SequenceGroup
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0.1856899618.6%
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jalview.ws.dbsources.EmblSource
jalview.ws.dbsources.EmblSource
|
0.1818181918.2%
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jalview.io.IdentifyFile
jalview.io.IdentifyFile
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0.1760563417.6%
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jalview.schemes.IdColourScheme
jalview.schemes.IdColourScheme
|
0.1739130517.4%
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jalview.ws.jws1.WS1Client
jalview.ws.jws1.WS1Client
|
0.1616%
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jalview.gui.AlignFrame
jalview.gui.AlignFrame
|
0.1569169915.7%
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jalview.gui.Desktop.MyDesktopManager
jalview.gui.Desktop.MyDesktopManager
|
0.1555555615.6%
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jalview.viewmodel.seqfeatures.FeatureRendererSettings
jalview.viewmodel.seqfeatures.FeatureRendererSettings
|
0.1555555615.6%
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jalview.ws.dbsources.EmblCdsSource
jalview.ws.dbsources.EmblCdsSource
|
0.1538461615.4%
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jalview.schemes.TCoffeeColourScheme
jalview.schemes.TCoffeeColourScheme
|
0.1475409914.8%
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jalview.gui.Desktop
jalview.gui.Desktop
|
0.1457550714.6%
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com.stevesoft.pat.Branch
com.stevesoft.pat.Branch
|
0.140939614.1%
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jalview.viewmodel.seqfeatures.FeaturesDisplayed
jalview.viewmodel.seqfeatures.FeaturesDisplayed
|
0.1379310313.8%
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jalview.io.AlignFile
jalview.io.AlignFile
|
0.1349206413.5%
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jalview.util.MapList
jalview.util.MapList
|
0.1339130413.4%
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jalview.gui.SplashScreen
jalview.gui.SplashScreen
|
0.1293103412.9%
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jalview.ws.rest.params.SeqGroupIndexVector
jalview.ws.rest.params.SeqGroupIndexVector
|
0.12408759412.4%
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jalview.gui.Console
jalview.gui.Console
|
0.12380952412.4%
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jalview.analysis.CrossRef
jalview.analysis.CrossRef
|
0.1229508212.3%
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jalview.gui.IdwidthAdjuster
jalview.gui.IdwidthAdjuster
|
0.1190476211.9%
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jalview.schemes.Blosum62ColourScheme
jalview.schemes.Blosum62ColourScheme
|
0.1176470611.8%
|
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jalview.ws.rest.RestClient
jalview.ws.rest.RestClient
|
0.11538461611.5%
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jalview.gui.BlogReader
jalview.gui.BlogReader
|
0.1142061311.4%
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jalview.util.ColorUtils
jalview.util.ColorUtils
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jalview.util.ShortcutKeyMaskExWrapper
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jalview.ws.sifts.SiftsSettings
jalview.ws.sifts.SiftsSettings
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jalview.gui.ProgressBar
jalview.gui.ProgressBar
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jalview.util.DBRefUtils
jalview.util.DBRefUtils
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jalview.analysis.scoremodels.ScoreMatrix
jalview.analysis.scoremodels.ScoreMatrix
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jalview.ws.rest.params.AnnotationFile
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jalview.datamodel.Mapping
jalview.datamodel.Mapping
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jalview.workers.AlignCalcWorker
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jalview.gui.TreeCanvas
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jalview.gui.AnnotationPanel
jalview.gui.AnnotationPanel
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com.stevesoft.pat.ReplaceRule
com.stevesoft.pat.ReplaceRule
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jalview.ext.ensembl.EnsemblSequenceFetcher
jalview.ext.ensembl.EnsemblSequenceFetcher
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jalview.schemes.RNAHelicesColour
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jalview.schemes.FeatureColour
jalview.schemes.FeatureColour
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jalview.ws.dbsources.Xfam
jalview.ws.dbsources.Xfam
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jalview.gui.SeqCanvas
jalview.gui.SeqCanvas
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jalview.bin.Cache
jalview.bin.Cache
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jalview.io.FileFormat
jalview.io.FileFormat
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jalview.schemes.PIDColourScheme
jalview.schemes.PIDColourScheme
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com.stevesoft.pat.RegOpt
com.stevesoft.pat.RegOpt
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jalview.gui.IdPanel
jalview.gui.IdPanel
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ext.vamsas.ServiceHandle
ext.vamsas.ServiceHandle
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jalview.util.Platform
jalview.util.Platform
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jalview.gui.ViewSelectionMenu
jalview.gui.ViewSelectionMenu
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jalview.datamodel.HiddenColumns
jalview.datamodel.HiddenColumns
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jalview.ws.seqfetcher.ASequenceFetcher
jalview.ws.seqfetcher.ASequenceFetcher
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jalview.gui.StructureViewerBase
jalview.gui.StructureViewerBase
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jalview.datamodel.ColumnSelection.IntList
jalview.datamodel.ColumnSelection.IntList
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jalview.ws.seqfetcher.DbSourceProxyImpl
jalview.ws.seqfetcher.DbSourceProxyImpl
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jalview.ws.jws1.Discoverer
jalview.ws.jws1.Discoverer
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jalview.gui.IdCanvas
jalview.gui.IdCanvas
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jalview.analysis.GeneticCodes
jalview.analysis.GeneticCodes
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jalview.gui.Desktop.MyDesktopPane
jalview.gui.Desktop.MyDesktopPane
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jalview.io.AppletFormatAdapter
jalview.io.AppletFormatAdapter
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jalview.ws.dbsources.Pdb
jalview.ws.dbsources.Pdb
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jalview.ws.jws2.JabaParamStore
jalview.ws.jws2.JabaParamStore
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jalview.gui.ScalePanel
jalview.gui.ScalePanel
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jalview.gui.SliderPanel
jalview.gui.SliderPanel
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jalview.ws.jws1.JPredClient
jalview.ws.jws1.JPredClient
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jalview.structures.models.AAStructureBindingModel
jalview.structures.models.AAStructureBindingModel
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jalview.controller.AlignViewController
jalview.controller.AlignViewController
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jalview.renderer.ResidueColourFinder
jalview.renderer.ResidueColourFinder
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jalview.schemes.ClustalxColourScheme
jalview.schemes.ClustalxColourScheme
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jalview.ws.dbsources.Uniprot
jalview.ws.dbsources.Uniprot
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jalview.datamodel.SearchResults
jalview.datamodel.SearchResults
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jalview.gui.AnnotationLabels
jalview.gui.AnnotationLabels
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mc_view.PDBfile
mc_view.PDBfile
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jalview.gui.SequenceRenderer
jalview.gui.SequenceRenderer
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jalview.gui.SeqPanel
jalview.gui.SeqPanel
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jalview.io.SequenceAnnotationReport
jalview.io.SequenceAnnotationReport
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jalview.datamodel.ColumnSelection
jalview.datamodel.ColumnSelection
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jalview.bin.Jalview
jalview.bin.Jalview
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jalview.viewmodel.seqfeatures.FeatureRendererModel
jalview.viewmodel.seqfeatures.FeatureRendererModel
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jalview.gui.SequenceFetcher
jalview.gui.SequenceFetcher
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jalview.ext.ensembl.EnsemblGene
jalview.ext.ensembl.EnsemblGene
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jalview.renderer.seqfeatures.FeatureRenderer
jalview.renderer.seqfeatures.FeatureRenderer
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jalview.gui.AppJmol
jalview.gui.AppJmol
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jalview.ext.jmol.JalviewJmolBinding
jalview.ext.jmol.JalviewJmolBinding
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jalview.renderer.AnnotationRenderer
jalview.renderer.AnnotationRenderer
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com.stevesoft.pat.CaseMgr
com.stevesoft.pat.CaseMgr
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jalview.schemes.ResidueProperties
jalview.schemes.ResidueProperties
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