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jalview.io.DataSourceType
jalview.io.DataSourceType
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1.0100%
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jalview.renderer.ScaleRenderer.ScaleMark
jalview.renderer.ScaleRenderer.ScaleMark
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1.0100%
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jalview.ws.WSClient
jalview.ws.WSClient
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1.0100%
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jalview.ws.SequenceFetcher
jalview.ws.SequenceFetcher
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1.0100%
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jalview.util.MathUtils
jalview.util.MathUtils
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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.Sequence.DBModList
jalview.datamodel.Sequence.DBModList
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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.workers.ComplementConsensusThread
jalview.workers.ComplementConsensusThread
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jalview.viewmodel.seqfeatures.FeatureRendererSettings
jalview.viewmodel.seqfeatures.FeatureRendererSettings
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0.888888988.9%
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jalview.gui.SplashScreen.SplashImage
jalview.gui.SplashScreen.SplashImage
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0.8823529588.2%
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jalview.analysis.CodonComparator
jalview.analysis.CodonComparator
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0.8709677587.1%
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jalview.io.JalviewFileChooser.recentlyOpenedCellRenderer
jalview.io.JalviewFileChooser.recentlyOpenedCellRenderer
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0.869565287%
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jalview.viewmodel.styles.ViewStyle
jalview.viewmodel.styles.ViewStyle
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0.858695685.9%
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jalview.json.binding.biojs.BioJSReleasePojo
jalview.json.binding.biojs.BioJSReleasePojo
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0.8461538684.6%
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jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids
jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids
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0.833333383.3%
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jalview.datamodel.DBRefSource
jalview.datamodel.DBRefSource
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0.833333383.3%
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jalview.datamodel.Profiles
jalview.datamodel.Profiles
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jalview.datamodel.GeneLocus
jalview.datamodel.GeneLocus
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0.812581.2%
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jalview.gui.ItemsRenderer
jalview.gui.ItemsRenderer
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0.777777877.8%
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jalview.ws.jws2.jabaws2.Jws2Instance
jalview.ws.jws2.jabaws2.Jws2Instance
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0.7701149677%
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jalview.analysis.Conservation
jalview.analysis.Conservation
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0.761083776.1%
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jalview.analysis.CodingUtils
jalview.analysis.CodingUtils
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0.758620775.9%
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jalview.workers.SecondaryStructureConsensusThread
jalview.workers.SecondaryStructureConsensusThread
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0.7555555775.6%
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jalview.ws.jws2.jabaws2.Jws2InstanceFactory
jalview.ws.jws2.jabaws2.Jws2InstanceFactory
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0.7575%
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jalview.datamodel.Mapping.AlignedCodonIterator
jalview.datamodel.Mapping.AlignedCodonIterator
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0.7575%
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jalview.xml.binding.jalview.SequenceSet
jalview.xml.binding.jalview.SequenceSet
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0.736842173.7%
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jalview.workers.ConsensusThread
jalview.workers.ConsensusThread
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0.7272727572.7%
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jalview.gui.FeatureRenderer
jalview.gui.FeatureRenderer
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0.7142857371.4%
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jalview.json.binding.biojs.BioJSRepositoryPojo
jalview.json.binding.biojs.BioJSRepositoryPojo
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0.687568.8%
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jalview.analysis.SequenceIdMatcher.SeqIdName
jalview.analysis.SequenceIdMatcher.SeqIdName
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jalview.datamodel.VisibleContigsIterator
jalview.datamodel.VisibleContigsIterator
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jalview.datamodel.Profile
jalview.datamodel.Profile
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jalview.xml.binding.jalview.JalviewModel.FeatureSettings
jalview.xml.binding.jalview.JalviewModel.FeatureSettings
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jalview.ws.dbsources.PfamSeed
jalview.ws.dbsources.PfamSeed
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0.636363663.6%
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jalview.xml.binding.jalview.JalviewModel
jalview.xml.binding.jalview.JalviewModel
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0.6153846461.5%
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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.datamodel.HiddenColumnsCursor
jalview.datamodel.HiddenColumnsCursor
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0.60937560.9%
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jalview.ws.dbsources.EmblSource
jalview.ws.dbsources.EmblSource
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0.660%
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jalview.xml.binding.jalview.MapListType
jalview.xml.binding.jalview.MapListType
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0.660%
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jalview.jbgui.GAlignFrame
jalview.jbgui.GAlignFrame
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0.580943658.1%
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jalview.xml.binding.jalview.Sequence
jalview.xml.binding.jalview.Sequence
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0.571428657.1%
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jalview.schemes.FeatureSettingsAdapter
jalview.schemes.FeatureSettingsAdapter
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0.571428657.1%
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jalview.workers.ConservationThread
jalview.workers.ConservationThread
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0.568965556.9%
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jalview.xml.binding.jalview.JalviewModel.JSeq
jalview.xml.binding.jalview.JalviewModel.JSeq
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0.562556.2%
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jalview.xml.binding.jalview.Sequence.DBRef
jalview.xml.binding.jalview.Sequence.DBRef
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0.562556.2%
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jalview.renderer.ScaleRenderer
jalview.renderer.ScaleRenderer
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0.5656%
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jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping
jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping
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0.5446428754.5%
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jalview.ws.dbsources.PfamFull
jalview.ws.dbsources.PfamFull
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0.5384615753.8%
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jalview.gui.SplashScreen
jalview.gui.SplashScreen
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0.5324675453.2%
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jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting
jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Setting
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0.532258153.2%
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jalview.datamodel.features.FeatureAttributes.AttributeData
jalview.datamodel.features.FeatureAttributes.AttributeData
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jalview.xml.binding.jalview.Feature
jalview.xml.binding.jalview.Feature
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0.529411852.9%
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jalview.util.MessageManager
jalview.util.MessageManager
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0.5238095552.4%
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jalview.analysis.AAFrequency
jalview.analysis.AAFrequency
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0.518518551.9%
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jalview.gui.CrossRefAction
jalview.gui.CrossRefAction
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0.5136363551.4%
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jalview.gui.JalviewChangeSupport
jalview.gui.JalviewChangeSupport
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0.550%
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jalview.viewmodel.seqfeatures.FeaturesDisplayed
jalview.viewmodel.seqfeatures.FeaturesDisplayed
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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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jalview.xml.binding.jalview.Feature.OtherData
jalview.xml.binding.jalview.Feature.OtherData
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0.550%
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jalview.xml.binding.jalview.AnnotationElement
jalview.xml.binding.jalview.AnnotationElement
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jalview.xml.binding.jalview.SequenceType
jalview.xml.binding.jalview.SequenceType
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jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group
jalview.xml.binding.jalview.JalviewModel.FeatureSettings.Group
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jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns
jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns
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0.550%
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jalview.xml.binding.jalview.MapListType.MapListFrom
jalview.xml.binding.jalview.MapListType.MapListFrom
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jalview.xml.binding.jalview.MapListType.MapListTo
jalview.xml.binding.jalview.MapListType.MapListTo
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jalview.io.gff.SequenceOntologyFactory
jalview.io.gff.SequenceOntologyFactory
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jalview.schemes.TaylorColourScheme
jalview.schemes.TaylorColourScheme
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jalview.schemes.FlowerColourScheme
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jalview.schemes.ZappoColourScheme
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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
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0.550%
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jalview.schemes.OceanColourScheme
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0.550%
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jalview.xml.binding.jalview.Annotation
jalview.xml.binding.jalview.Annotation
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0.4818181748.2%
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jalview.xml.binding.jalview.JalviewModel.Viewport
jalview.xml.binding.jalview.JalviewModel.Viewport
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0.4771241847.7%
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jalview.jbgui.GSplitFrame
jalview.jbgui.GSplitFrame
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0.4657534446.6%
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jalview.datamodel.DBRefEntry
jalview.datamodel.DBRefEntry
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0.4657534446.6%
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jalview.io.BioJsHTMLOutput
jalview.io.BioJsHTMLOutput
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0.46446.4%
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jalview.datamodel.AlignedCodonFrame
jalview.datamodel.AlignedCodonFrame
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0.4607508546.1%
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jalview.ws.jws2.JabaWsServerQuery
jalview.ws.jws2.JabaWsServerQuery
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0.4583333445.8%
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jalview.gui.AlignViewport
jalview.gui.AlignViewport
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0.45662145.7%
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jalview.datamodel.StartRegionIterator
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0.4444444544.4%
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jalview.ws.jws2.MsaWSClient
jalview.ws.jws2.MsaWSClient
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0.4429530244.3%
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jalview.workers.AlignCalcManager
jalview.workers.AlignCalcManager
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0.4345238243.5%
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jalview.gui.ColourMenuHelper
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0.4322033843.2%
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jalview.datamodel.Sequence
jalview.datamodel.Sequence
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0.4290657342.9%
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jalview.ws.utils.UrlDownloadClient
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jalview.ws.dbsources.EmblCdsSource
jalview.ws.dbsources.EmblCdsSource
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jalview.ws.dbsources.RfamSeed
jalview.ws.dbsources.RfamSeed
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0.4285714342.9%
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jalview.util.QuickSort.IntComparator
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0.4285714342.9%
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jalview.viewmodel.AlignmentViewport
jalview.viewmodel.AlignmentViewport
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0.4266862342.7%
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jalview.util.ShortcutKeyMaskExWrapper11
jalview.util.ShortcutKeyMaskExWrapper11
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0.4166666641.7%
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jalview.gui.ProgressBar
jalview.gui.ProgressBar
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jalview.datamodel.SequenceFeature
jalview.datamodel.SequenceFeature
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0.4100719441%
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jalview.ws.jws2.JabaPreset
jalview.ws.jws2.JabaPreset
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0.409090940.9%
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jalview.gui.SequenceRenderer
jalview.gui.SequenceRenderer
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0.4086538640.9%
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jalview.datamodel.features.SequenceFeatures
jalview.datamodel.features.SequenceFeatures
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0.4012738840.1%
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jalview.ws.jws2.Jws2Discoverer
jalview.ws.jws2.Jws2Discoverer
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jalview.schemes.HydrophobicColourScheme
jalview.schemes.HydrophobicColourScheme
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jalview.schemes.HelixColourScheme
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0.440%
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jalview.schemes.TurnColourScheme
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0.440%
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jalview.schemes.StrandColourScheme
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0.440%
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jalview.schemes.BuriedColourScheme
jalview.schemes.BuriedColourScheme
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0.440%
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jalview.datamodel.AlignedCodon
jalview.datamodel.AlignedCodon
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0.393939439.4%
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jalview.log.JalviewAppender
jalview.log.JalviewAppender
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0.388888938.9%
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jalview.datamodel.Range
jalview.datamodel.Range
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0.388888938.9%
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jalview.datamodel.ResidueCount
jalview.datamodel.ResidueCount
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0.3854545438.5%
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org.json.simple.parser.Yylex
org.json.simple.parser.Yylex
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0.3853503238.5%
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jalview.util.QuickSort
jalview.util.QuickSort
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0.3851132738.5%
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jalview.gui.AlignmentPanel
jalview.gui.AlignmentPanel
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0.3698468837%
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jalview.util.MapList
jalview.util.MapList
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0.3629283636.3%
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jalview.viewmodel.seqfeatures.FeatureRendererModel
jalview.viewmodel.seqfeatures.FeatureRendererModel
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0.359937436%
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jalview.schemes.ResidueColourScheme
jalview.schemes.ResidueColourScheme
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0.3571428735.7%
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jalview.analysis.SequenceIdMatcher
jalview.analysis.SequenceIdMatcher
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0.350877235.1%
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jalview.analysis.CrossRef
jalview.analysis.CrossRef
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0.3483606634.8%
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jalview.util.Comparison
jalview.util.Comparison
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0.3425196734.3%
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jalview.gui.SplitFrame
jalview.gui.SplitFrame
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0.3421633534.2%
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jalview.util.DBRefUtils
jalview.util.DBRefUtils
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0.3413897234.1%
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jalview.ext.so.SequenceOntology
jalview.ext.so.SequenceOntology
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0.337533.8%
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jalview.viewmodel.ViewportRanges
jalview.viewmodel.ViewportRanges
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0.3333333433.3%
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jalview.xml.binding.jalview.VAMSAS
jalview.xml.binding.jalview.VAMSAS
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0.3333333433.3%
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jalview.xml.binding.jalview.Mapping
jalview.xml.binding.jalview.Mapping
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0.3333333433.3%
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jalview.renderer.seqfeatures.FeatureRenderer
jalview.renderer.seqfeatures.FeatureRenderer
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0.320754732.1%
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jalview.ws.rest.RestServiceDescription
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0.31531.5%
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jalview.datamodel.SearchResults
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0.3141025631.4%
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jalview.io.FileLoader
jalview.io.FileLoader
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0.3076923230.8%
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jalview.gui.IdCanvas
jalview.gui.IdCanvas
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0.3052631630.5%
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jalview.analysis.AlignmentUtils
jalview.analysis.AlignmentUtils
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0.2962707329.6%
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org.json.simple.parser.JSONParser
org.json.simple.parser.JSONParser
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0.2945544429.5%
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jalview.ws.jws2.SequenceAnnotationWSClient
jalview.ws.jws2.SequenceAnnotationWSClient
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0.2903225729%
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jalview.datamodel.features.FeatureStore
jalview.datamodel.features.FeatureStore
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0.290030229%
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jalview.datamodel.features.FeatureAttributes
jalview.datamodel.features.FeatureAttributes
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0.286821728.7%
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jalview.renderer.ResidueColourFinder
jalview.renderer.ResidueColourFinder
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0.285714328.6%
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jalview.schemes.JalviewColourScheme
jalview.schemes.JalviewColourScheme
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0.285714328.6%
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jalview.datamodel.PDBEntry
jalview.datamodel.PDBEntry
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0.282608728.3%
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jalview.gui.JvSwingUtils
jalview.gui.JvSwingUtils
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0.258503425.9%
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jalview.ext.ensembl.EnsemblSequenceFetcher
jalview.ext.ensembl.EnsemblSequenceFetcher
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0.2525%
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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
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0.2435897424.4%
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jalview.gui.BlogReader
jalview.gui.BlogReader
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0.2430939224.3%
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jalview.gui.ScalePanel
jalview.gui.ScalePanel
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0.242187524.2%
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jalview.io.FileFormats
jalview.io.FileFormats
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0.2424%
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jalview.datamodel.SequenceCursor
jalview.datamodel.SequenceCursor
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0.2333333323.3%
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jalview.datamodel.Alignment
jalview.datamodel.Alignment
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0.2318435823.2%
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jalview.gui.IdwidthAdjuster
jalview.gui.IdwidthAdjuster
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0.223684222.4%
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jalview.ws.jws2.Jws2Client
jalview.ws.jws2.Jws2Client
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0.2228915722.3%
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jalview.util.ColorUtils
jalview.util.ColorUtils
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0.220430122%
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jalview.project.Jalview2XML
jalview.project.Jalview2XML
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0.2185666921.9%
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jalview.schemes.FeatureColour
jalview.schemes.FeatureColour
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0.216842121.7%
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jalview.gui.PromptUserConfig
jalview.gui.PromptUserConfig
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0.215909121.6%
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jalview.controller.AlignViewController
jalview.controller.AlignViewController
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0.2081911320.8%
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jalview.ws.rest.InputType
jalview.ws.rest.InputType
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0.2056074720.6%
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jalview.ws.seqfetcher.ASequenceFetcher
jalview.ws.seqfetcher.ASequenceFetcher
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0.1866666718.7%
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jalview.io.FileParse
jalview.io.FileParse
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0.1866295318.7%
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jalview.util.MappingUtils
jalview.util.MappingUtils
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0.1853448318.5%
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jalview.datamodel.SearchResults.Match
jalview.datamodel.SearchResults.Match
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0.1818181918.2%
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jalview.ws.dbsources.Xfam
jalview.ws.dbsources.Xfam
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0.1739130517.4%
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jalview.schemes.IdColourScheme
jalview.schemes.IdColourScheme
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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.datamodel.ColumnSelection.IntList
jalview.datamodel.ColumnSelection.IntList
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jalview.analysis.AnnotationSorter
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jalview.io.IdentifyFile
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jalview.gui.PaintRefresher
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jalview.ws.jws1.WS1Client
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jalview.gui.Desktop.MyDesktopManager
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jalview.util.Format
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jalview.schemes.TCoffeeColourScheme
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jalview.ws.jws2.JabaParamStore
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jalview.log.JLogger
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jalview.gui.Desktop.MyDesktopPane
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jalview.datamodel.Mapping
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jalview.ws.seqfetcher.DbSourceProxyImpl
jalview.ws.seqfetcher.DbSourceProxyImpl
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jalview.datamodel.HiddenColumns
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jalview.bin.Console
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jalview.gui.AlignFrame
jalview.gui.AlignFrame
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jalview.datamodel.AlignmentAnnotation
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jalview.renderer.ResidueShader
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jalview.ws.dbsources.Rfam
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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.gui.SeqCanvas
jalview.gui.SeqCanvas
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jalview.schemes.Blosum62ColourScheme
jalview.schemes.Blosum62ColourScheme
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jalview.datamodel.ColumnSelection
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jalview.analysis.scoremodels.ScoreModels
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jalview.ws.rest.RestClient
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0.11538461611.5%
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jalview.ext.ensembl.EnsemblGene
jalview.ext.ensembl.EnsemblGene
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0.11428571511.4%
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jalview.datamodel.Annotation
jalview.datamodel.Annotation
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jalview.util.ShortcutKeyMaskExWrapper
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jalview.schemes.ColourSchemeProperty
jalview.schemes.ColourSchemeProperty
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jalview.log.JLoggerLog4j
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jalview.ws.rest.params.AnnotationFile
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jalview.gui.Desktop
jalview.gui.Desktop
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org.json.simple.parser.Yytoken
org.json.simple.parser.Yytoken
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0.096774199.7%
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jalview.workers.AlignCalcWorker
jalview.workers.AlignCalcWorker
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jalview.util.JSONUtils
jalview.util.JSONUtils
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jalview.util.Platform
jalview.util.Platform
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jalview.ws.dbsources.Pfam
jalview.ws.dbsources.Pfam
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jalview.gui.Console
jalview.gui.Console
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jalview.datamodel.HiddenSequences
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jalview.schemes.RNAHelicesColour
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jalview.schemes.ColourSchemes
jalview.schemes.ColourSchemes
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jalview.gui.IdPanel
jalview.gui.IdPanel
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junit.extensions.PrivilegedAccessor
junit.extensions.PrivilegedAccessor
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jalview.io.JalviewFileChooser.RecentlyOpened
jalview.io.JalviewFileChooser.RecentlyOpened
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jalview.schemes.PIDColourScheme
jalview.schemes.PIDColourScheme
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jalview.ws.dbsources.Pdb
jalview.ws.dbsources.Pdb
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jalview.io.FileFormat
jalview.io.FileFormat
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0.0620155046.2%
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jalview.analysis.scoremodels.ScoreMatrix
jalview.analysis.scoremodels.ScoreMatrix
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0.0617283966.2%
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ext.vamsas.ServiceHandle
ext.vamsas.ServiceHandle
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0.061224496.1%
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jalview.gui.ViewSelectionMenu
jalview.gui.ViewSelectionMenu
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0.059405945.9%
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junit.extensions.PA
junit.extensions.PA
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0.0576923085.8%
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jalview.bin.Cache
jalview.bin.Cache
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0.056473835.6%
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jalview.structure.StructureSelectionManager
jalview.structure.StructureSelectionManager
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0.0549169855.5%
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jalview.gui.AnnotationPanel
jalview.gui.AnnotationPanel
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jalview.ws.jws1.Discoverer
jalview.ws.jws1.Discoverer
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0.0512820525.1%
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jalview.analysis.GeneticCodes
jalview.analysis.GeneticCodes
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0.0496894425%
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jalview.datamodel.SecondaryStructureCount
jalview.datamodel.SecondaryStructureCount
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0.0468754.7%
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jalview.gui.WsParamSetManager
jalview.gui.WsParamSetManager
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0.0429447854.3%
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org.json.simple.JSONObject
org.json.simple.JSONObject
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jalview.ws.jws1.JPredClient
jalview.ws.jws1.JPredClient
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0.0310559013.1%
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jalview.ext.ensembl.EnsemblRestClient
jalview.ext.ensembl.EnsemblRestClient
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0.0283018872.8%
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jalview.ws.dbsources.Uniprot
jalview.ws.dbsources.Uniprot
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jalview.util.HttpUtils
jalview.util.HttpUtils
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0.0196078442%
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jalview.schemes.ClustalxColourScheme
jalview.schemes.ClustalxColourScheme
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jalview.analysis.AlignSeq
jalview.analysis.AlignSeq
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jalview.gui.SeqPanel
jalview.gui.SeqPanel
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jalview.io.SequenceAnnotationReport
jalview.io.SequenceAnnotationReport
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0.0122699381.2%
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jalview.bin.Jalview
jalview.bin.Jalview
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0.0117328521.2%
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jalview.gui.AnnotationLabels
jalview.gui.AnnotationLabels
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0.0110497241.1%
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jalview.gui.SequenceFetcher
jalview.gui.SequenceFetcher
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jalview.bin.argparser.BootstrapArgs
jalview.bin.argparser.BootstrapArgs
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0.0082644620.8%
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org.json.simple.JSONArray
org.json.simple.JSONArray
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jalview.gui.QuitHandler
jalview.gui.QuitHandler
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jalview.ext.ensembl.EnsemblSeqProxy
jalview.ext.ensembl.EnsemblSeqProxy
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jalview.renderer.AnnotationRenderer
jalview.renderer.AnnotationRenderer
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0.00357142860.4%
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