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jalview.ws.params.simple.StringParameter.Builder
jalview.ws.params.simple.StringParameter.Builder
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1.0100%
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jalview.io.DataSourceType
jalview.io.DataSourceType
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1.0100%
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jalview.ws2.actions.alignment.AlignmentAction.Builder
jalview.ws2.actions.alignment.AlignmentAction.Builder
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1.0100%
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jalview.ws2.api.WebService.Builder
jalview.ws2.api.WebService.Builder
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1.0100%
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jalview.ws.params.ParamDatastoreI
jalview.ws.params.ParamDatastoreI
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1.0100%
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jalview.datamodel.SecondaryStructureCount.SymbolCounts
jalview.datamodel.SecondaryStructureCount.SymbolCounts
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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.ws2.actions.annotation.AnnotationAction.Builder
jalview.ws2.actions.annotation.AnnotationAction.Builder
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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.datamodel.Profiles
jalview.datamodel.Profiles
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jalview.ws.params.simple.BooleanOption.Builder
jalview.ws.params.simple.BooleanOption.Builder
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0.8571428785.7%
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jalview.ws2.client.slivka.SlivkaWSDiscoverer
jalview.ws2.client.slivka.SlivkaWSDiscoverer
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0.85234985.2%
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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.workers.ConsensusThread
jalview.workers.ConsensusThread
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0.880%
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jalview.ws.params.simple.Option.Builder
jalview.ws.params.simple.Option.Builder
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0.880%
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jalview.ws2.api.WebService
jalview.ws2.api.WebService
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0.880%
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jalview.analysis.Conservation
jalview.analysis.Conservation
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0.782608778.3%
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jalview.gui.ItemsRenderer
jalview.gui.ItemsRenderer
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0.777777877.8%
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jalview.util.LinkedIdentityHashSet
jalview.util.LinkedIdentityHashSet
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0.7727272577.3%
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jalview.ws2.actions.BaseAction
jalview.ws2.actions.BaseAction
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0.771428677.1%
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jalview.workers.SecondaryStructureConsensusThread
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0.75471775.5%
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jalview.workers.AlignCalcManager2.WorkerManager
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0.7575%
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jalview.schemes.ZappoColourScheme
jalview.schemes.ZappoColourScheme
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0.7575%
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jalview.schemes.NucleotideColourScheme
jalview.schemes.NucleotideColourScheme
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0.7575%
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jalview.workers.AlignCalcManager2.SimpleWorkerManager
jalview.workers.AlignCalcManager2.SimpleWorkerManager
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0.7142857371.4%
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jalview.gui.FeatureRenderer
jalview.gui.FeatureRenderer
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0.7142857371.4%
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jalview.util.LinkedIdentityHashSet.IdentityWrapper
jalview.util.LinkedIdentityHashSet.IdentityWrapper
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0.7142857371.4%
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jalview.datamodel.Profile
jalview.datamodel.Profile
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0.70491870.5%
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jalview.ws2.client.slivka.SlivkaParamStoreFactory
jalview.ws2.client.slivka.SlivkaParamStoreFactory
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0.7028985670.3%
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jalview.ws.jws2.jabaws2.Jws2InstanceFactory
jalview.ws.jws2.jabaws2.Jws2InstanceFactory
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0.695652269.6%
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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.workers.ConservationThread
jalview.workers.ConservationThread
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0.666666766.7%
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jalview.schemes.ResidueColourScheme
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jalview.ws.params.simple.IntegerParameter.Builder
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0.655172465.5%
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jalview.ws.SequenceFetcher
jalview.ws.SequenceFetcher
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0.6470588464.7%
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jalview.bin.Cache.VersionChecker
jalview.bin.Cache.VersionChecker
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0.629629663%
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jalview.ws.jws2.JabaWsServerQuery
jalview.ws.jws2.JabaWsServerQuery
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0.62562.5%
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jalview.datamodel.AlignmentExportData
jalview.datamodel.AlignmentExportData
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0.62562.5%
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jalview.ws2.actions.BaseAction.Builder
jalview.ws2.actions.BaseAction.Builder
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0.6190476461.9%
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jalview.ws2.actions.alignment.AlignmentAction
jalview.ws2.actions.alignment.AlignmentAction
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0.660%
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jalview.util.ParseHtmlBodyAndLinks
jalview.util.ParseHtmlBodyAndLinks
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0.594202959.4%
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jalview.ws.sifts.SiftsSettings
jalview.ws.sifts.SiftsSettings
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0.571428657.1%
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jalview.jbgui.GAlignFrame
jalview.jbgui.GAlignFrame
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0.567556.7%
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jalview.io.BioJsHTMLOutput
jalview.io.BioJsHTMLOutput
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0.5656%
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jalview.urls.IdOrgSettings
jalview.urls.IdOrgSettings
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0.5454545654.5%
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jalview.ws2.gui.WebServicesMenuManager
jalview.ws2.gui.WebServicesMenuManager
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0.5428571754.3%
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jalview.ws2.client.api.AbstractWebServiceDiscoverer
jalview.ws2.client.api.AbstractWebServiceDiscoverer
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0.537735853.8%
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jalview.util.MessageManager
jalview.util.MessageManager
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0.5238095552.4%
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jalview.gui.JalviewChangeSupport
jalview.gui.JalviewChangeSupport
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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.schemes.TaylorColourScheme
jalview.schemes.TaylorColourScheme
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0.550%
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jalview.schemes.FlowerColourScheme
jalview.schemes.FlowerColourScheme
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0.550%
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jalview.schemes.NucleotideAmbiguityColourScheme
jalview.schemes.NucleotideAmbiguityColourScheme
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0.550%
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jalview.schemes.PurinePyrimidineColourScheme
jalview.schemes.PurinePyrimidineColourScheme
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0.550%
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jalview.schemes.BlossomColourScheme
jalview.schemes.BlossomColourScheme
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0.550%
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jalview.schemes.SunsetColourScheme
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0.550%
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jalview.schemes.OceanColourScheme
jalview.schemes.OceanColourScheme
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0.550%
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jalview.bin.argparser.ArgParser
jalview.bin.argparser.ArgParser
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jalview.bin.argparser.BootstrapArgs
jalview.bin.argparser.BootstrapArgs
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0.4917355549.2%
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jalview.gui.BlogReader
jalview.gui.BlogReader
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0.483425448.3%
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jalview.ws.jws2.jabaws2.Jws2Instance
jalview.ws.jws2.jabaws2.Jws2Instance
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0.4711538647.1%
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jalview.io.FileFormats
jalview.io.FileFormats
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0.4646%
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jalview.ws2.gui.WebServicesMenuManager.InteractiveServiceEntryGroup
jalview.ws2.gui.WebServicesMenuManager.InteractiveServiceEntryGroup
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0.4579439245.8%
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jalview.ws2.actions.annotation.AnnotationAction
jalview.ws2.actions.annotation.AnnotationAction
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0.4444444544.4%
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jalview.bin.ArgsParser
jalview.bin.ArgsParser
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0.4426229644.3%
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jalview.bin.argparser.SubVals
jalview.bin.argparser.SubVals
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0.432989743.3%
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jalview.gui.ColourMenuHelper
jalview.gui.ColourMenuHelper
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0.4322033843.2%
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jalview.ws.api.UIinfo
jalview.ws.api.UIinfo
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0.4313725543.1%
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jalview.util.QuickSort.IntComparator
jalview.util.QuickSort.IntComparator
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0.4285714342.9%
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jalview.datamodel.HiddenCursorPosition
jalview.datamodel.HiddenCursorPosition
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0.4285714342.9%
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jalview.ws.params.simple.BooleanOption
jalview.ws.params.simple.BooleanOption
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0.4242424442.4%
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jalview.bin.argparser.ArgValue
jalview.bin.argparser.ArgValue
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0.4179104641.8%
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jalview.gui.SequenceRenderer
jalview.gui.SequenceRenderer
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0.4134615441.3%
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org.json.JSONTokener
org.json.JSONTokener
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0.4132841241.3%
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jalview.ext.so.SequenceOntology
jalview.ext.so.SequenceOntology
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0.412541.2%
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jalview.ws.dbsources.EmblSource
jalview.ws.dbsources.EmblSource
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0.440%
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jalview.io.gff.SequenceOntologyFactory
jalview.io.gff.SequenceOntologyFactory
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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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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.ws.jws2.Jws2Discoverer
jalview.ws.jws2.Jws2Discoverer
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0.397435939.7%
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jalview.workers.AlignCalcManager2
jalview.workers.AlignCalcManager2
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0.3904109639%
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jalview.datamodel.ResidueCount
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0.390243939%
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jalview.log.JalviewAppender
jalview.log.JalviewAppender
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0.388888938.9%
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jalview.io.FileLoader
jalview.io.FileLoader
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0.387195138.7%
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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.bin.Cache
jalview.bin.Cache
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0.379403837.9%
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jalview.io.AlignFile
jalview.io.AlignFile
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0.378378437.8%
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jalview.ws.jws2.MsaWSClient
jalview.ws.jws2.MsaWSClient
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0.37537.5%
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jalview.ws.jws2.JabaPreset
jalview.ws.jws2.JabaPreset
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jalview.bin.ApplicationSingletonProvider
jalview.bin.ApplicationSingletonProvider
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0.37537.5%
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jalview.io.BackupFilesPresetEntry
jalview.io.BackupFilesPresetEntry
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0.3676470536.8%
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jalview.renderer.ScaleRenderer
jalview.renderer.ScaleRenderer
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0.3636%
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jalview.util.HttpUtils
jalview.util.HttpUtils
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0.3585858635.9%
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jalview.ws.jws1.Discoverer
jalview.ws.jws1.Discoverer
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0.3575757435.8%
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jalview.gui.UserQuestionnaireCheck
jalview.gui.UserQuestionnaireCheck
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0.349397634.9%
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jalview.bin.argparser.ArgValues
jalview.bin.argparser.ArgValues
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0.3412698534.1%
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jalview.bin.argparser.ArgValuesMap
jalview.bin.argparser.ArgValuesMap
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0.3403755734%
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jalview.viewmodel.styles.ViewStyle
jalview.viewmodel.styles.ViewStyle
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0.3369565333.7%
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jalview.viewmodel.AlignmentViewport
jalview.viewmodel.AlignmentViewport
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0.335737733.6%
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jalview.ws.api.ServiceWithParameters
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0.3333333433.3%
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jalview.ws.jws2.Jws2Client
jalview.ws.jws2.Jws2Client
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0.3333333433.3%
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jalview.gui.IdwidthAdjuster
jalview.gui.IdwidthAdjuster
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0.3289473732.9%
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jalview.ws.jws2.PreferredServiceRegistry
jalview.ws.jws2.PreferredServiceRegistry
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0.3280423332.8%
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jalview.ws.rest.RestServiceDescription
jalview.ws.rest.RestServiceDescription
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0.3221649532.2%
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jalview.util.FileUtils
jalview.util.FileUtils
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0.3214285732.1%
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jalview.util.Format
jalview.util.Format
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0.3209109632.1%
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jalview.io.FastaFile
jalview.io.FastaFile
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0.315315331.5%
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jalview.util.Comparison
jalview.util.Comparison
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0.3149606331.5%
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jalview.analysis.AAFrequency
jalview.analysis.AAFrequency
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0.3099510731%
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jalview.bin.Commands
jalview.bin.Commands
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0.300982830.1%
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jalview.gui.AlignViewport
jalview.gui.AlignViewport
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0.3002309530%
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jalview.renderer.AnnotationRenderer
jalview.renderer.AnnotationRenderer
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0.2967515329.7%
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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.gui.JvSwingUtils
jalview.gui.JvSwingUtils
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0.2896551829%
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jalview.gui.AlignmentPanel
jalview.gui.AlignmentPanel
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0.288278828.8%
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jalview.ws.dbsources.EmblCdsSource
jalview.ws.dbsources.EmblCdsSource
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0.285714328.6%
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jalview.renderer.ResidueColourFinder
jalview.renderer.ResidueColourFinder
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0.285714328.6%
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ext.vamsas.ServiceHandle
ext.vamsas.ServiceHandle
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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.io.FileParse
jalview.io.FileParse
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0.2853185528.5%
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jalview.bin.Jalview
jalview.bin.Jalview
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0.2740501227.4%
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jalview.io.IdentifyFile
jalview.io.IdentifyFile
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0.2737752227.4%
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jalview.viewmodel.ViewportRanges
jalview.viewmodel.ViewportRanges
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0.261589426.2%
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org.json.JSONObject.Null
org.json.JSONObject.Null
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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.renderer.ResidueShader
jalview.renderer.ResidueShader
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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.gui.IdCanvas
jalview.gui.IdCanvas
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0.2425249224.3%
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jalview.io.BackupFiles
jalview.io.BackupFiles
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0.23623.6%
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jalview.ws.WSClient
jalview.ws.WSClient
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0.2352941223.5%
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jalview.util.ErrorLog
jalview.util.ErrorLog
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0.2352941223.5%
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jalview.bin.BuildDetails
jalview.bin.BuildDetails
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0.2352941223.5%
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jalview.ws.params.simple.Option
jalview.ws.params.simple.Option
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0.2333333323.3%
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jalview.datamodel.AlignExportSettingsAdapter
jalview.datamodel.AlignExportSettingsAdapter
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0.2307692323.1%
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jalview.bin.Console
jalview.bin.Console
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0.226415122.6%
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jalview.io.FormatAdapter
jalview.io.FormatAdapter
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0.2222%
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jalview.ws.params.simple.IntegerParameter
jalview.ws.params.simple.IntegerParameter
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0.2142857221.4%
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jalview.gui.BlogReader.LaunchJvBrowserOnItem
jalview.gui.BlogReader.LaunchJvBrowserOnItem
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0.2083333320.8%
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jalview.ws.rest.InputType
jalview.ws.rest.InputType
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0.2056074720.6%
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jalview.bin.JalviewTaskbar
jalview.bin.JalviewTaskbar
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0.220%
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jalview.ws.params.simple.DoubleParameter
jalview.ws.params.simple.DoubleParameter
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0.1956521719.6%
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jalview.io.AppletFormatAdapter
jalview.io.AppletFormatAdapter
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0.1956521719.6%
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jalview.datamodel.SecondaryStructureCount
jalview.datamodel.SecondaryStructureCount
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0.1914062519.1%
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jalview.ws.params.simple.StringParameter
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0.190476219%
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jalview.log.JLogger
jalview.log.JLogger
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0.1868131918.7%
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jalview.util.QuickSort
jalview.util.QuickSort
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0.1844660218.4%
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jalview.gui.AnnotationLabels
jalview.gui.AnnotationLabels
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0.1771653617.7%
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jalview.schemes.IdColourScheme
jalview.schemes.IdColourScheme
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0.1739130517.4%
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jalview.datamodel.Alignment
jalview.datamodel.Alignment
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0.1712756517.1%
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jalview.util.UserAgent
jalview.util.UserAgent
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0.1666666716.7%
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jalview.ws.jws1.WS1Client
jalview.ws.jws1.WS1Client
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0.1616%
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jalview.gui.PaintRefresher
jalview.gui.PaintRefresher
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0.1578947315.8%
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jalview.gui.Desktop.MyDesktopManager
jalview.gui.Desktop.MyDesktopManager
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0.1555555615.6%
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jalview.structure.StructureImportSettings
jalview.structure.StructureImportSettings
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0.1538461615.4%
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jalview.gui.AlignFrame
jalview.gui.AlignFrame
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0.1505948615.1%
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jalview.gui.ScalePanel
jalview.gui.ScalePanel
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0.1490196114.9%
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jalview.schemes.TCoffeeColourScheme
jalview.schemes.TCoffeeColourScheme
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0.1475409914.8%
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jalview.ws.rest.RestClient
jalview.ws.rest.RestClient
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0.1466666614.7%
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jalview.ws.jws2.JabaParamStore
jalview.ws.jws2.JabaParamStore
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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.AnnotationPanel
jalview.gui.AnnotationPanel
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0.1406411514.1%
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jalview.io.FileFormat
jalview.io.FileFormat
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0.1379310313.8%
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jalview.workers.AlignCalcWorker
jalview.workers.AlignCalcWorker
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0.1333333413.3%
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jalview.schemes.HmmerGlobalBackground
jalview.schemes.HmmerGlobalBackground
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0.1333333413.3%
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jalview.analysis.AnnotationSorter
jalview.analysis.AnnotationSorter
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0.132812513.3%
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org.json.JSONObject
org.json.JSONObject
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0.1322549913.2%
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jalview.ws.rest.params.SeqGroupIndexVector
jalview.ws.rest.params.SeqGroupIndexVector
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jalview.gui.Desktop
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jalview.schemes.Blosum62ColourScheme
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jalview.ws2.params.SimpleParamDatastore
jalview.ws2.params.SimpleParamDatastore
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jalview.datamodel.Annotation
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jalview.gui.PromptUserConfig
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jalview.schemes.ColourSchemeProperty
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jalview.util.StringUtils
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jalview.log.JLoggerLog4j
jalview.log.JLoggerLog4j
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jalview.util.Platform
jalview.util.Platform
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jalview.ws.rest.params.AnnotationFile
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jalview.datamodel.Sequence
jalview.datamodel.Sequence
|
0.1020920510.2%
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org.json.JSONArray
org.json.JSONArray
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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.ws2.client.jpred4.JPred4WSDiscoverer
jalview.ws2.client.jpred4.JPred4WSDiscoverer
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jalview.util.JSONUtils
jalview.util.JSONUtils
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jalview.ws2.client.slivka.SlivkaAlignmentWSClient
jalview.ws2.client.slivka.SlivkaAlignmentWSClient
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jalview.ws.dbsources.Xfam
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jalview.ext.ensembl.EnsemblSequenceFetcher
jalview.ext.ensembl.EnsemblSequenceFetcher
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0.0833333368.3%
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jalview.analysis.scoremodels.ScoreModels
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0.0833333368.3%
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jalview.schemes.RNAHelicesColour
jalview.schemes.RNAHelicesColour
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0.082191788.2%
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jalview.datamodel.AlignmentAnnotation
jalview.datamodel.AlignmentAnnotation
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jalview.ws2.client.ebi.JobDispatcherWSDiscoverer
jalview.ws2.client.ebi.JobDispatcherWSDiscoverer
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0.081632658.2%
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jalview.gui.SeqCanvas
jalview.gui.SeqCanvas
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0.080971668.1%
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jalview.schemes.HmmerLocalBackground
jalview.schemes.HmmerLocalBackground
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jalview.util.ChannelProperties
jalview.util.ChannelProperties
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jalview.analysis.CrossRef
jalview.analysis.CrossRef
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jalview.gui.ProgressBar
jalview.gui.ProgressBar
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0.068965526.9%
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jalview.io.StockholmFile
jalview.io.StockholmFile
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0.068407966.8%
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jalview.gui.IdPanel
jalview.gui.IdPanel
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0.067264576.7%
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jalview.schemes.PIDColourScheme
jalview.schemes.PIDColourScheme
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0.066666676.7%
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jalview.util.LaunchUtils
jalview.util.LaunchUtils
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0.066339076.6%
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jalview.util.ColorUtils
jalview.util.ColorUtils
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0.0635359146.4%
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jalview.bin.argparser.Arg
jalview.bin.argparser.Arg
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0.0619469026.2%
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jalview.analysis.scoremodels.ScoreMatrix
jalview.analysis.scoremodels.ScoreMatrix
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0.0617283966.2%
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jalview.structure.StructureSelectionManager
jalview.structure.StructureSelectionManager
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0.0597964386%
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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
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0.0577777775.8%
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jalview.datamodel.ColumnSelection.IntList
jalview.datamodel.ColumnSelection.IntList
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0.0560747655.6%
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jalview.workers.InformationThread
jalview.workers.InformationThread
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0.0555555565.6%
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jalview.ws.seqfetcher.DbSourceProxyImpl
jalview.ws.seqfetcher.DbSourceProxyImpl
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0.0540540555.4%
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jalview.schemes.ColourSchemes
jalview.schemes.ColourSchemes
|
0.0512820525.1%
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jalview.ws2.client.slivka.SlivkaAnnotationWSClient
jalview.ws2.client.slivka.SlivkaAnnotationWSClient
|
0.055%
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jalview.analysis.GeneticCodes
jalview.analysis.GeneticCodes
|
0.0496894425%
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jalview.util.DBRefUtils
jalview.util.DBRefUtils
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0.044642864.5%
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jalview.gui.WsParamSetManager
jalview.gui.WsParamSetManager
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0.0429447854.3%
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jalview.schemes.HMMMatchScoreColourScheme
jalview.schemes.HMMMatchScoreColourScheme
|
0.042553194.3%
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jalview.ws.dbsources.Pdb
jalview.ws.dbsources.Pdb
|
0.0408163264.1%
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jalview.datamodel.HiddenColumns
jalview.datamodel.HiddenColumns
|
0.040094344%
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jalview.ws.jws2.Jws2ClientFactory
jalview.ws.jws2.Jws2ClientFactory
|
0.044%
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jalview.schemes.HmmerColourScheme
jalview.schemes.HmmerColourScheme
|
0.038461543.8%
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org.json.simple.JSONObject
org.json.simple.JSONObject
|
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jalview.ws.jws1.JPredClient
jalview.ws.jws1.JPredClient
|
0.0310559013.1%
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jalview.ws2.client.slivka.SlivkaWSClient
jalview.ws2.client.slivka.SlivkaWSClient
|
0.033%
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jalview.analysis.AlignmentAnnotationUtils
jalview.analysis.AlignmentAnnotationUtils
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0.0296610173%
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jalview.datamodel.HiddenSequences
jalview.datamodel.HiddenSequences
|
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jalview.gui.AlignExportOptions
jalview.gui.AlignExportOptions
|
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jalview.analysis.AlignmentUtils
jalview.analysis.AlignmentUtils
|
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jalview.schemes.ClustalxColourScheme
jalview.schemes.ClustalxColourScheme
|
0.0169491531.7%
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jalview.datamodel.HiddenColumnsCursor
jalview.datamodel.HiddenColumnsCursor
|
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jalview.ws.dbsources.Uniprot
jalview.ws.dbsources.Uniprot
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jalview.hmmer.HmmerCommand
jalview.hmmer.HmmerCommand
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0.0141509441.4%
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jalview.controller.AlignViewController
jalview.controller.AlignViewController
|
0.0135593221.4%
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jalview.gui.SeqPanel
jalview.gui.SeqPanel
|
0.0129954521.3%
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jalview.analysis.AlignSeq
jalview.analysis.AlignSeq
|
0.01275510251.3%
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jalview.datamodel.features.SequenceFeatures
jalview.datamodel.features.SequenceFeatures
|
0.0127388541.3%
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jalview.io.SequenceAnnotationReport
jalview.io.SequenceAnnotationReport
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0.0112359551.1%
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jalview.datamodel.ColumnSelection
jalview.datamodel.ColumnSelection
|
0.0103092781%
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jalview.ext.ensembl.EnsemblGene
jalview.ext.ensembl.EnsemblGene
|
0.0081632650.8%
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org.json.simple.JSONArray
org.json.simple.JSONArray
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0.0080645160.8%
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jalview.renderer.seqfeatures.FeatureRenderer
jalview.renderer.seqfeatures.FeatureRenderer
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0.007547170.8%
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jalview.gui.QuitHandler
jalview.gui.QuitHandler
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0.00722021660.7%
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