Hierarchy For All Packages

Package Hierarchies:

• io.repseq.cli,
• io.repseq.core,
• io.repseq.dto,
• io.repseq.gen,
• io.repseq.gen.dist,
• io.repseq.maven,
• io.repseq.seqbase,
• io.repseq.util

Class Hierarchy

• java.lang.Object
  • io.repseq.seqbase.AbstractRAFastaResolver (implements io.repseq.seqbase.SequenceResolver)
    • io.repseq.seqbase.HTTPFastaSequenceResolver (implements io.repseq.seqbase.OptionalSequenceResolver)
      • io.repseq.seqbase.HTTPSequenceResolvers.NucCoreResolver
    • io.repseq.seqbase.LocalFileResolver (implements io.repseq.seqbase.OptionalSequenceResolver)
  • io.repseq.core.AbstractReferencePointsBuilder<T>
    • io.repseq.core.ExtendedReferencePointsBuilder
    • io.repseq.core.ReferencePointsBuilder
  • com.milaboratory.cli.ActionParameters
    • com.milaboratory.cli.ActionParametersWithOutput
      • io.repseq.cli.CompileAction.Params
      • io.repseq.cli.ExportCloneSequencesAction.Params
      • io.repseq.cli.FastaAction.Params
      • io.repseq.cli.FilterAction.Params
      • io.repseq.cli.FromPaddedFastaAction.Params
      • io.repseq.cli.GenerateClonesAction.Params
      • io.repseq.cli.InferAnchorPointsAction.Params
      • io.repseq.cli.MergeAction.Params
      • io.repseq.cli.NormalizeCloneAbundancesAction.Params
      • io.repseq.cli.TsvAction.Params
    • io.repseq.cli.CheckAction.Params
    • io.repseq.cli.DebugAction.Params
    • io.repseq.cli.FormatAction.Params
    • io.repseq.cli.ListAction.Params
    • io.repseq.cli.StatAction.Params
  • io.repseq.seqbase.AnySequenceResolver (implements io.repseq.seqbase.OptionalSequenceResolver)
  • io.repseq.core.BaseSequence
  • io.repseq.gen.dist.BasicGCloneModel (implements io.repseq.gen.dist.GCloneModel)
  • io.repseq.gen.dist.BasicGGeneModel (implements io.repseq.gen.dist.GGeneModel)
  • io.repseq.gen.dist.CategoricalIndependentIntModel (implements io.repseq.gen.dist.IndependentIntModel)
    • io.repseq.gen.dist.CommonCategoricalGeneTrimmingModel (implements io.repseq.gen.dist.GeneTrimmingModel)
  • io.repseq.core.Chains (implements java.lang.Iterable<T>)
  • io.repseq.cli.CheckAction (implements com.milaboratory.cli.Action)
  • io.repseq.cli.CLIUtils
  • io.repseq.cli.CLIUtils.GeneFeatureConverter (implements com.beust.jcommander.IStringConverter<T>)
  • io.repseq.cli.CLIUtils.GeneFeatureSplitter (implements com.beust.jcommander.converters.IParameterSplitter)
  • io.repseq.cli.CLIUtils.GeneFeatureValidator (implements com.beust.jcommander.IParameterValidator)
  • io.repseq.cli.CLIUtils.GeneFeatureWithOriginalName
  • io.repseq.gen.dist.CommonCategoricalDGeneTrimmingModel (implements io.repseq.gen.dist.DTrimmingModel)
  • io.repseq.gen.dist.CommonNormalDTrimmingModel (implements io.repseq.gen.dist.DTrimmingModel)
  • io.repseq.gen.dist.CommonNormalGeneTrimmingModel (implements io.repseq.gen.dist.GeneTrimmingModel)
  • io.repseq.cli.CompileAction (implements com.milaboratory.cli.Action)
  • io.repseq.maven.CompileLibraryMavenStage
  • io.repseq.gen.ConcatenatedLazySequence<S> (implements com.milaboratory.core.sequence.provider.SequenceProvider<S>)
  • io.repseq.cli.DebugAction (implements com.milaboratory.cli.Action)
  • io.repseq.gen.dist.DJCDependentVDJCGenesModel (implements io.repseq.gen.dist.VDJCGenesModel)
  • io.repseq.gen.dist.DJCDependentVDJCGenesModel.VDJCGene3
  • io.repseq.gen.dist.DJDependentVDJCGenesModel (implements io.repseq.gen.dist.VDJCGenesModel)
  • io.repseq.gen.dist.DJDependentVDJCGenesModel.VDJCGene2
  • io.repseq.gen.dist.DoubleTensor
  • io.repseq.gen.DTrimming
  • io.repseq.cli.ExportCloneSequencesAction (implements com.milaboratory.cli.Action)
  • io.repseq.cli.FastaAction (implements com.milaboratory.cli.Action)
  • io.repseq.cli.FilterAction (implements com.milaboratory.cli.Action)
  • io.repseq.gen.dist.FixedInsertModel (implements io.repseq.gen.dist.InsertModel)
  • io.repseq.gen.dist.FixedRealModel (implements io.repseq.gen.dist.IndependentRealModel)
  • io.repseq.cli.FormatAction (implements com.milaboratory.cli.Action)
  • io.repseq.cli.FromPaddedFastaAction (implements com.milaboratory.cli.Action)
  • io.repseq.gen.GClone
  • io.repseq.core.GeneFeature (implements java.lang.Comparable<T>, java.lang.Iterable<T>, java.io.Serializable)
  • io.repseq.core.GeneFeature.ReferenceRange (implements java.io.Serializable)
  • io.repseq.core.GeneFeatureSerializer (implements com.milaboratory.primitivio.Serializer<T>)
  • io.repseq.cli.GenerateClonesAction (implements com.milaboratory.cli.Action)
  • io.repseq.gen.dist.GeneTrimmingGeneratorEnumerated (implements io.repseq.gen.dist.GeneTrimmingGenerator)
  • io.repseq.gen.dist.GModels
  • io.repseq.gen.GRepertoire
  • io.repseq.gen.GRepertoireReader (implements cc.redberry.pipe.OutputPortCloseable<T>)
  • io.repseq.gen.GRepertoireWriter (implements java.lang.AutoCloseable)
  • io.repseq.seqbase.HTTPRedirectSequenceResolver (implements io.repseq.seqbase.OptionalSequenceResolver, io.repseq.seqbase.ParentAwareResolver)
  • io.repseq.seqbase.HTTPResolversContext
  • io.repseq.seqbase.HTTPSequenceResolvers
  • io.repseq.gen.dist.IndependentVDJCGenesModel (implements io.repseq.gen.dist.VDJCGenesModel)
  • io.repseq.gen.dist.IndependentVDJTrimmingModel (implements io.repseq.gen.dist.VDJTrimmingModel)
  • io.repseq.cli.InferAnchorPointsAction (implements com.milaboratory.cli.Action)
  • com.fasterxml.jackson.databind.JsonDeserializer<T>
    • io.repseq.core.BaseSequence.Deserializer
    • io.repseq.core.GeneFeature.Deserializer
    • io.repseq.core.GeneType.Deserializer
    • io.repseq.core.ReferencePoint.Deserializer
    • io.repseq.core.ReferencePoints.JDeserializer
  • com.fasterxml.jackson.databind.JsonSerializer<T> (implements com.fasterxml.jackson.databind.jsonFormatVisitors.JsonFormatVisitable)
    • io.repseq.core.BaseSequence.Serializer
    • io.repseq.core.GeneFeature.Serializer
    • io.repseq.core.GeneType.Serializer
    • io.repseq.core.ReferencePoint.JsonKeySerializer
    • io.repseq.core.ReferencePoint.Serializer
    • io.repseq.core.ReferencePoints.JSerializer
  • com.fasterxml.jackson.databind.KeyDeserializer
    • io.repseq.core.ReferencePoint.JsonKeyDeserializer
  • io.repseq.dto.KnownSequenceFragmentData (implements java.lang.Comparable<T>)
  • io.repseq.cli.ListAction (implements com.milaboratory.cli.Action)
  • io.repseq.cli.Main
  • io.repseq.gen.dist.MarkovInsertModel (implements io.repseq.gen.dist.InsertModel)
    • io.repseq.gen.dist.MarkovInsertModel.Model3
    • io.repseq.gen.dist.MarkovInsertModel.Model5
  • io.repseq.cli.MergeAction (implements com.milaboratory.cli.Action)
  • io.repseq.cli.ModifyLibraryAction
  • io.repseq.seqbase.MultiSequenceResolver (implements io.repseq.seqbase.SequenceResolver)
  • io.repseq.gen.dist.NormalDistributionParameters
  • io.repseq.cli.NormalizeCloneAbundancesAction (implements com.milaboratory.cli.Action)
  • io.repseq.gen.dist.ParetoModel (implements io.repseq.gen.dist.IndependentRealModel)
  • io.repseq.core.PartitionedSequence<S>
    • io.repseq.core.PartitionedSequenceCached<S>
      • io.repseq.gen.GGene
      • io.repseq.core.SequenceProviderAndReferencePoints
      • io.repseq.core.VDJCGene (implements java.lang.Comparable<T>)
  • io.repseq.core.ReferencePoint (implements java.lang.Comparable<T>, java.io.Serializable)
  • io.repseq.core.ReferenceUtil
  • io.repseq.gen.dist.SeparateCategoricalDGeneTrimmingModel (implements io.repseq.gen.dist.DTrimmingModel)
  • io.repseq.gen.dist.SeparateCategoricalGeneTrimmingModel (implements io.repseq.gen.dist.GeneTrimmingModel)
  • io.repseq.seqbase.SequenceAddress
  • io.repseq.util.SequenceBase
  • io.repseq.core.SequencePartitioning
    • io.repseq.core.AbstractReferencePoints<T>
      • io.repseq.core.ExtendedReferencePoints
      • io.repseq.core.ReferencePoints (implements java.io.Serializable)
  • io.repseq.seqbase.SequenceResolvers
  • io.repseq.cli.StatAction (implements com.milaboratory.cli.Action)
  • io.repseq.util.StringWithMapping
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.lang.RuntimeException
        • io.repseq.core.GeneNotFoundException
  • io.repseq.cli.TsvAction (implements com.milaboratory.cli.Action)
  • io.repseq.cli.TsvAction.NameAndGeneFeature
  • io.repseq.dto.VDJCDataUtils
  • io.repseq.dto.VDJCDataUtils.FragmentsBuilder
  • io.repseq.dto.VDJCGeneData (implements java.lang.Comparable<T>)
  • io.repseq.core.VDJCGeneId (implements java.lang.Comparable<T>)
  • io.repseq.gen.VDJCGenes
  • io.repseq.core.VDJCLibrary (implements java.lang.Comparable<T>)
  • io.repseq.dto.VDJCLibraryData (implements java.lang.Comparable<T>)
  • io.repseq.core.VDJCLibraryId (implements java.lang.Comparable<T>)
  • io.repseq.dto.VDJCLibraryNote (implements java.lang.Comparable<T>)
  • io.repseq.core.VDJCLibraryRegistry
  • io.repseq.core.VDJCLibraryRegistry.ClasspathLibraryResolver (implements io.repseq.core.VDJCLibraryRegistry.AliasResolver, io.repseq.core.VDJCLibraryRegistry.LibraryNameListProvider, io.repseq.core.VDJCLibraryRegistry.LibraryResolver)
  • io.repseq.core.VDJCLibraryRegistry.FolderLibraryResolver (implements io.repseq.core.VDJCLibraryRegistry.AliasResolver, io.repseq.core.VDJCLibraryRegistry.LibraryNameListProvider, io.repseq.core.VDJCLibraryRegistry.LibraryResolver)
  • io.repseq.gen.VDJTrimming

Interface Hierarchy

• io.repseq.gen.dist.DTrimmingGenerator
• io.repseq.gen.dist.GCloneGenerator
• io.repseq.gen.dist.GCloneModel
• io.repseq.gen.dist.GeneTrimmingGenerator
• io.repseq.gen.dist.GGeneGenerator
• io.repseq.gen.dist.IndependentIntGenerator
• io.repseq.gen.dist.IndependentRealGenerator
• io.repseq.gen.dist.InsertGenerator
• io.repseq.gen.dist.Model
  • io.repseq.gen.dist.DTrimmingModel
  • io.repseq.gen.dist.GeneTrimmingModel
  • io.repseq.gen.dist.GGeneModel
  • io.repseq.gen.dist.IndependentIntModel
  • io.repseq.gen.dist.IndependentRealModel
  • io.repseq.gen.dist.InsertModel
  • io.repseq.gen.dist.VDJCGenesModel
  • io.repseq.gen.dist.VDJTrimmingModel
• io.repseq.seqbase.ParentAwareResolver
• io.repseq.seqbase.SequenceResolver
  • io.repseq.seqbase.OptionalSequenceResolver
• io.repseq.gen.dist.VDJCGenesGenerator
• io.repseq.core.VDJCLibraryRegistry.AliasResolver
• io.repseq.core.VDJCLibraryRegistry.LibraryNameListProvider
• io.repseq.core.VDJCLibraryRegistry.LibraryResolver
• io.repseq.gen.VDJCUsageDistribution
• io.repseq.gen.VDJCUsageDistributionInstance
• io.repseq.gen.dist.VDJTrimmingGenerator

Annotation Type Hierarchy

• io.repseq.util.Doc (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • io.repseq.core.GeneType (implements java.io.Serializable)
    • io.repseq.dto.VDJCLibraryNoteType
    • io.repseq.dto.GeneTag