Hierarchy For All Packages
Package Hierarchies:Class Hierarchy
- java.lang.Object
- vcf.AllData (implements vcf.Data)
- phase.AlleleImputer
- bref.AsIsBref3Writer (implements bref.BrefWriter)
- vcf.BasicGT (implements vcf.GT)
- vcf.BasicMarker (implements vcf.Marker)
- phase.BestMatch
- vcf.BitSetGTRec (implements vcf.GTRec)
- bref.Bref3
- bref.Bref3It (implements blbutil.SampleFileIt<E>)
- bref.Bref3Reader
- bref.BrefBlock
- ints.CharArray (implements ints.IntArray)
- beagleutil.ChromIds
- beagleutil.ChromInterval (implements java.lang.Comparable<T>, beagleutil.IntInterval)
- imp.CodedSteps
- phase.CodedSteps
- main.CompHapSegment (implements java.lang.Comparable<T>)
- bref.CompressBref3Writer (implements bref.BrefWriter)
- blbutil.Const
- blbutil.DoubleArray
- phase.EstPhase
- blbutil.FileUtil
- vcf.FilterUtil
- phase.FixedPhaseData
- blbutil.FloatArray
- blbutil.FloatList
- phase.FwdBwd
- phase.HapImputer
- imp.HaplotypeCoder
- vcf.HapsGT (implements vcf.GT)
- phase.HmmUpdater
- phase.Ibs2
- imp.ImpData
- imp.ImpIbs
- imp.ImpLS
- imp.ImpLSBaum
- imp.ImpStates
- phase.ImputeBaum
- imp.ImputedRecBuilder
- imp.ImputedVcfWriter
- ints.IndexArray (implements ints.IntArray)
- blbutil.InputIt (implements blbutil.FileIt<E>)
- vcf.IntervalVcfIt<E> (implements blbutil.SampleFileIt<E>)
- ints.IntIntMap
- ints.IntList
- ints.LongArray
- phase.LowFreqPhaseIbs (implements phase.PhaseIbs)
- vcf.LowMafRefDiallelicGTRec (implements vcf.RefGTRec)
- vcf.LowMafRefGTRec (implements vcf.RefGTRec)
- main.Main
- main.MainHelper
- vcf.MarkerIndices
- vcf.MarkerMap
- vcf.Markers
- blbutil.MultiThreadUtils
- java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
- blbutil.BGZIPOutputStream
- ints.PackedIntArray (implements ints.IntArray)
- blbutil.Pair<F,S>
- main.Par
- phase.PbwtPhaseIbs (implements phase.PhaseIbs)
- beagleutil.PbwtUpdater
- main.Pedigree
- phase.PhaseBaum1
- phase.PhaseData
- phase.PhaseLS
- phase.PhaseStates
- vcf.PlinkGenMap (implements vcf.GeneticMap)
- vcf.PositionMap (implements vcf.GeneticMap)
- phase.RecombRegress
- vcf.RefGT (implements vcf.GT)
- imp.RefHapHash
- vcf.RefIt (implements blbutil.SampleFileIt<E>)
- math.Regress
- vcf.RestrictedGT (implements vcf.GT)
- vcf.RestrictedVcfWindow (implements java.io.Closeable)
- main.RunStats
- beagleutil.SampleIds
- vcf.Samples
- phase.SampleSeg (implements java.lang.Comparable<T>, beagleutil.IntInterval)
- vcf.SeqCodedRefGTRec (implements vcf.RefGTRec)
- bref.SeqCoder3
- vcf.SplicedGT (implements vcf.GT)
- imp.StateProbsFactory
- blbutil.StringUtil
- vcf.TargetData (implements vcf.Data)
- beagleutil.ThreadSafeIndexer<T>
- bref.UnBref3
- ints.UnsignedByteArray (implements ints.IntArray)
- blbutil.Utilities
- blbutil.Validate
- vcf.VcfHeader
- vcf.VcfIt<E> (implements blbutil.SampleFileIt<E>)
- vcf.VcfMetaInfo
- vcf.VcfRec (implements vcf.GTRec)
- vcf.VcfRecBuilder
- vcf.VcfRecGTParser
- vcf.VcfWriter
- vcf.Window<E>
- vcf.WindowIt<E> (implements blbutil.SampleFileIt<E>)
- main.WindowWriter (implements java.io.Closeable)
- ints.WrappedIntArray (implements ints.IntArray)
Interface Hierarchy
- java.lang.AutoCloseable
- java.io.Closeable
- bref.BrefWriter
- vcf.Data
- blbutil.FileIt<E> (also extends java.util.Iterator<E>)
- blbutil.SampleFileIt<E>
- java.io.Closeable
- java.lang.Comparable<T>
- vcf.Marker
- blbutil.Filter<E>
- vcf.GeneticMap
- vcf.GT
- ints.IntArray
- vcf.DuplicatesGTRec (also extends vcf.MarkerContainer)
- beagleutil.IntInterval
- java.util.Iterator<E>
- blbutil.FileIt<E> (also extends java.io.Closeable)
- blbutil.SampleFileIt<E>
- blbutil.FileIt<E> (also extends java.io.Closeable)
- vcf.MarkerContainer
- vcf.DuplicatesGTRec (also extends ints.IntArray)
- phase.PhaseIbs
- imp.StateProbs