# Hierarchy For All Packages

Package Hierarchies:

- org.snpsift,
- org.snpsift.annotate,
- org.snpsift.annotate.mem,
- org.snpsift.annotate.mem.arrays,
- org.snpsift.annotate.mem.database,
- org.snpsift.annotate.mem.dataFrame,
- org.snpsift.annotate.mem.dataFrame.dataFrameColumn,
- org.snpsift.annotate.mem.variantTypeCounter,
- org.snpsift.antlr,
- org.snpsift.caseControl,
- org.snpsift.fileIterator,
- org.snpsift.gwasCatalog,
- org.snpsift.hwe,
- org.snpsift.lang,
- org.snpsift.lang.expression,
- org.snpsift.lang.function,
- org.snpsift.pedigree,
- org.snpsift.phatsCons,
- org.snpsift.util

## Class Hierarchy

- java.lang.Object
  - org.antlr.v4.runtime.tree.AbstractParseTreeVisitor<T> (implements org.antlr.v4.runtime.tree.ParseTreeVisitor<T>)
    - org.snpsift.antlr.SnpSiftBaseVisitor<T> (implements org.snpsift.antlr.SnpSiftVisitor<T>)
  - org.snpsift.annotate.AnnotateVcfDb
    - org.snpsift.annotate.AnnotateVcfDbMem
    - org.snpsift.annotate.AnnotateVcfDbSorted
    - org.snpsift.annotate.AnnotateVcfDbTabix
  - org.snpsift.annotate.mem.arrays.BoolArray (implements java.io.Serializable)
  - org.snpsift.annotate.mem.dataFrame.DataFrame (implements java.io.Serializable)
    - org.snpsift.annotate.mem.dataFrame.DataFrameDel
    - org.snpsift.annotate.mem.dataFrame.DataFrameIns
    - org.snpsift.annotate.mem.dataFrame.DataFrameMixed
    - org.snpsift.annotate.mem.dataFrame.DataFrameMnp
    - org.snpsift.annotate.mem.dataFrame.DataFrameOther
    - org.snpsift.annotate.mem.dataFrame.DataFrameSnp
  - org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumn<T> (implements java.io.Serializable)
    - org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnBool
    - org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnChar
    - org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnDouble
    - org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnInt
    - org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnLong
    - org.snpsift.annotate.mem.dataFrame.dataFrameColumn.DataFrameColumnString
  - org.snpsift.annotate.mem.dataFrame.DataFrameRow (implements java.lang.Iterable<T>, java.io.Serializable)
  - org.snpsift.fileIterator.DbNsfp (implements org.snpsift.annotate.DbMarker<Q,R>)
  - org.snpsift.annotate.DbVcf (implements org.snpsift.annotate.DbMarker<Q,R>)
    - org.snpsift.annotate.DbVcfMem
    - org.snpsift.annotate.DbVcfSorted
    - org.snpsift.annotate.DbVcfTabix
  - org.snpsift.lang.expression.Expression
    - org.snpsift.lang.expression.ExpressionBinary
      - org.snpsift.lang.expression.And
      - org.snpsift.lang.expression.Div
      - org.snpsift.lang.expression.Eq
        - org.snpsift.lang.expression.Neq
      - org.snpsift.lang.expression.Ge
      - org.snpsift.lang.expression.Gt
      - org.snpsift.lang.expression.Has
      - org.snpsift.lang.expression.Le
      - org.snpsift.lang.expression.Lt
      - org.snpsift.lang.expression.Match
        - org.snpsift.lang.expression.NotMatch
      - org.snpsift.lang.expression.Minus
      - org.snpsift.lang.expression.Mod
      - org.snpsift.lang.expression.Or
      - org.snpsift.lang.expression.Plus
      - org.snpsift.lang.expression.Times
      - org.snpsift.lang.expression.Xor
    - org.snpsift.lang.expression.ExpressionUnary
      - org.snpsift.lang.expression.Exists
        - org.snpsift.lang.expression.Na
      - org.snpsift.lang.expression.Not
    - org.snpsift.lang.expression.Field
      - org.snpsift.lang.expression.FieldConstant
        - org.snpsift.lang.expression.FieldConstantFloat
      - org.snpsift.lang.expression.FieldSub
        - org.snpsift.lang.expression.FieldEff
        - org.snpsift.lang.expression.FieldGenotype
          - org.snpsift.lang.expression.FieldGenotypeSub
        - org.snpsift.lang.expression.FieldLof
          - org.snpsift.lang.expression.FieldNmd
    - org.snpsift.lang.function.Function
      - org.snpsift.lang.function.CountHet
      - org.snpsift.lang.function.CountHom
      - org.snpsift.lang.function.CountRef
      - org.snpsift.lang.function.CountVariant
      - org.snpsift.lang.function.FunctionBoolGenotype
        - org.snpsift.lang.function.IsHet
        - org.snpsift.lang.function.IsHom
        - org.snpsift.lang.function.IsRef
        - org.snpsift.lang.function.IsVariant
      - org.snpsift.lang.function.In
    - org.snpsift.lang.expression.Literal
  - org.snpsift.util.FastaSample
  - org.snpsift.lang.expression.FieldIterator
  - org.snpsift.annotate.mem.Fields (implements java.lang.Iterable<T>, java.io.Serializable)
  - org.snpeff.fileIterator.FileIterator<T> (implements java.lang.Iterable<T>, java.util.Iterator<E>)
    - org.snpeff.fileIterator.LineClassFileIterator<T>
      - org.snpsift.gwasCatalog.GwasCatalogFileIterator
  - org.snpsift.util.FormatUtil
  - org.snpsift.gwasCatalog.GwasCatalog (implements java.lang.Iterable<T>)
  - org.snpsift.gwasCatalog.GwasCatalogEntry
  - org.snpsift.pedigree.Individual (implements java.lang.Comparable<T>)
  - org.snpeff.interval.Interval (implements java.lang.Cloneable, java.lang.Comparable<T>, java.io.Serializable)
    - org.snpeff.interval.Marker (implements org.snpeff.serializer.TxtSerializable)
      - org.snpsift.annotate.MarkerFile
      - org.snpeff.interval.Variant
        - org.snpsift.fileIterator.DbNsfpEntry
  - org.snpsift.lang.LangFactory
  - org.snpsift.pedigree.PedigreeDraw
  - org.snpsift.phatsCons.PhastCons
  - org.snpsift.annotate.mem.arrays.PosIndex (implements java.io.Serializable)
  - org.snpsift.annotate.QueryResult
  - org.snpsift.util.RandomUtil
  - org.antlr.v4.runtime.Recognizer<Symbol,ATNInterpreter>
    - org.antlr.v4.runtime.Lexer (implements org.antlr.v4.runtime.TokenSource)
      - org.snpsift.antlr.SnpSiftLexer
    - org.antlr.v4.runtime.Parser
      - org.snpsift.antlr.SnpSiftParser
  - org.antlr.v4.runtime.RuleContext (implements org.antlr.v4.runtime.tree.RuleNode)
    - org.antlr.v4.runtime.ParserRuleContext
      - org.snpsift.antlr.SnpSiftParser.CompilationUnitContext
      - org.snpsift.antlr.SnpSiftParser.ExpressionContext
        - org.snpsift.antlr.SnpSiftParser.ExpressionCompContext
        - org.snpsift.antlr.SnpSiftParser.ExpressionCondContext
        - org.snpsift.antlr.SnpSiftParser.ExpressionExistsContext
        - org.snpsift.antlr.SnpSiftParser.ExpressionLogicContext
        - org.snpsift.antlr.SnpSiftParser.ExpressionParenContext
        - org.snpsift.antlr.SnpSiftParser.ExpressionPlusContext
        - org.snpsift.antlr.SnpSiftParser.ExpressionSetContext
        - org.snpsift.antlr.SnpSiftParser.ExpressionTimesContext
        - org.snpsift.antlr.SnpSiftParser.ExpressionUnaryContext
        - org.snpsift.antlr.SnpSiftParser.FunctionCallContext
        - org.snpsift.antlr.SnpSiftParser.LiteralBoolContext
        - org.snpsift.antlr.SnpSiftParser.LiteralFloatContext
        - org.snpsift.antlr.SnpSiftParser.LiteralIndexContext
        - org.snpsift.antlr.SnpSiftParser.LiteralIntContext
        - org.snpsift.antlr.SnpSiftParser.LiteralStringContext
        - org.snpsift.antlr.SnpSiftParser.VarReferenceContext
        - org.snpsift.antlr.SnpSiftParser.VarReferenceListContext
        - org.snpsift.antlr.SnpSiftParser.VarReferenceListSubContext
  - org.snpsift.util.ShowProgress
  - org.snpsift.SnpSift (implements org.snpeff.snpEffect.VcfAnnotator)
    - org.snpsift.SnpSiftCmdAlleleMatrix
    - org.snpsift.SnpSiftCmdAnnotate
    - org.snpsift.SnpSiftCmdAnnotateMem
    - org.snpsift.SnpSiftCmdCaseControl
    - org.snpsift.caseControl.SnpSiftCmdCaseControlSummary
    - org.snpsift.SnpSiftCmdConcordance
    - org.snpsift.SnpSiftCmdCovarianceMatrix
    - org.snpsift.SnpSiftCmdDbNsfp
    - org.snpsift.SnpSiftCmdExtractFields
    - org.snpsift.SnpSiftCmdFilter
    - org.snpsift.SnpSiftCmdFilterChrPos
    - org.snpsift.SnpSiftCmdFilterGt
    - org.snpsift.SnpSiftCmdGeneSets
    - org.snpsift.SnpSiftCmdGt
    - org.snpsift.SnpSiftCmdGwasCatalog
    - org.snpsift.hwe.SnpSiftCmdHwe
    - org.snpsift.SnpSiftCmdIntersect
    - org.snpsift.SnpSiftCmdIntervals
    - org.snpsift.SnpSiftCmdIntervalsIndex
    - org.snpsift.SnpSiftCmdJoin
    - org.snpsift.SnpSiftCmdPedShow
    - org.snpsift.SnpSiftCmdPhastCons
    - org.snpsift.SnpSiftCmdPrivate
    - org.snpsift.SnpSiftCmdRemoveReferenceGenotypes
    - org.snpsift.SnpSiftCmdRmInfo
    - org.snpsift.SnpSiftCmdSort
    - org.snpsift.SnpSiftCmdSplit
    - org.snpsift.SnpSiftCmdTsTv
    - org.snpsift.SnpSiftCmdVarType
    - org.snpsift.SnpSiftCmdVcf2Tped
    - org.snpsift.SnpSiftCmdVcfCheck
    - org.snpsift.SnpSiftCmdVcfOperator
  - org.snpsift.antlr.SnpSiftBaseListener (implements org.snpsift.antlr.SnpSiftListener)
  - org.snpsift.annotate.mem.SortedVariantsVcfIterator (implements java.lang.Iterable<T>, java.util.Iterator<E>)
  - org.snpsift.annotate.mem.arrays.StringArrayBase (implements java.lang.Iterable<T>, java.io.Serializable)
    - org.snpsift.annotate.mem.arrays.EnumArray
    - org.snpsift.annotate.mem.arrays.StringArray
  - org.snpsift.caseControl.Summary
  - org.snpsift.lang.Value
  - org.snpsift.caseControl.VariantCounter
  - org.snpsift.annotate.mem.database.VariantDatabase
  - org.snpsift.annotate.mem.database.VariantDataFrame (implements java.io.Serializable)
  - org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounter (implements java.io.Serializable)
  - org.snpsift.annotate.mem.variantTypeCounter.VariantTypeCounters
  - org.snpsift.hwe.VcfHwe
  - org.snpsift.annotate.VcfIndex
  - org.snpsift.annotate.VcfIndexDataChromo
  - org.snpsift.annotate.VcfIndexTree (implements org.snpeff.interval.tree.Itree)
  - org.snpsift.VcfLd
  - org.snpsift.annotate.mem.Zzz

## Interface Hierarchy

- org.snpsift.annotate.DbMarker<Q,R>
- org.antlr.v4.runtime.tree.ParseTreeListener
  - org.snpsift.antlr.SnpSiftListener
- org.antlr.v4.runtime.tree.ParseTreeVisitor<T>
  - org.snpsift.antlr.SnpSiftVisitor<T>

## Enum Class Hierarchy

- java.lang.Object
  - java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    - org.snpsift.lang.expression.FieldConstant.FieldConstantNames
    - org.snpsift.lang.expression.FieldIterator.IteratorType
    - org.snpsift.SnpSiftCmdVcf2Tped.UseMissing
    - org.snpsift.SnpSiftCmdVcfOperator.Operator
    - org.snpsift.annotate.mem.VariantCategory