Hierarchy For All Packages
- org.snpsift,
- org.snpsift.annotate,
- 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.testCases,
- org.snpsift.testCases.unit,
- 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.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.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.expression.FieldConstant
- 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.In
- org.snpsift.lang.expression.Literal
- org.snpsift.lang.expression.ExpressionBinary
- org.snpsift.util.FastaSample
- org.snpsift.lang.expression.FieldIterator
- org.snpeff.fileIterator.FileIterator<T> (implements java.lang.Iterable<T>, java.util.Iterator<E>)
- org.snpeff.fileIterator.LineClassFileIterator<T>
- org.snpsift.gwasCatalog.GwasCatalogFileIterator
- org.snpeff.fileIterator.LineClassFileIterator<T>
- 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.snpeff.interval.Marker (implements org.snpeff.serializer.TxtSerializable)
- org.snpsift.lang.LangFactory
- org.snpsift.pedigree.PedigreeDraw
- org.snpsift.phatsCons.PhastCons
- org.snpsift.annotate.QueryResult
- 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.Lexer (implements org.antlr.v4.runtime.TokenSource)
- 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.antlr.v4.runtime.ParserRuleContext
- org.snpsift.SnpSift (implements org.snpeff.snpEffect.commandLine.CommandLine, org.snpeff.snpEffect.VcfAnnotator)
- org.snpsift.SnpSiftCmdAlleleMatrix
- org.snpsift.SnpSiftCmdAnnotate
- 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.caseControl.Summary
- org.snpsift.testCases.unit.TestCasesAnnotate
- org.snpsift.testCases.unit.TestCasesAnnotateCreateIndex
- org.snpsift.testCases.unit.TestCasesAnnotateMem
- org.snpsift.testCases.unit.TestCasesAnnotateTabix
- org.snpsift.testCases.unit.TestCasesAnnotateUseIndex
- org.snpsift.testCases.unit.TestCasesCaseControl
- org.snpsift.testCases.unit.TestCasesConcordance
- org.snpsift.testCases.unit.TestCasesDbNsfp
- org.snpsift.testCases.unit.TestCasesDbNsfpDeleteCache
- org.snpsift.testCases.unit.TestCasesExtractFields
- org.snpsift.testCases.unit.TestCasesFilter
- org.snpsift.testCases.unit.TestCasesFilterALL
- org.snpsift.testCases.unit.TestCasesFilterChrPos
- org.snpsift.testCases.unit.TestCasesFilterGt
- org.snpsift.testCases.unit.TestCasesGeneSets
- org.snpsift.testCases.unit.TestCasesGt
- org.snpsift.testCases.unit.TestCasesGwasCatalog
- org.snpsift.testCases.unit.TestCasesHwe
- org.snpsift.testCases.unit.TestCasesIndex
- org.snpsift.testCases.unit.TestCasesIntervals
- org.snpsift.testCases.unit.TestCasesLd
- org.snpsift.testCases.unit.TestCasesPrivate
- org.snpsift.testCases.unit.TestCasesSort
- org.snpsift.testCases.unit.TestCasesSplit
- org.snpsift.testCases.unit.TestCasesVarType
- org.snpsift.testCases.unit.TestCasesVcfCheck
- org.snpsift.testCases.TestCasesZzz
- org.snpsift.testCases.TestSuiteAll
- org.snpsift.lang.Value
- org.snpsift.caseControl.VariantCounter
- 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.antlr.v4.runtime.tree.AbstractParseTreeVisitor<T> (implements org.antlr.v4.runtime.tree.ParseTreeVisitor<T>)
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
- java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)