Uses of Class
org.snpsift.lang.expression.Expression

Packages that use Expression

Package	Description
org.snpsift
org.snpsift.lang
org.snpsift.lang.expression
org.snpsift.lang.function

Uses of Expression in org.snpsift

Methods in org.snpsift that return Expression

Modifier and Type	Method	Description
Expression	SnpSiftCmdFilter.parseExpression(java.lang.String expression)	Parse expression
Expression	SnpSiftCmdFilterGt.parseExpression(java.lang.String expression)	Parse expression

Uses of Expression in org.snpsift.lang

Methods in org.snpsift.lang that return Expression

Modifier and Type	Method	Description
Expression	LangFactory.compile(java.lang.String expression)	Create an AST from a program (using ANTLR lexer & parser) Returns null if error Use 'alreadyIncluded' to keep track of from 'include' statements
Expression	LangFactory.expressionFactory(org.antlr.v4.runtime.tree.ParseTree tree)	Create 'Expressions' from Tree

Uses of Expression in org.snpsift.lang.expression

Subclasses of Expression in org.snpsift.lang.expression

Modifier and Type	Class	Description
class	And	And expression
class	Div	And expression
class	Eq	Equal
class	Exists	Exists operator (true if a field exists)
class	ExpressionBinary	Binary condition
class	ExpressionUnary	An expression that can be negated
class	Field	A field: E.g.: 'DP', 'CHROM'
class	FieldConstant	A 'constant' field: e.g.
class	FieldConstantFloat	A 'constant' field: e.g.
class	FieldEff	An 'EFF' field form SnpEff: E.g.: 'EFF[2].GENE'
class	FieldGenotype	A field: E.g.: 'GEN[2].GT'
class	FieldGenotypeSub	A field: E.g.: 'GEN[2].PL[3]'
class	FieldLof	A LOF field form SnpEff: E.g.: 'LOF[2].GENE'
class	FieldNmd	A NMD field form SnpEff: E.g.: 'NMD[2].GENE'
class	FieldSub	A field that has sub fields (e.g.
class	Ge	Greater equal
class	Gt	Greater equal
class	Has	Equal
class	Le	Less or equal than
class	Literal
class	Lt	Greater equal
class	Match	Match a regular expression (string)
class	Minus	And expression
class	Mod	And expression
class	Na	Exists operator (true if a field exists)
class	Neq	Not equal
class	Not	Not expression
class	NotMatch	Match a regular expression (string)
class	Or	Or expression
class	Plus	And expression
class	Times	And expression
class	Xor	Or expression

Fields in org.snpsift.lang.expression declared as Expression

Modifier and Type	Field	Description
protected Expression	ExpressionUnary.expr
protected Expression	ExpressionBinary.left
protected Expression	ExpressionBinary.right

Methods in org.snpsift.lang.expression with parameters of type Expression

Modifier and Type	Method	Description
protected int	FieldSub.evalIndex(org.snpeff.vcf.VcfEntry vcfEntry, Expression idxExpr)	Evaluate index expression (VCF entry)
protected int	FieldSub.evalIndex(org.snpeff.vcf.VcfGenotype vcfGenotype, Expression idxExpr)	Evaluate index expression (VCF genotype)

Constructors in org.snpsift.lang.expression with parameters of type Expression

Constructor	Description
And(Expression left, Expression right)
Div(Expression left, Expression right)
Eq(Expression left, Expression right)
Exists(Expression expr)
ExpressionBinary(Expression left, Expression right, java.lang.String operator)
ExpressionUnary(Expression expr, java.lang.String operator)
FieldEff(java.lang.String name, Expression idxExpr, org.snpeff.vcf.EffFormatVersion formatVersion, java.lang.String fieldName)	Constructor
FieldGenotype(java.lang.String name, Expression indexExpr)
FieldGenotypeSub(java.lang.String name, Expression indexExpr, Expression indexExpr2)
FieldLof(java.lang.String name, Expression indexExpr)
FieldNmd(java.lang.String name, Expression indexExpr)
FieldSub(java.lang.String name, Expression indexExpr)
Ge(Expression left, Expression right)
Gt(Expression left, Expression right)
Has(Expression left, Expression right)
Le(Expression left, Expression right)
Lt(Expression left, Expression right)
Match(Expression left, Expression right)
Minus(Expression left)
Minus(Expression left, Expression right)
Mod(Expression left, Expression right)
Na(Expression expr)
Neq(Expression left, Expression right)
Not(Expression expr)
NotMatch(Expression left, Expression right)
Or(Expression left, Expression right)
Plus(Expression left)
Plus(Expression left, Expression right)
Times(Expression left, Expression right)
Xor(Expression left, Expression right)

Uses of Expression in org.snpsift.lang.function

Subclasses of Expression in org.snpsift.lang.function

Modifier and Type	Class	Description
class	CountHet	Count number of heterozygous samples
class	CountHom	Count number of homozygous samples
class	CountRef	Count number of refernces samples
class	CountVariant	Count number of ALT samples
class	Function	A function that returns an expression (i.e.
class	FunctionBoolGenotype	A function that returns a bool type (i.e.
class	In	Is an expression in a set?
class	IsHet	Is 'genotypeNum' heterozygous?
class	IsHom	Is 'genotypeNum' homozygous?
class	IsRef	Is 'genotypeNum' reference?
class	IsVariant	Is 'genotypeNum' reference?

Constructors in org.snpsift.lang.function with parameters of type Expression

Constructor	Description
FunctionBoolGenotype(java.lang.String functionName, Expression exprIdx)
In(java.util.ArrayList<java.util.HashSet<java.lang.String>> sets, Expression expression, Expression setIdxExpr)
IsHet(Expression exprIdx)
IsHom(Expression exprIdx)
IsRef(Expression exprIdx)
IsVariant(Expression exprIdx)