Uses of Class
org.snpsift.lang.expression.Expression
Packages that use Expression
Package
Description
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Uses of Expression in org.snpsift
Methods in org.snpsift that return ExpressionModifier and TypeMethodDescriptionSnpSiftCmdFilter.parseExpression
(String expression) Parse expressionSnpSiftCmdFilterGt.parseExpression
(String expression) Parse expression -
Uses of Expression in org.snpsift.lang
Methods in org.snpsift.lang that return ExpressionModifier and TypeMethodDescriptionCreate an AST from a program (using ANTLR lexer invalid input: '&' parser) Returns null if error Use 'alreadyIncluded' to keep track of from 'include' statementsLangFactory.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.expressionModifier and TypeClassDescriptionclass
And expressionclass
And expressionclass
Equalclass
Exists operator (true if a field exists)class
Binary conditionclass
An expression that can be negatedclass
A field: E.g.: 'DP', 'CHROM'class
A 'constant' field: e.g.class
A 'constant' field: e.g.class
An 'EFF' field form SnpEff: E.g.: 'EFF[2].GENE'class
A field: E.g.: 'GEN[2].GT'class
A field: E.g.: 'GEN[2].PL[3]'class
A LOF field form SnpEff: E.g.: 'LOF[2].GENE'class
A NMD field form SnpEff: E.g.: 'NMD[2].GENE'class
A field that has sub fields (e.g.class
Greater equalclass
Greater equalclass
Equalclass
Less or equal thanclass
class
Greater equalclass
Match a regular expression (string)class
And expressionclass
And expressionclass
Exists operator (true if a field exists)class
Not equalclass
Not expressionclass
Match a regular expression (string)class
Or expressionclass
And expressionclass
And expressionclass
Or expressionFields in org.snpsift.lang.expression declared as ExpressionModifier and TypeFieldDescriptionprotected Expression
ExpressionUnary.expr
protected Expression
ExpressionBinary.left
protected Expression
ExpressionBinary.right
Methods in org.snpsift.lang.expression with parameters of type ExpressionModifier and TypeMethodDescriptionprotected 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 ExpressionModifierConstructorDescriptionAnd
(Expression left, Expression right) Div
(Expression left, Expression right) Eq
(Expression left, Expression right) Exists
(Expression expr) ExpressionBinary
(Expression left, Expression right, String operator) ExpressionUnary
(Expression expr, String operator) FieldEff
(String name, Expression idxExpr, org.snpeff.vcf.EffFormatVersion formatVersion, String fieldName) ConstructorFieldGenotype
(String name, Expression indexExpr) FieldGenotypeSub
(String name, Expression indexExpr, Expression indexExpr2) FieldLof
(String name, Expression indexExpr) FieldNmd
(String name, Expression indexExpr) FieldSub
(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.functionModifier and TypeClassDescriptionclass
Count number of heterozygous samplesclass
Count number of homozygous samplesclass
Count number of refernces samplesclass
Count number of ALT samplesclass
A function that returns an expression (i.e.class
A function that returns a bool type (i.e.class
Is an expression in a set?class
Is 'genotypeNum' heterozygous?class
Is 'genotypeNum' homozygous?class
Is 'genotypeNum' reference?class
Is 'genotypeNum' reference?Constructors in org.snpsift.lang.function with parameters of type ExpressionModifierConstructorDescriptionFunctionBoolGenotype
(String functionName, Expression exprIdx) In
(ArrayList<HashSet<String>> sets, Expression expression, Expression setIdxExpr) IsHet
(Expression exprIdx) IsHom
(Expression exprIdx) IsRef
(Expression exprIdx) IsVariant
(Expression exprIdx)