Uses of Class
org.snpsift.lang.expression.Expression
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Packages that use Expression Package Description org.snpsift org.snpsift.lang org.snpsift.lang.expression org.snpsift.lang.function -
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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 expressionExpression
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' statementsExpression
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 expressionclass
Div
And expressionclass
Eq
Equalclass
Exists
Exists operator (true if a field exists)class
ExpressionBinary
Binary conditionclass
ExpressionUnary
An expression that can be negatedclass
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 equalclass
Gt
Greater equalclass
Has
Equalclass
Le
Less or equal thanclass
Literal
class
Lt
Greater equalclass
Match
Match a regular expression (string)class
Minus
And expressionclass
Mod
And expressionclass
Na
Exists operator (true if a field exists)class
Neq
Not equalclass
Not
Not expressionclass
NotMatch
Match a regular expression (string)class
Or
Or expressionclass
Plus
And expressionclass
Times
And expressionclass
Xor
Or expressionFields 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)
ConstructorFieldGenotype(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)
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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 samplesclass
CountHom
Count number of homozygous samplesclass
CountRef
Count number of refernces samplesclass
CountVariant
Count number of ALT samplesclass
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)
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