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 TypeClassDescriptionclassAnd expressionclassAnd expressionclassEqualclassExists operator (true if a field exists)classBinary conditionclassAn expression that can be negatedclassA field: E.g.: 'DP', 'CHROM'classA 'constant' field: e.g.classA 'constant' field: e.g.classAn 'EFF' field form SnpEff: E.g.: 'EFF[2].GENE'classA field: E.g.: 'GEN[2].GT'classA field: E.g.: 'GEN[2].PL[3]'classA LOF field form SnpEff: E.g.: 'LOF[2].GENE'classA NMD field form SnpEff: E.g.: 'NMD[2].GENE'classA field that has sub fields (e.g.classGreater equalclassGreater equalclassEqualclassLess or equal thanclassclassGreater equalclassMatch a regular expression (string)classAnd expressionclassAnd expressionclassExists operator (true if a field exists)classNot equalclassNot expressionclassMatch a regular expression (string)classOr expressionclassAnd expressionclassAnd expressionclassOr expressionFields in org.snpsift.lang.expression declared as ExpressionModifier and TypeFieldDescriptionprotected ExpressionExpressionUnary.exprprotected ExpressionExpressionBinary.leftprotected ExpressionExpressionBinary.rightMethods in org.snpsift.lang.expression with parameters of type ExpressionModifier and TypeMethodDescriptionprotected intFieldSub.evalIndex(org.snpeff.vcf.VcfEntry vcfEntry, Expression idxExpr) Evaluate index expression (VCF entry)protected intFieldSub.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 TypeClassDescriptionclassCount number of heterozygous samplesclassCount number of homozygous samplesclassCount number of refernces samplesclassCount number of ALT samplesclassA function that returns an expression (i.e.classA function that returns a bool type (i.e.classIs an expression in a set?classIs 'genotypeNum' heterozygous?classIs 'genotypeNum' homozygous?classIs 'genotypeNum' reference?classIs '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)