Package org.snpsift.lang.expression
Class FieldSub
java.lang.Object
org.snpsift.lang.expression.Expression
org.snpsift.lang.expression.Field
org.snpsift.lang.expression.FieldSub
- Direct Known Subclasses:
FieldEff
,FieldGenotype
,FieldLof
A field that has sub fields (e.g. comma separated list of parameters):
E.g.: 'AF1[2]'
- Author:
- pablocingolani
-
Field Summary
Fields inherited from class org.snpsift.lang.expression.Field
exceptionIfNotFound, name, number, returnType, TYPE_ALL, TYPE_ANY, vcfInfo, vcfInfoNumber
Fields inherited from class org.snpsift.lang.expression.Expression
debug, negated, operator
-
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
evalIndex
(org.snpeff.vcf.VcfEntry vcfEntry) Evaluate index expressionprotected int
evalIndex
(org.snpeff.vcf.VcfEntry vcfEntry, Expression idxExpr) Evaluate index expression (VCF entry)protected int
evalIndex
(org.snpeff.vcf.VcfGenotype vcfGenotype) Evaluate index expression (VCF genotype)protected int
evalIndex
(org.snpeff.vcf.VcfGenotype vcfGenotype, Expression idxExpr) Evaluate index expression (VCF genotype)getFieldString
(org.snpeff.vcf.VcfEntry vcfEntry) Get a field from VcfEntrygetFieldString
(org.snpeff.vcf.VcfGenotype vcfGenotype) Get a field from VcfEntryprotected boolean
isSub()
toString()
Methods inherited from class org.snpsift.lang.expression.Field
eval, eval, fieldHeaderNotFound, fieldNotFound, getName, getReturnType, getSampleNum, gtFieldNotFound, indexStr, isSampleName, returnType, returnType, setExceptionIfNotFound
Methods inherited from class org.snpsift.lang.expression.Expression
setNegated
-
Constructor Details
-
FieldSub
-
-
Method Details
-
evalIndex
protected int evalIndex(org.snpeff.vcf.VcfEntry vcfEntry) Evaluate index expression -
evalIndex
Evaluate index expression (VCF entry) -
evalIndex
protected int evalIndex(org.snpeff.vcf.VcfGenotype vcfGenotype) Evaluate index expression (VCF genotype) -
evalIndex
Evaluate index expression (VCF genotype) -
getFieldString
Get a field from VcfEntry -
getFieldString
Get a field from VcfEntry- Overrides:
getFieldString
in classField
-
isSub
protected boolean isSub() -
toString
-