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

public class FieldSub
extends Field

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

Constructor	Description
FieldSub(java.lang.String name, Expression indexExpr)

Method Summary

Modifier and Type	Method	Description
protected int	evalIndex(org.snpeff.vcf.VcfEntry vcfEntry)	Evaluate index expression
protected 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)
java.lang.String	getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)	Get a field from VcfEntry
java.lang.String	getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)	Get a field from VcfEntry
protected boolean	isSub()
java.lang.String	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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

FieldSub

public FieldSub(java.lang.String name,
                Expression indexExpr)

Method Detail

evalIndex

protected int evalIndex(org.snpeff.vcf.VcfEntry vcfEntry)

Evaluate index expression

evalIndex

protected int evalIndex(org.snpeff.vcf.VcfEntry vcfEntry,
                        Expression idxExpr)

Evaluate index expression (VCF entry)

evalIndex

protected int evalIndex(org.snpeff.vcf.VcfGenotype vcfGenotype)

Evaluate index expression (VCF genotype)

evalIndex

protected int evalIndex(org.snpeff.vcf.VcfGenotype vcfGenotype,
                        Expression idxExpr)

Evaluate index expression (VCF genotype)

getFieldString

public java.lang.String getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)

Get a field from VcfEntry

getFieldString

public java.lang.String getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)

Get a field from VcfEntry

Overrides:

getFieldString in class Field

isSub

protected boolean isSub()

Overrides:

isSub in class Field

toString

public java.lang.String toString()

Overrides:

toString in class Field