Package org.snpsift.lang.expression
Class FieldSub
- java.lang.Object
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- org.snpsift.lang.expression.Expression
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- org.snpsift.lang.expression.Field
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- org.snpsift.lang.expression.FieldSub
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- 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
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Field Summary
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Fields inherited from class org.snpsift.lang.expression.Field
exceptionIfNotFound, name, number, returnType, TYPE_ALL, TYPE_ANY, vcfInfo, vcfInfoNumber
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Fields inherited from class org.snpsift.lang.expression.Expression
debug, negated, operator
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Constructor Summary
Constructors Constructor Description FieldSub(java.lang.String name, Expression indexExpr)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected 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)java.lang.String
getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)
Get a field from VcfEntryjava.lang.String
getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)
Get a field from VcfEntryprotected boolean
isSub()
java.lang.String
toString()
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Methods inherited from class org.snpsift.lang.expression.Field
eval, eval, fieldHeaderNotFound, fieldNotFound, getName, getReturnType, getSampleNum, gtFieldNotFound, indexStr, isSampleName, returnType, returnType, setExceptionIfNotFound
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Methods inherited from class org.snpsift.lang.expression.Expression
setNegated
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Constructor Detail
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FieldSub
public FieldSub(java.lang.String name, Expression indexExpr)
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Method Detail
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evalIndex
protected int evalIndex(org.snpeff.vcf.VcfEntry vcfEntry)
Evaluate index expression
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evalIndex
protected int evalIndex(org.snpeff.vcf.VcfEntry vcfEntry, Expression idxExpr)
Evaluate index expression (VCF entry)
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evalIndex
protected int evalIndex(org.snpeff.vcf.VcfGenotype vcfGenotype)
Evaluate index expression (VCF genotype)
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evalIndex
protected int evalIndex(org.snpeff.vcf.VcfGenotype vcfGenotype, Expression idxExpr)
Evaluate index expression (VCF genotype)
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getFieldString
public java.lang.String getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)
Get a field from VcfEntry
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getFieldString
public java.lang.String getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)
Get a field from VcfEntry- Overrides:
getFieldString
in classField
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