Package org.snpsift.lang.expression
Class FieldGenotype
- 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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- org.snpsift.lang.expression.FieldGenotype
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- Direct Known Subclasses:
FieldGenotypeSub
public class FieldGenotype extends FieldSub
A field: E.g.: 'GEN[2].GT'- 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 FieldGenotype(java.lang.String name, Expression indexExpr)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected org.snpeff.vcf.VcfGenotype
evalGenotype(org.snpeff.vcf.VcfEntry vcfEntry)
Evaluate expressions and return VcfGenotypejava.lang.String
getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)
Get a field from VcfEntryjava.lang.String
getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)
Get a field (as a Float) from VcfEntryprotected boolean
isSub()
java.lang.String
toString()
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Methods inherited from class org.snpsift.lang.expression.FieldSub
evalIndex, evalIndex, evalIndex, evalIndex
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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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FieldGenotype
public FieldGenotype(java.lang.String name, Expression indexExpr)
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Method Detail
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evalGenotype
protected org.snpeff.vcf.VcfGenotype evalGenotype(org.snpeff.vcf.VcfEntry vcfEntry)
Evaluate expressions and return VcfGenotype
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getFieldString
public java.lang.String getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)
Get a field from VcfEntry- Overrides:
getFieldString
in classFieldSub
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getFieldString
public java.lang.String getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)
Get a field (as a Float) from VcfEntry- Overrides:
getFieldString
in classFieldSub
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