Package org.snpsift.lang.expression
Class FieldEff
- 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.FieldEff
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public class FieldEff extends FieldSub
An 'EFF' field form SnpEff: E.g.: 'EFF[2].GENE'- 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 FieldEff(java.lang.String name, Expression idxExpr, org.snpeff.vcf.EffFormatVersion formatVersion, java.lang.String fieldName)
Constructor
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)
Get a field from VcfEntryjava.lang.String
getName()
org.snpeff.vcf.VcfInfoType
getReturnType(org.snpeff.vcf.VcfEntry vcfEntry)
java.lang.String
toString()
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Methods inherited from class org.snpsift.lang.expression.FieldSub
evalIndex, evalIndex, evalIndex, evalIndex, getFieldString, isSub
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Methods inherited from class org.snpsift.lang.expression.Field
eval, eval, fieldHeaderNotFound, fieldNotFound, 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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FieldEff
public FieldEff(java.lang.String name, Expression idxExpr, org.snpeff.vcf.EffFormatVersion formatVersion, java.lang.String fieldName)
Constructor- Parameters:
formatVersion
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Method Detail
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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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getReturnType
public org.snpeff.vcf.VcfInfoType getReturnType(org.snpeff.vcf.VcfEntry vcfEntry)
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