Package org.snpsift.lang.expression
Class Field
java.lang.Object
org.snpsift.lang.expression.Expression
org.snpsift.lang.expression.Field
- Direct Known Subclasses:
FieldConstant
,FieldSub
A field:
E.g.: 'DP', 'CHROM'
- Author:
- pablocingolani
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected boolean
protected String
protected int
protected org.snpeff.vcf.VcfInfoType
static final int
static final int
protected org.snpeff.vcf.VcfHeaderInfo
protected org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber
Fields inherited from class org.snpsift.lang.expression.Expression
debug, negated, operator
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioneval
(org.snpeff.vcf.VcfEntry vcfEntry) Evaluate expression using VcfEntryeval
(org.snpeff.vcf.VcfGenotype vcfGenotype) Evaluate expression using genotypeprotected Object
fieldHeaderNotFound
(org.snpeff.vcf.VcfEntry vcfEntry) protected Object
fieldNotFound
(org.snpeff.vcf.VcfEntry vcfEntry) getFieldString
(org.snpeff.vcf.VcfGenotype vcfGenotype) getName()
org.snpeff.vcf.VcfInfoType
getReturnType
(org.snpeff.vcf.VcfGenotype vcfGenotype) protected int
getSampleNum
(org.snpeff.vcf.VcfEntry vcfEntry, String name) protected Object
gtFieldNotFound
(org.snpeff.vcf.VcfGenotype vcfGenotype) indexStr
(int index) Convert and index to a stringprotected boolean
isSampleName
(org.snpeff.vcf.VcfEntry vcfEntry, String name) protected boolean
isSub()
org.snpeff.vcf.VcfInfoType
returnType
(org.snpeff.vcf.VcfEntry vcfEntry) org.snpeff.vcf.VcfInfoType
returnType
(org.snpeff.vcf.VcfGenotype vcfGenotype) void
setExceptionIfNotFound
(boolean exceptionIfNotFound) toString()
Methods inherited from class org.snpsift.lang.expression.Expression
setNegated
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Field Details
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TYPE_ALL
public static final int TYPE_ALL- See Also:
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TYPE_ANY
public static final int TYPE_ANY- See Also:
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name
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returnType
protected org.snpeff.vcf.VcfInfoType returnType -
exceptionIfNotFound
protected boolean exceptionIfNotFound -
vcfInfo
protected org.snpeff.vcf.VcfHeaderInfo vcfInfo -
number
protected int number -
vcfInfoNumber
protected org.snpeff.vcf.VcfHeaderInfo.VcfInfoNumber vcfInfoNumber
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Constructor Details
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Field
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Method Details
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eval
Description copied from class:Expression
Evaluate expression using VcfEntry- Specified by:
eval
in classExpression
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eval
Description copied from class:Expression
Evaluate expression using genotype- Specified by:
eval
in classExpression
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fieldHeaderNotFound
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fieldNotFound
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getFieldString
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getName
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getReturnType
public org.snpeff.vcf.VcfInfoType getReturnType(org.snpeff.vcf.VcfGenotype vcfGenotype) -
getSampleNum
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gtFieldNotFound
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indexStr
Convert and index to a string -
isSampleName
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isSub
protected boolean isSub() -
returnType
public org.snpeff.vcf.VcfInfoType returnType(org.snpeff.vcf.VcfEntry vcfEntry) -
returnType
public org.snpeff.vcf.VcfInfoType returnType(org.snpeff.vcf.VcfGenotype vcfGenotype) -
setExceptionIfNotFound
public void setExceptionIfNotFound(boolean exceptionIfNotFound) -
toString
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