FieldGenotypeSub (SnpSift 5.2 API)

java.lang.Object

org.snpsift.lang.expression.Expression

org.snpsift.lang.expression.Field

org.snpsift.lang.expression.FieldSub

org.snpsift.lang.expression.FieldGenotype

org.snpsift.lang.expression.FieldGenotypeSub

public class FieldGenotypeSub extends FieldGenotype

A field: E.g.: 'GEN[2].PL[3]'

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

FieldGenotypeSub(String name, Expression indexExpr, Expression indexExpr2)
Method Summary

Modifier and Type

Method

Description

String

getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)

Get a field from VcfEntry

String

getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)

Get a field from VcfGenotype

protected boolean

isSub()

String

toString()

Methods inherited from class org.snpsift.lang.expression.FieldGenotype
evalGenotype

Methods inherited from class org.snpsift.lang.expression.FieldSub
evalIndex, evalIndex, evalIndex, evalIndex

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 Details
- FieldGenotypeSub
  
  public FieldGenotypeSub(String name, Expression indexExpr, Expression indexExpr2)
Method Details
- getFieldString
  
  public String getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)
  
  Get a field from VcfEntry
  
  Overrides:
  
  getFieldString in class FieldGenotype
- getFieldString
  
  public String getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)
  
  Get a field from VcfGenotype
  
  Overrides:
  
  getFieldString in class FieldGenotype
- isSub
  
  protected boolean isSub()
  
  Overrides:
  
  isSub in class FieldGenotype
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class FieldGenotype