FieldGenotype (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

Direct Known Subclasses:: FieldGenotypeSub

public class FieldGenotype extends FieldSub

A field: E.g.: 'GEN[2].GT'

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

FieldGenotype(String name, Expression indexExpr)
Method Summary

Modifier and Type

Method

Description

protected org.snpeff.vcf.VcfGenotype

evalGenotype(org.snpeff.vcf.VcfEntry vcfEntry)

Evaluate expressions and return VcfGenotype

String

getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)

Get a field from VcfEntry

String

getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)

Get a field (as a Float) from VcfEntry

protected boolean

isSub()

String

toString()

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
- FieldGenotype
  
  public FieldGenotype(String name, Expression indexExpr)
Method Details
- evalGenotype
  
  protected org.snpeff.vcf.VcfGenotype evalGenotype(org.snpeff.vcf.VcfEntry vcfEntry)
  
  Evaluate expressions and return VcfGenotype
- getFieldString
  
  public String getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)
  
  Get a field from VcfEntry
  
  Overrides:
  
  getFieldString in class FieldSub
- getFieldString
  
  public String getFieldString(org.snpeff.vcf.VcfGenotype vcfGenotype)
  
  Get a field (as a Float) from VcfEntry
  
  Overrides:
  
  getFieldString in class FieldSub
- isSub
  
  protected boolean isSub()
  
  Overrides:
  
  isSub in class FieldSub
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class FieldSub