FieldEff (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.FieldEff

public class FieldEff extends FieldSub

An 'EFF' field form SnpEff: E.g.: 'EFF[2].GENE'

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

FieldEff(String name, Expression idxExpr, org.snpeff.vcf.EffFormatVersion formatVersion, String fieldName)

Constructor
Method Summary

Modifier and Type

Method

Description

String

getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)

Get a field from VcfEntry

String

getName()

org.snpeff.vcf.VcfInfoType

getReturnType(org.snpeff.vcf.VcfEntry vcfEntry)

String

toString()

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

Methods inherited from class org.snpsift.lang.expression.Field
eval, eval, fieldHeaderNotFound, fieldNotFound, 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
- FieldEff
  
  public FieldEff(String name, Expression idxExpr, org.snpeff.vcf.EffFormatVersion formatVersion, String fieldName)
  
  Constructor
  
  Parameters:
  
  formatVersion - : Can be null (it will be guessed)
Method Details
- getFieldString
  
  public String getFieldString(org.snpeff.vcf.VcfEntry vcfEntry)
  
  Get a field from VcfEntry
  
  Overrides:
  
  getFieldString in class FieldSub
- getName
  
  public String getName()
  
  Overrides:
  
  getName in class Field
- getReturnType
  
  public org.snpeff.vcf.VcfInfoType getReturnType(org.snpeff.vcf.VcfEntry vcfEntry)
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class FieldSub