org.snpeff.snpEffect.VariantEffectFusion

All Implemented Interfaces:: Cloneable, Comparable<VariantEffect>

public class VariantEffectFusion extends VariantEffectStructural

Effect of a structural variant (fusion) affecting two genes

Author:: pcingola

Nested Class Summary

Nested classes/interfaces inherited from class VariantEffect
VariantEffect.Coding, VariantEffect.EffectImpact, VariantEffect.FunctionalClass
Field Summary

Fields inherited from class VariantEffect
aaAlt, aaRef, aasAroundNew, aasAroundOld, cDnaPos, codonDegeneracy, codonIndex, codonNum, codonsAlt, codonsAroundNew, codonsAroundOld, codonsRef, distance, effectImpact, effectImpacts, effectType, effectTypes, error, marker, MAX_CODON_SEQUENCE_LEN, message, variant, warning
Constructor Summary

Constructors

Constructor

Description

VariantEffectFusion(Variant variant, Marker mLeft, Marker mRight)
Method Summary

Modifier and Type

Method

Description

int

getAaNumLeftEnd()

int

getAaNumLeftStart()

int

getAaNumRightEnd()

int

getAaNumRightStart()

Gene

getGene()

Gene

getGeneLeft()

Gene

getGeneRight()

Marker

getMarker()

Transcript

getTrLeft()

Transcript

getTrRight()

boolean

isGeneGeneFusion()

String

toString()

Methods inherited from class VariantEffectStructural
countGenes, effect, fusions, getGenes, isGene, isMultipleGenes, isTranscript

Methods inherited from class VariantEffect
addEffect, addEffectImpact, addEffectType, addErrorMessage, addErrorWarningInfo, addInfoMessage, addWarningMessge, clone, compareTo, effect, getAaAlt, getAaChange, getAaChangeOld, getAaLength, getAaNetChange, getAaRef, getBiotype, getcDnaPos, getCdsLength, getCodonChange, getCodonChangeMax, getCodonIndex, getCodonNum, getCodonsAlt, getCodonsRef, getDistance, getEffectImpact, getEffectType, getEffectTypes, getEffectTypeString, getEffectTypeString, getEffectTypeString, getError, getExon, getFunctionalClass, getGeneRegion, getGenotype, getHgvs, getHgvsDna, getHgvsProt, getIntron, getTranscript, getVariant, getWarning, hasAdditionalAnnotations, hasEffectImpact, hasEffectType, hasError, hasWarning, isCustom, isExon, isIntergenic, isIntron, isMotif, isNextProt, isRegulation, isSpliceSite, isSpliceSiteCore, isSpliceSiteRegion, isUtr3, isUtr5, set, setCodons, setCodonsAround, setDistance, setEffect, setEffectImpact, setEffectType, setMarker, toStr, toString, toStringSimple

Methods inherited from class Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details
- VariantEffectFusion
  
  public VariantEffectFusion(Variant variant, Marker mLeft, Marker mRight)
Method Details
- getAaNumLeftEnd
  
  public int getAaNumLeftEnd()
- getAaNumLeftStart
  
  public int getAaNumLeftStart()
- getAaNumRightEnd
  
  public int getAaNumRightEnd()
- getAaNumRightStart
  
  public int getAaNumRightStart()
- getGene
  
  public Gene getGene()
  
  Overrides:
  
  getGene in class VariantEffectStructural
- getGeneLeft
  
  public Gene getGeneLeft()
- getGeneRight
  
  public Gene getGeneRight()
- getMarker
  
  public Marker getMarker()
  
  Overrides:
  
  getMarker in class VariantEffectStructural
- getTrLeft
  
  public Transcript getTrLeft()
- getTrRight
  
  public Transcript getTrRight()
- isGeneGeneFusion
  
  public boolean isGeneGeneFusion()
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class VariantEffectStructural

Class VariantEffectFusion

Nested Class Summary

Nested classes/interfaces inherited from class VariantEffect

Field Summary

Fields inherited from class VariantEffect

Constructor Summary

Method Summary

Methods inherited from class VariantEffectStructural

Methods inherited from class VariantEffect

Methods inherited from class Object

Constructor Details

VariantEffectFusion

Method Details

getAaNumLeftEnd

getAaNumLeftStart

getAaNumRightEnd

getAaNumRightStart

getGene

getGeneLeft

getGeneRight

getMarker

getTrLeft

getTrRight

isGeneGeneFusion

toString