Package org.snpeff.snpEffect

Class VariantEffectFusion

java.lang.Object

org.snpeff.snpEffect.VariantEffect

org.snpeff.snpEffect.VariantEffectStructural

org.snpeff.snpEffect.VariantEffectFusion

All Implemented Interfaces:

java.lang.Cloneable, java.lang.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 org.snpeff.snpEffect.VariantEffect

VariantEffect.Coding, VariantEffect.EffectImpact, VariantEffect.FunctionalClass

Field Summary

Fields inherited from class org.snpeff.snpEffect.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()
java.lang.String	toString()

Methods inherited from class org.snpeff.snpEffect.VariantEffectStructural

countGenes, effect, fusions, getGenes, isGene, isMultipleGenes, isTranscript

Methods inherited from class org.snpeff.snpEffect.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 java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

VariantEffectFusion

public VariantEffectFusion(Variant variant,
                           Marker mLeft,
                           Marker mRight)

Method Detail

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 java.lang.String toString()

Overrides:

toString in class VariantEffectStructural