Package org.snpeff.snpEffect
Class VariantEffectFusion
- java.lang.Object
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- org.snpeff.snpEffect.VariantEffect
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- org.snpeff.snpEffect.VariantEffectStructural
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- org.snpeff.snpEffect.VariantEffectFusion
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from class org.snpeff.snpEffect.VariantEffect
VariantEffect.Coding, VariantEffect.EffectImpact, VariantEffect.ErrorWarningType, VariantEffect.FunctionalClass
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Field Summary
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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
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Constructor Summary
Constructors Constructor Description VariantEffectFusion(Variant variant, Marker mLeft, Marker mRight)
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Method Summary
All Methods Instance Methods Concrete Methods 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()
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Methods inherited from class org.snpeff.snpEffect.VariantEffectStructural
countGenes, effect, fusions, getGenes, isGene, isMultipleGenes, isTranscript
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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
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Method Detail
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getAaNumLeftEnd
public int getAaNumLeftEnd()
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getAaNumLeftStart
public int getAaNumLeftStart()
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getAaNumRightEnd
public int getAaNumRightEnd()
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getAaNumRightStart
public int getAaNumRightStart()
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getGene
public Gene getGene()
- Overrides:
getGene
in classVariantEffectStructural
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getGeneLeft
public Gene getGeneLeft()
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getGeneRight
public Gene getGeneRight()
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getMarker
public Marker getMarker()
- Overrides:
getMarker
in classVariantEffectStructural
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getTrLeft
public Transcript getTrLeft()
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getTrRight
public Transcript getTrRight()
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isGeneGeneFusion
public boolean isGeneGeneFusion()
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toString
public java.lang.String toString()
- Overrides:
toString
in classVariantEffectStructural
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