Package org.snpeff.snpEffect
Class VariantEffectFusion
java.lang.Object
org.snpeff.snpEffect.VariantEffect
org.snpeff.snpEffect.VariantEffectStructural
org.snpeff.snpEffect.VariantEffectFusion
- All Implemented Interfaces:
Cloneable
,Comparable<VariantEffect>
Effect of a structural variant (fusion) affecting two genes
- Author:
- pcingola
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Nested Class Summary
Nested classes/interfaces inherited from class org.snpeff.snpEffect.VariantEffect
VariantEffect.Coding, VariantEffect.EffectImpact, VariantEffect.FunctionalClass
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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
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Constructor Summary
Constructors -
Method Summary
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
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Constructor Details
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VariantEffectFusion
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Method Details
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getAaNumLeftEnd
public int getAaNumLeftEnd() -
getAaNumLeftStart
public int getAaNumLeftStart() -
getAaNumRightEnd
public int getAaNumRightEnd() -
getAaNumRightStart
public int getAaNumRightStart() -
getGene
- Overrides:
getGene
in classVariantEffectStructural
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getGeneLeft
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getGeneRight
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getMarker
- Overrides:
getMarker
in classVariantEffectStructural
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getTrLeft
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getTrRight
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isGeneGeneFusion
public boolean isGeneGeneFusion() -
toString
- Overrides:
toString
in classVariantEffectStructural
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