Package org.snpeff.snpEffect
Class VariantEffectStructural
java.lang.Object
org.snpeff.snpEffect.VariantEffect
org.snpeff.snpEffect.VariantEffectStructural
- All Implemented Interfaces:
Cloneable
,Comparable<VariantEffect>
- Direct Known Subclasses:
VariantEffectFusion
Effect of a structural variant affecting multiple 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
ConstructorsConstructorDescriptionVariantEffectStructural
(Variant variant) VariantEffectStructural
(Variant variant, Markers intersects) -
Method Summary
Modifier and TypeMethodDescriptionprotected int
countGenes
(List<Marker> features) protected EffectType
effect()
fusions()
Is there another 'fusion' effect?getGene()
getGenes()
protected boolean
boolean
protected boolean
toString()
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
-
Constructor Details
-
VariantEffectStructural
-
VariantEffectStructural
-
-
Method Details
-
countGenes
-
effect
-
fusions
Is there another 'fusion' effect? -
getGene
- Overrides:
getGene
in classVariantEffect
-
getGenes
- Overrides:
getGenes
in classVariantEffect
-
getMarker
- Overrides:
getMarker
in classVariantEffect
-
isGene
-
isMultipleGenes
public boolean isMultipleGenes()- Overrides:
isMultipleGenes
in classVariantEffect
-
isTranscript
-
toString
- Overrides:
toString
in classVariantEffect
-