Package org.snpeff.snpEffect
Class VariantEffectStructural
- java.lang.Object
-
- org.snpeff.snpEffect.VariantEffect
-
- org.snpeff.snpEffect.VariantEffectStructural
-
- All Implemented Interfaces:
java.lang.Cloneable
,java.lang.Comparable<VariantEffect>
- Direct Known Subclasses:
VariantEffectFusion
public class VariantEffectStructural extends VariantEffect
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
Constructors Constructor Description VariantEffectStructural(Variant variant)
VariantEffectStructural(Variant variant, Markers intersects)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
countGenes(java.util.List<Marker> features)
protected EffectType
effect()
java.util.List<VariantEffect>
fusions()
Is there another 'fusion' effect?Gene
getGene()
java.util.List<Gene>
getGenes()
Marker
getMarker()
protected boolean
isGene(Marker m)
boolean
isMultipleGenes()
protected boolean
isTranscript(Marker m)
java.lang.String
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
-
-
-
-
Method Detail
-
countGenes
protected int countGenes(java.util.List<Marker> features)
-
effect
protected EffectType effect()
-
fusions
public java.util.List<VariantEffect> fusions()
Is there another 'fusion' effect?
-
getGene
public Gene getGene()
- Overrides:
getGene
in classVariantEffect
-
getGenes
public java.util.List<Gene> getGenes()
- Overrides:
getGenes
in classVariantEffect
-
getMarker
public Marker getMarker()
- Overrides:
getMarker
in classVariantEffect
-
isGene
protected boolean isGene(Marker m)
-
isMultipleGenes
public boolean isMultipleGenes()
- Overrides:
isMultipleGenes
in classVariantEffect
-
isTranscript
protected boolean isTranscript(Marker m)
-
toString
public java.lang.String toString()
- Overrides:
toString
in classVariantEffect
-
-