java.lang.Object

org.snpeff.snpEffect.VariantEffect

org.snpeff.snpEffect.VariantEffectStructural

All Implemented Interfaces:: Cloneable, 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

Modifier and Type

Method

Description

protected int

countGenes(List<Marker> features)

protected EffectType

effect()

List<VariantEffect>

fusions()

Is there another 'fusion' effect?

Gene

getGene()

List<Gene>

getGenes()

Marker

getMarker()

protected boolean

isGene(Marker m)

boolean

isMultipleGenes()

protected boolean

isTranscript(Marker m)

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

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details
- VariantEffectStructural
  
  public VariantEffectStructural(Variant variant)
- VariantEffectStructural
  
  public VariantEffectStructural(Variant variant, Markers intersects)
Method Details
- countGenes
  
  protected int countGenes(List<Marker> features)
- effect
  
  protected EffectType effect()
- fusions
  
  public List<VariantEffect> fusions()
  
  Is there another 'fusion' effect?
- getGene
  
  public Gene getGene()
  
  Overrides:
  
  getGene in class VariantEffect
- getGenes
  
  public List<Gene> getGenes()
  
  Overrides:
  
  getGenes in class VariantEffect
- getMarker
  
  public Marker getMarker()
  
  Overrides:
  
  getMarker in class VariantEffect
- isGene
  
  protected boolean isGene(Marker m)
- isMultipleGenes
  
  public boolean isMultipleGenes()
  
  Overrides:
  
  isMultipleGenes in class VariantEffect
- isTranscript
  
  protected boolean isTranscript(Marker m)
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class VariantEffect

Class VariantEffectStructural

Nested Class Summary

Nested classes/interfaces inherited from class org.snpeff.snpEffect.VariantEffect

Field Summary

Fields inherited from class org.snpeff.snpEffect.VariantEffect

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.snpEffect.VariantEffect

Methods inherited from class java.lang.Object

Constructor Details

VariantEffectStructural

VariantEffectStructural

Method Details

countGenes

effect

fusions

getGene

getGenes

getMarker

isGene

isMultipleGenes

isTranscript

toString