org.snpeff.interval.codonChange.CodonChangeDel

public class CodonChangeDel extends CodonChangeStructural

Calculate codon changes produced by a deletion

Author:: pcingola

Field Summary

Fields inherited from class org.snpeff.interval.codonChange.CodonChangeStructural
cdsAlt, cdsRef, coding, debug, exonFull, exonPartial

Fields inherited from class org.snpeff.interval.codonChange.CodonChange
CODON_SIZE, showCodonChange
Constructor Summary

Constructors

Constructor

Description

CodonChangeDel(Variant variant, Transcript transcript, VariantEffects variantEffects)
Method Summary

Modifier and Type

Method

Description

protected boolean

codonChange(Exon exon)

Analyze deletions in this transcript.

protected String

codonsAlt()

Get alternative codons

protected String

codonsRef()

Get original codons in CDS

protected void

effectTranscript()

protected void

exons()

Deletion analysis using full transcript information.

protected void

exonsCoding()

Variant affect one or more coding exons

protected void

exonsNoncoding()

Variant affect one or more non-coding exons

protected void

intron()

Variant affect one intron

Methods inherited from class org.snpeff.interval.codonChange.CodonChangeStructural
cdsDiff, codonChange, codonChangeSuper, codonsRefAlt, countAffectedExons

Methods inherited from class org.snpeff.interval.codonChange.CodonChange
additionalEffect, cdsBaseNumber, codonsRef, effect, effectNoCodon, effectNoCodon, factory, intersectsExons, netCdsChange, toString

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

Constructor Details
- CodonChangeDel
  
  public CodonChangeDel(Variant variant, Transcript transcript, VariantEffects variantEffects)
Method Details
- codonChange
  
  protected boolean codonChange(Exon exon)
  
  Analyze deletions in this transcript.
  
  Overrides:
  
  codonChange in class CodonChange
- codonsAlt
  
  protected String codonsAlt()
  
  Get alternative codons
  
  Overrides:
  
  codonsAlt in class CodonChange
- codonsRef
  
  protected String codonsRef()
  
  Get original codons in CDS
  
  Overrides:
  
  codonsRef in class CodonChange
- effectTranscript
  
  protected void effectTranscript()
  
  Specified by:
  
  effectTranscript in class CodonChangeStructural
- exons
  
  protected void exons()
  
  Deletion analysis using full transcript information. This is done only when the variant affects more than one exons.
  
  Specified by:
  
  exons in class CodonChangeStructural
- exonsCoding
  
  protected void exonsCoding()
  
  Description copied from class: CodonChangeStructural
  
  Variant affect one or more coding exons
  
  Specified by:
  
  exonsCoding in class CodonChangeStructural
- exonsNoncoding
  
  protected void exonsNoncoding()
  
  Description copied from class: CodonChangeStructural
  
  Variant affect one or more non-coding exons
  
  Specified by:
  
  exonsNoncoding in class CodonChangeStructural
- intron
  
  protected void intron()
  
  Description copied from class: CodonChangeStructural
  
  Variant affect one intron
  
  Specified by:
  
  intron in class CodonChangeStructural

Class CodonChangeDel

Field Summary

Fields inherited from class org.snpeff.interval.codonChange.CodonChangeStructural

Fields inherited from class org.snpeff.interval.codonChange.CodonChange

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.interval.codonChange.CodonChangeStructural

Methods inherited from class org.snpeff.interval.codonChange.CodonChange

Methods inherited from class java.lang.Object

Constructor Details

CodonChangeDel

Method Details

codonChange

codonsAlt

codonsRef

effectTranscript

exons

exonsCoding

exonsNoncoding

intron