Package org.snpeff.interval.codonChange

Class CodonChangeDup

java.lang.Object

org.snpeff.interval.codonChange.CodonChange

org.snpeff.interval.codonChange.CodonChangeStructural

org.snpeff.interval.codonChange.CodonChangeDup

public class CodonChangeDup
extends CodonChangeStructural

Calculate codon changes produced by a duplication

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
CodonChangeDup(Variant variant, Transcript transcript, VariantEffects variantEffects)

Method Summary

Modifier and Type	Method	Description
protected void	effectTranscript()
protected void	exons()	Variant affect one or more exons
protected void	exonsCoding()	One or more exons fully included (no partial overlap)
protected void	exonsNoncoding()	Effects for non-coding transcripts
protected void	intron()	Inversion does not intersect any exon

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, codonChange, codonsAlt, codonsRef, 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 Detail

CodonChangeDup

public CodonChangeDup(Variant variant,
                      Transcript transcript,
                      VariantEffects variantEffects)

Method Detail

effectTranscript

protected void effectTranscript()

Specified by:

effectTranscript in class CodonChangeStructural

exons

protected void exons()

Description copied from class: CodonChangeStructural

Variant affect one or more exons

Specified by:

exons in class CodonChangeStructural

exonsCoding

protected void exonsCoding()

One or more exons fully included (no partial overlap)

Specified by:

exonsCoding in class CodonChangeStructural

exonsNoncoding

protected void exonsNoncoding()

Effects for non-coding transcripts

Specified by:

exonsNoncoding in class CodonChangeStructural

intron

protected void intron()

Inversion does not intersect any exon

Specified by:

intron in class CodonChangeStructural