Package org.snpeff.interval.codonChange

Class CodonChangeDel

java.lang.Object

org.snpeff.interval.codonChange.CodonChange

org.snpeff.interval.codonChange.CodonChangeStructural

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 java.lang.String	codonsAlt()	Get alternative codons
protected java.lang.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 Detail

CodonChangeDel

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

Method Detail

codonChange

protected boolean codonChange(Exon exon)

Analyze deletions in this transcript.

Overrides:

codonChange in class CodonChange

codonsAlt

protected java.lang.String codonsAlt()

Get alternative codons

Overrides:

codonsAlt in class CodonChange

codonsRef

protected java.lang.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