Package org.snpeff.interval.codonChange

Class CodonChangeSnp

java.lang.Object

org.snpeff.interval.codonChange.CodonChange

org.snpeff.interval.codonChange.CodonChangeSnp

public class CodonChangeSnp
extends CodonChange

Calculate codon changes produced by a SNP

Author:

pcingola

Field Summary

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

CODON_SIZE, showCodonChange

Constructor Summary

Constructors

Constructor	Description
CodonChangeSnp(Variant variant, Transcript transcript, VariantEffects variantEffects)

Method Summary

Modifier and Type	Method	Description
protected boolean	codonChange(Exon exon)	Analyze SNPs in this transcript.
protected java.lang.String	codonsAlt()	Get new (modified) codons
protected java.lang.String	codonsRef()	Get original codons in CDS

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

additionalEffect, cdsBaseNumber, codonChange, 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

CodonChangeSnp

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

Method Detail

codonChange

protected boolean codonChange(Exon exon)

Analyze SNPs in this transcript. Add changeEffect to 'changeEffect'

Overrides:

codonChange in class CodonChange

codonsAlt

protected java.lang.String codonsAlt()

Get new (modified) codons

Overrides:

codonsAlt in class CodonChange

codonsRef

protected java.lang.String codonsRef()

Get original codons in CDS

Overrides:

codonsRef in class CodonChange