Package org.snpeff.interval.codonChange

Class CodonChangeMnp

java.lang.Object

org.snpeff.interval.codonChange.CodonChange

org.snpeff.interval.codonChange.CodonChangeMnp

Direct Known Subclasses:

CodonChangeMixed

public class CodonChangeMnp
extends CodonChange

Calculate codon changes produced by a MNP

Author:

pcingola

Field Summary

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

CODON_SIZE, showCodonChange

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
void	codonChange()	Calculate a list of codon changes
protected void	codonOldNew()	Calculate codons old / codons new
protected java.lang.String	codonsAlt()	Calculate new codons
protected java.lang.String	codonsRef()	Calculate old codons
protected java.lang.String	netCdsChange()	We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exons

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

additionalEffect, cdsBaseNumber, codonChange, codonsRef, effect, effectNoCodon, effectNoCodon, factory, intersectsExons, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

CodonChangeMnp

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

Method Detail

codonChange

public void codonChange()

Calculate a list of codon changes

Overrides:

codonChange in class CodonChange

codonOldNew

protected void codonOldNew()

Calculate codons old / codons new

codonsAlt

protected java.lang.String codonsAlt()

Description copied from class: CodonChange

Calculate new codons

Overrides:

codonsAlt in class CodonChange

codonsRef

protected java.lang.String codonsRef()

Calculate old codons

Overrides:

codonsRef in class CodonChange

netCdsChange

protected java.lang.String netCdsChange()

We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exons

Overrides:

netCdsChange in class CodonChange

Returns: