Package org.snpeff.interval.codonChange

Class CodonChangeStructural

java.lang.Object

org.snpeff.interval.codonChange.CodonChange

org.snpeff.interval.codonChange.CodonChangeStructural

Direct Known Subclasses:

CodonChangeDel, CodonChangeDup

public abstract class CodonChangeStructural
extends CodonChange

Calculate codon changes produced by a duplication

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
protected java.lang.String	cdsAlt
protected java.lang.String	cdsRef
protected boolean	coding
static boolean	debug
protected int	exonFull
protected int	exonPartial

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

CODON_SIZE, showCodonChange

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected void	cdsDiff()	Differences between two CDSs after removing equal codons from the beginning and from the end of both strings
void	codonChange()	Calculate a list of codon changes
protected void	codonChangeSuper()
protected void	codonsRefAlt()	Calculate codons by applying the variant and calculating the differences in CDS sequences This is a slow method, makes sense only for complex variants
protected void	countAffectedExons()	How many full / partial exons does the variant affect?
protected abstract void	effectTranscript()
protected abstract void	exons()	Variant affect one or more exons
protected abstract void	exonsCoding()	Variant affect one or more coding exons
protected abstract void	exonsNoncoding()	Variant affect one or more non-coding exons
protected abstract void	intron()	Variant affect one intron

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

Field Detail

debug

public static boolean debug

coding

protected boolean coding

exonFull

protected int exonFull

exonPartial

protected int exonPartial

cdsAlt

protected java.lang.String cdsAlt

cdsRef

protected java.lang.String cdsRef

Constructor Detail

CodonChangeStructural

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

Method Detail

cdsDiff

protected void cdsDiff()

Differences between two CDSs after removing equal codons from the beginning and from the end of both strings

codonChange

public void codonChange()

Description copied from class: CodonChange

Calculate a list of codon changes

Overrides:

codonChange in class CodonChange

codonChangeSuper

protected void codonChangeSuper()

codonsRefAlt

protected void codonsRefAlt()

Calculate codons by applying the variant and calculating the differences in CDS sequences This is a slow method, makes sense only for complex variants

countAffectedExons

protected void countAffectedExons()

How many full / partial exons does the variant affect?

effectTranscript

protected abstract void effectTranscript()

exons

protected abstract void exons()

Variant affect one or more exons

exonsCoding

protected abstract void exonsCoding()

Variant affect one or more coding exons

exonsNoncoding

protected abstract void exonsNoncoding()

Variant affect one or more non-coding exons

intron

protected abstract void intron()

Variant affect one intron