Package org.snpeff.interval.codonChange

Class CodonChange

java.lang.Object

org.snpeff.interval.codonChange.CodonChange

Direct Known Subclasses:

CodonChangeIns, CodonChangeInterval, CodonChangeInv, CodonChangeMnp, CodonChangeSnp, CodonChangeStructural

public class CodonChange
extends java.lang.Object

Analyze codon changes based on a variant and a Transcript

Author:

pcingola

Field Summary

Fields

Modifier and Type	Field	Description
static int	CODON_SIZE
static boolean	showCodonChange

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	CodonChange(Variant variant, Transcript transcript, VariantEffects variantEffects)

Method Summary

Modifier and Type	Method	Description
protected EffectType	additionalEffect(java.lang.String codonsOld, java.lang.String codonsNew, int codonNum, int codonIndex, java.lang.String aaOld, java.lang.String aaNew)	Calculate additional effect due to codon changes E.g.
protected int	cdsBaseNumber(int pos)	Calculate base number in a cds where 'pos' is
void	codonChange()	Calculate a list of codon changes
protected boolean	codonChange(Exon exon)	Calculate the effect on an exon
protected java.lang.String	codonsAlt()	Calculate new codons
protected java.lang.String	codonsRef()	Calculate 'reference' codons
protected java.lang.String	codonsRef(int numCodons)	Calculate 'reference' codons
protected VariantEffect	effect(Marker marker, EffectType effectType, boolean allowReplace)	Calculate variant effect
protected VariantEffect	effectNoCodon(Marker marker, EffectType effectType)
protected VariantEffect	effectNoCodon(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact)
static CodonChange	factory(Variant variant, Transcript transcript, VariantEffects variantEffects)	Create a specific codon change for a variant
protected boolean	intersectsExons()	Does the variant intersect any exons?
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
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

CODON_SIZE

public static final int CODON_SIZE

See Also:

Constant Field Values

showCodonChange

public static boolean showCodonChange

Constructor Detail

CodonChange

protected CodonChange(Variant variant,
                      Transcript transcript,
                      VariantEffects variantEffects)

Method Detail

factory

public static CodonChange factory(Variant variant,
                                  Transcript transcript,
                                  VariantEffects variantEffects)

Create a specific codon change for a variant

additionalEffect

protected EffectType additionalEffect(java.lang.String codonsOld,
                                      java.lang.String codonsNew,
                                      int codonNum,
                                      int codonIndex,
                                      java.lang.String aaOld,
                                      java.lang.String aaNew)

Calculate additional effect due to codon changes E.g. A frame-shift that also affects a stop codon

cdsBaseNumber

protected int cdsBaseNumber(int pos)

Calculate base number in a cds where 'pos' is

codonChange

public void codonChange()

Calculate a list of codon changes

codonChange

protected boolean codonChange(Exon exon)

Calculate the effect on an exon

codonsAlt

protected java.lang.String codonsAlt()

Calculate new codons

codonsRef

protected java.lang.String codonsRef()

Calculate 'reference' codons

codonsRef

protected java.lang.String codonsRef(int numCodons)

Calculate 'reference' codons

effect

protected VariantEffect effect(Marker marker,
                               EffectType effectType,
                               boolean allowReplace)

Calculate variant effect

Parameters:

marker - : Genomic marker affected by this variant (e.g. exon, transcript, etc)

effectType - : Effect type

allowReplace - : Can another variant effect replace this one?

Returns:

A new VariantEffect object

effectNoCodon

protected VariantEffect effectNoCodon(Marker marker,
                                      EffectType effectType)

effectNoCodon

protected VariantEffect effectNoCodon(Marker marker,
                                      EffectType effectType,
                                      VariantEffect.EffectImpact effectImpact)

intersectsExons

protected boolean intersectsExons()

Does the variant intersect any exons?

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

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object