Package org.snpeff.interval.codonChange
Class CodonChange
java.lang.Object
org.snpeff.interval.codonChange.CodonChange
- Direct Known Subclasses:
CodonChangeIns
,CodonChangeInterval
,CodonChangeInv
,CodonChangeMnp
,CodonChangeSnp
,CodonChangeStructural
Analyze codon changes based on a variant and a Transcript
- Author:
- pcingola
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Field Summary
Fields -
Constructor Summary
ConstructorsModifierConstructorDescriptionprotected
CodonChange
(Variant variant, Transcript transcript, VariantEffects variantEffects) -
Method Summary
Modifier and TypeMethodDescriptionprotected EffectType
additionalEffect
(String codonsOld, String codonsNew, int codonNum, int codonIndex, String aaOld, String aaNew) Calculate additional effect due to codon changes E.g.protected int
cdsBaseNumber
(int pos) Calculate base number in a cds where 'pos' isvoid
Calculate a list of codon changesprotected boolean
codonChange
(Exon exon) Calculate the effect on an exonprotected String
Calculate new codonsprotected String
Calculate 'reference' codonsprotected String
codonsRef
(int numCodons) Calculate 'reference' codonsprotected VariantEffect
effect
(Marker marker, EffectType effectType, boolean allowReplace) Calculate variant effectprotected 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 variantprotected boolean
Does the variant intersect any exons?protected String
We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exonstoString()
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Field Details
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CODON_SIZE
public static final int CODON_SIZE- See Also:
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showCodonChange
public static boolean showCodonChange
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Constructor Details
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CodonChange
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Method Details
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factory
public static CodonChange factory(Variant variant, Transcript transcript, VariantEffects variantEffects) Create a specific codon change for a variant -
additionalEffect
protected EffectType additionalEffect(String codonsOld, String codonsNew, int codonNum, int codonIndex, String aaOld, 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
Calculate the effect on an exon -
codonsAlt
Calculate new codons -
codonsRef
Calculate 'reference' codons -
codonsRef
Calculate 'reference' codons -
effect
Calculate variant effect- Parameters:
marker
- : Genomic marker affected by this variant (e.g. exon, transcript, etc)effectType
- : Effect typeallowReplace
- : Can another variant effect replace this one?- Returns:
- A new VariantEffect object
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effectNoCodon
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effectNoCodon
protected VariantEffect effectNoCodon(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact) -
intersectsExons
protected boolean intersectsExons()Does the variant intersect any exons? -
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
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