Package org.snpeff.interval.codonChange
Class CodonChangeMnp
java.lang.Object
org.snpeff.interval.codonChange.CodonChange
org.snpeff.interval.codonChange.CodonChangeMnp
- Direct Known Subclasses:
CodonChangeMixed
Calculate codon changes produced by a MNP
- Author:
- pcingola
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Field Summary
Fields inherited from class org.snpeff.interval.codonChange.CodonChange
CODON_SIZE, showCodonChange
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Constructor Summary
ConstructorsConstructorDescriptionCodonChangeMnp
(Variant variant, Transcript transcript, VariantEffects variantEffects) -
Method Summary
Modifier and TypeMethodDescriptionvoid
Calculate a list of codon changesprotected void
Calculate codons old / codons newprotected String
Calculate new codonsprotected String
Calculate old codonsprotected String
We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exonsMethods inherited from class org.snpeff.interval.codonChange.CodonChange
additionalEffect, cdsBaseNumber, codonChange, codonsRef, effect, effectNoCodon, effectNoCodon, factory, intersectsExons, toString
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Constructor Details
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CodonChangeMnp
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Method Details
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codonChange
public void codonChange()Calculate a list of codon changes- Overrides:
codonChange
in classCodonChange
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codonOldNew
protected void codonOldNew()Calculate codons old / codons new -
codonsAlt
Description copied from class:CodonChange
Calculate new codons- Overrides:
codonsAlt
in classCodonChange
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codonsRef
Calculate old codons- Overrides:
codonsRef
in classCodonChange
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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 classCodonChange
- Returns:
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