Package org.snpeff.interval.codonChange
Class CodonChangeMnp
- java.lang.Object
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- org.snpeff.interval.codonChange.CodonChange
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- org.snpeff.interval.codonChange.CodonChangeMnp
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- Direct Known Subclasses:
CodonChangeMixed
public class CodonChangeMnp extends CodonChange
Calculate codon changes produced by a MNP- Author:
- pcingola
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Field Summary
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Fields inherited from class org.snpeff.interval.codonChange.CodonChange
CODON_SIZE, showCodonChange
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Constructor Summary
Constructors Constructor Description CodonChangeMnp(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
codonChange()
Calculate a list of codon changesprotected void
codonOldNew()
Calculate codons old / codons newprotected java.lang.String
codonsAlt()
Calculate new codonsprotected java.lang.String
codonsRef()
Calculate old codonsprotected 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
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Constructor Detail
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CodonChangeMnp
public CodonChangeMnp(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Detail
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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
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codonsAlt
protected java.lang.String codonsAlt()
Description copied from class:CodonChange
Calculate new codons- Overrides:
codonsAlt
in classCodonChange
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codonsRef
protected java.lang.String codonsRef()
Calculate old codons- Overrides:
codonsRef
in classCodonChange
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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 classCodonChange
- Returns:
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