Package org.snpeff.interval.codonChange
Class CodonChangeSnp
- java.lang.Object
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- org.snpeff.interval.codonChange.CodonChange
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- org.snpeff.interval.codonChange.CodonChangeSnp
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public class CodonChangeSnp extends CodonChange
Calculate codon changes produced by a SNP- 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 CodonChangeSnp(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
codonChange(Exon exon)
Analyze SNPs in this transcript.protected java.lang.String
codonsAlt()
Get new (modified) codonsprotected java.lang.String
codonsRef()
Get original codons in CDS-
Methods inherited from class org.snpeff.interval.codonChange.CodonChange
additionalEffect, cdsBaseNumber, codonChange, codonsRef, effect, effectNoCodon, effectNoCodon, factory, intersectsExons, netCdsChange, toString
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Constructor Detail
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CodonChangeSnp
public CodonChangeSnp(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Detail
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codonChange
protected boolean codonChange(Exon exon)
Analyze SNPs in this transcript. Add changeEffect to 'changeEffect'- Overrides:
codonChange
in classCodonChange
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codonsAlt
protected java.lang.String codonsAlt()
Get new (modified) codons- Overrides:
codonsAlt
in classCodonChange
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codonsRef
protected java.lang.String codonsRef()
Get original codons in CDS- Overrides:
codonsRef
in classCodonChange
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