Package org.snpeff.interval.codonChange
Class CodonChangeMixed
- 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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- org.snpeff.interval.codonChange.CodonChangeMixed
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public class CodonChangeMixed extends CodonChangeMnp
Calculate codon changes produced by a 'mixed' variant Essentially every 'mixed' variant can be represented as a concatenation of a SNP/MNP + an INS/DEL- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
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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 CodonChangeMixed(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 changes-
Methods inherited from class org.snpeff.interval.codonChange.CodonChangeMnp
codonOldNew, codonsAlt, codonsRef, netCdsChange
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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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CodonChangeMixed
public CodonChangeMixed(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Detail
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codonChange
public void codonChange()
Description copied from class:CodonChangeMnp
Calculate a list of codon changes- Overrides:
codonChange
in classCodonChangeMnp
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