Package org.snpeff.interval.codonChange
Class CodonChangeDup
java.lang.Object
org.snpeff.interval.codonChange.CodonChange
org.snpeff.interval.codonChange.CodonChangeStructural
org.snpeff.interval.codonChange.CodonChangeDup
Calculate codon changes produced by a duplication
- Author:
- pcingola
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Field Summary
Fields inherited from class org.snpeff.interval.codonChange.CodonChangeStructural
cdsAlt, cdsRef, coding, debug, exonFull, exonPartial
Fields inherited from class org.snpeff.interval.codonChange.CodonChange
CODON_SIZE, showCodonChange
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Constructor Summary
ConstructorsConstructorDescriptionCodonChangeDup
(Variant variant, Transcript transcript, VariantEffects variantEffects) -
Method Summary
Methods inherited from class org.snpeff.interval.codonChange.CodonChangeStructural
cdsDiff, codonChange, codonChangeSuper, codonsRefAlt, countAffectedExons
Methods inherited from class org.snpeff.interval.codonChange.CodonChange
additionalEffect, cdsBaseNumber, codonChange, codonsAlt, codonsRef, codonsRef, effect, effectNoCodon, effectNoCodon, factory, intersectsExons, netCdsChange, toString
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Constructor Details
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CodonChangeDup
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Method Details
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effectTranscript
protected void effectTranscript()- Specified by:
effectTranscript
in classCodonChangeStructural
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exons
protected void exons()Description copied from class:CodonChangeStructural
Variant affect one or more exons- Specified by:
exons
in classCodonChangeStructural
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exonsCoding
protected void exonsCoding()One or more exons fully included (no partial overlap)- Specified by:
exonsCoding
in classCodonChangeStructural
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exonsNoncoding
protected void exonsNoncoding()Effects for non-coding transcripts- Specified by:
exonsNoncoding
in classCodonChangeStructural
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intron
protected void intron()Inversion does not intersect any exon- Specified by:
intron
in classCodonChangeStructural
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