Package org.snpeff.interval.codonChange
Class CodonChangeDup
- java.lang.Object
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- org.snpeff.interval.codonChange.CodonChange
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- org.snpeff.interval.codonChange.CodonChangeStructural
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- org.snpeff.interval.codonChange.CodonChangeDup
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public class CodonChangeDup extends CodonChangeStructural
Calculate codon changes produced by a duplication- Author:
- pcingola
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Field Summary
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Fields inherited from class org.snpeff.interval.codonChange.CodonChangeStructural
cdsAlt, cdsRef, coding, debug, exonFull, exonPartial
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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 CodonChangeDup(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
effectTranscript()
protected void
exons()
Variant affect one or more exonsprotected void
exonsCoding()
One or more exons fully included (no partial overlap)protected void
exonsNoncoding()
Effects for non-coding transcriptsprotected void
intron()
Inversion does not intersect any exon-
Methods inherited from class org.snpeff.interval.codonChange.CodonChangeStructural
cdsDiff, codonChange, codonChangeSuper, codonsRefAlt, countAffectedExons
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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 Detail
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CodonChangeDup
public CodonChangeDup(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Detail
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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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