Package org.snpeff.interval.codonChange
Class CodonChangeDel
java.lang.Object
org.snpeff.interval.codonChange.CodonChange
org.snpeff.interval.codonChange.CodonChangeStructural
org.snpeff.interval.codonChange.CodonChangeDel
Calculate codon changes produced by a deletion
- 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
ConstructorsConstructorDescriptionCodonChangeDel
(Variant variant, Transcript transcript, VariantEffects variantEffects) -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
codonChange
(Exon exon) Analyze deletions in this transcript.protected String
Get alternative codonsprotected String
Get original codons in CDSprotected void
protected void
exons()
Deletion analysis using full transcript information.protected void
Variant affect one or more coding exonsprotected void
Variant affect one or more non-coding exonsprotected void
intron()
Variant affect one intronMethods inherited from class org.snpeff.interval.codonChange.CodonChangeStructural
cdsDiff, codonChange, codonChangeSuper, codonsRefAlt, countAffectedExons
Methods inherited from class org.snpeff.interval.codonChange.CodonChange
additionalEffect, cdsBaseNumber, codonsRef, effect, effectNoCodon, effectNoCodon, factory, intersectsExons, netCdsChange, toString
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Constructor Details
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CodonChangeDel
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Method Details
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codonChange
Analyze deletions in this transcript.- Overrides:
codonChange
in classCodonChange
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codonsAlt
Get alternative codons- Overrides:
codonsAlt
in classCodonChange
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codonsRef
Get original codons in CDS- Overrides:
codonsRef
in classCodonChange
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effectTranscript
protected void effectTranscript()- Specified by:
effectTranscript
in classCodonChangeStructural
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exons
protected void exons()Deletion analysis using full transcript information. This is done only when the variant affects more than one exons.- Specified by:
exons
in classCodonChangeStructural
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exonsCoding
protected void exonsCoding()Description copied from class:CodonChangeStructural
Variant affect one or more coding exons- Specified by:
exonsCoding
in classCodonChangeStructural
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exonsNoncoding
protected void exonsNoncoding()Description copied from class:CodonChangeStructural
Variant affect one or more non-coding exons- Specified by:
exonsNoncoding
in classCodonChangeStructural
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intron
protected void intron()Description copied from class:CodonChangeStructural
Variant affect one intron- Specified by:
intron
in classCodonChangeStructural
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