Package org.snpeff.interval.codonChange
Class CodonChangeDel
- 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.CodonChangeDel
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public class CodonChangeDel extends CodonChangeStructural
Calculate codon changes produced by a deletion- 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 CodonChangeDel(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 deletions in this transcript.protected java.lang.String
codonsAlt()
Get alternative codonsprotected java.lang.String
codonsRef()
Get original codons in CDSprotected void
effectTranscript()
protected void
exons()
Deletion analysis using full transcript information.protected void
exonsCoding()
Variant affect one or more coding exonsprotected void
exonsNoncoding()
Variant affect one or more non-coding exonsprotected void
intron()
Variant affect one intron-
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, codonsRef, effect, effectNoCodon, effectNoCodon, factory, intersectsExons, netCdsChange, toString
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Constructor Detail
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CodonChangeDel
public CodonChangeDel(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Detail
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codonChange
protected boolean codonChange(Exon exon)
Analyze deletions in this transcript.- Overrides:
codonChange
in classCodonChange
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codonsAlt
protected java.lang.String codonsAlt()
Get alternative 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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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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