Package org.snpeff.interval.codonChange
Class CodonChangeStructural
- 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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- Direct Known Subclasses:
CodonChangeDel
,CodonChangeDup
public abstract class CodonChangeStructural extends CodonChange
Calculate codon changes produced by a duplication- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description protected java.lang.String
cdsAlt
protected java.lang.String
cdsRef
protected boolean
coding
static boolean
debug
protected int
exonFull
protected int
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 CodonChangeStructural(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description protected void
cdsDiff()
Differences between two CDSs after removing equal codons from the beginning and from the end of both stringsvoid
codonChange()
Calculate a list of codon changesprotected void
codonChangeSuper()
protected void
codonsRefAlt()
Calculate codons by applying the variant and calculating the differences in CDS sequences This is a slow method, makes sense only for complex variantsprotected void
countAffectedExons()
How many full / partial exons does the variant affect?protected abstract void
effectTranscript()
protected abstract void
exons()
Variant affect one or more exonsprotected abstract void
exonsCoding()
Variant affect one or more coding exonsprotected abstract void
exonsNoncoding()
Variant affect one or more non-coding exonsprotected abstract void
intron()
Variant affect one intron-
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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CodonChangeStructural
public CodonChangeStructural(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Detail
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cdsDiff
protected void cdsDiff()
Differences between two CDSs after removing equal codons from the beginning and from the end of both strings
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codonChange
public void codonChange()
Description copied from class:CodonChange
Calculate a list of codon changes- Overrides:
codonChange
in classCodonChange
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codonChangeSuper
protected void codonChangeSuper()
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codonsRefAlt
protected void codonsRefAlt()
Calculate codons by applying the variant and calculating the differences in CDS sequences This is a slow method, makes sense only for complex variants
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countAffectedExons
protected void countAffectedExons()
How many full / partial exons does the variant affect?
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effectTranscript
protected abstract void effectTranscript()
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exons
protected abstract void exons()
Variant affect one or more exons
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exonsCoding
protected abstract void exonsCoding()
Variant affect one or more coding exons
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exonsNoncoding
protected abstract void exonsNoncoding()
Variant affect one or more non-coding exons
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intron
protected abstract void intron()
Variant affect one intron
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