Package org.snpeff.interval.codonChange
Class CodonChangeStructural
java.lang.Object
org.snpeff.interval.codonChange.CodonChange
org.snpeff.interval.codonChange.CodonChangeStructural
- Direct Known Subclasses:
CodonChangeDel
,CodonChangeDup
Calculate codon changes produced by a duplication
- Author:
- pcingola
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected String
protected String
protected boolean
static boolean
protected int
protected int
Fields inherited from class org.snpeff.interval.codonChange.CodonChange
CODON_SIZE, showCodonChange
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Constructor Summary
ConstructorsConstructorDescriptionCodonChangeStructural
(Variant variant, Transcript transcript, VariantEffects variantEffects) -
Method Summary
Modifier and TypeMethodDescriptionprotected void
cdsDiff()
Differences between two CDSs after removing equal codons from the beginning and from the end of both stringsvoid
Calculate a list of codon changesprotected void
protected void
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
How many full / partial exons does the variant affect?protected abstract void
protected abstract void
exons()
Variant affect one or more exonsprotected abstract void
Variant affect one or more coding exonsprotected abstract void
Variant affect one or more non-coding exonsprotected abstract void
intron()
Variant affect one intronMethods 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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Field Details
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debug
public static boolean debug -
coding
protected boolean coding -
exonFull
protected int exonFull -
exonPartial
protected int exonPartial -
cdsAlt
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cdsRef
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Constructor Details
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CodonChangeStructural
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Method Details
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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 -
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() -
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 -
countAffectedExons
protected void countAffectedExons()How many full / partial exons does the variant affect? -
effectTranscript
protected abstract void effectTranscript() -
exons
protected abstract void exons()Variant affect one or more exons -
exonsCoding
protected abstract void exonsCoding()Variant affect one or more coding exons -
exonsNoncoding
protected abstract void exonsNoncoding()Variant affect one or more non-coding exons -
intron
protected abstract void intron()Variant affect one intron
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