Package org.snpeff.interval.codonChange
Class CodonChange
- java.lang.Object
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- org.snpeff.interval.codonChange.CodonChange
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- Direct Known Subclasses:
CodonChangeIns
,CodonChangeInterval
,CodonChangeInv
,CodonChangeMnp
,CodonChangeSnp
,CodonChangeStructural
public class CodonChange extends java.lang.Object
Analyze codon changes based on a variant and a Transcript- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static int
CODON_SIZE
static boolean
showCodonChange
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Constructor Summary
Constructors Modifier Constructor Description protected
CodonChange(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected EffectType
additionalEffect(java.lang.String codonsOld, java.lang.String codonsNew, int codonNum, int codonIndex, java.lang.String aaOld, java.lang.String aaNew)
Calculate additional effect due to codon changes E.g.protected int
cdsBaseNumber(int pos)
Calculate base number in a cds where 'pos' isvoid
codonChange()
Calculate a list of codon changesprotected boolean
codonChange(Exon exon)
Calculate the effect on an exonprotected java.lang.String
codonsAlt()
Calculate new codonsprotected java.lang.String
codonsRef()
Calculate 'reference' codonsprotected java.lang.String
codonsRef(int numCodons)
Calculate 'reference' codonsprotected VariantEffect
effect(Marker marker, EffectType effectType, boolean allowReplace)
protected VariantEffect
effectNoCodon(Marker marker, EffectType effectType)
protected VariantEffect
effectNoCodon(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact)
static CodonChange
factory(Variant variant, Transcript transcript, VariantEffects variantEffects)
Create a specific codon change for a variantprotected boolean
intersectsExons()
Does the variant intersect any exons?protected java.lang.String
netCdsChange()
We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exonsjava.lang.String
toString()
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Field Detail
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showCodonChange
public static boolean showCodonChange
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CODON_SIZE
public static final int CODON_SIZE
- See Also:
- Constant Field Values
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Constructor Detail
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CodonChange
protected CodonChange(Variant variant, Transcript transcript, VariantEffects variantEffects)
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Method Detail
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factory
public static CodonChange factory(Variant variant, Transcript transcript, VariantEffects variantEffects)
Create a specific codon change for a variant
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additionalEffect
protected EffectType additionalEffect(java.lang.String codonsOld, java.lang.String codonsNew, int codonNum, int codonIndex, java.lang.String aaOld, java.lang.String aaNew)
Calculate additional effect due to codon changes E.g. A frame-shift that also affects a stop codon
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cdsBaseNumber
protected int cdsBaseNumber(int pos)
Calculate base number in a cds where 'pos' is
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codonChange
public void codonChange()
Calculate a list of codon changes
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codonChange
protected boolean codonChange(Exon exon)
Calculate the effect on an exon
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codonsAlt
protected java.lang.String codonsAlt()
Calculate new codons
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codonsRef
protected java.lang.String codonsRef()
Calculate 'reference' codons
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codonsRef
protected java.lang.String codonsRef(int numCodons)
Calculate 'reference' codons
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effect
protected VariantEffect effect(Marker marker, EffectType effectType, boolean allowReplace)
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effectNoCodon
protected VariantEffect effectNoCodon(Marker marker, EffectType effectType)
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effectNoCodon
protected VariantEffect effectNoCodon(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact)
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intersectsExons
protected boolean intersectsExons()
Does the variant intersect any exons?
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netCdsChange
protected java.lang.String netCdsChange()
We may have to calculate 'netCdsChange', which is the effect on the CDS Note: A deletion or a MNP might affect several exons
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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