Package org.snpeff.snpEffect
Class VariantEffect
java.lang.Object
org.snpeff.snpEffect.VariantEffect
- All Implemented Interfaces:
Cloneable
,Comparable<VariantEffect>
- Direct Known Subclasses:
VariantEffectStructural
Effect of a variant.
- Author:
- pcingola
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic enum
static enum
static enum
This class is only getFused for SNPs -
Field Summary
FieldsModifier and TypeFieldDescriptionprotected String
protected String
protected String
protected String
protected int
protected int
protected int
protected int
protected String
protected String
protected String
protected String
protected int
protected VariantEffect.EffectImpact
protected List<VariantEffect.EffectImpact>
protected EffectType
protected List<EffectType>
protected String
protected Marker
static final int
protected String
protected Variant
protected String
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Constructor Summary
ConstructorsConstructorDescriptionVariantEffect
(Variant variant) VariantEffect
(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String codonsOld, String codonsNew, int codonNum, int codonIndex, int cDnaPos) -
Method Summary
Modifier and TypeMethodDescriptionvoid
addEffect
(EffectType effectType) void
addEffectImpact
(VariantEffect.EffectImpact effectImpact) void
addEffectType
(EffectType effectType) void
addErrorMessage
(ErrorWarningType errmsg) void
addErrorWarningInfo
(ErrorWarningType errwarn) Add an error or warningvoid
addInfoMessage
(ErrorWarningType infomsg) void
addWarningMessge
(ErrorWarningType warnmsg) clone()
int
compareTo
(VariantEffect varEffOther) effect
(boolean shortFormat, boolean showAaChange, boolean showBioType, boolean useSeqOntology, boolean useFirstEffect) Show a string with overall effectgetAaAlt()
Amino acid change string (HGVS style)Amino acid change string (old style)int
Amino acid length (negative if there is none)Net AA change (InDels)getAaRef()
Get biotypeint
int
CDS length (negative if there is none)Codon change stringCodon change string (if it's not too long)int
int
int
Return impact of this effectHighest effect typeHighest effect typegetEffectTypeString
(boolean useSeqOntology) getEffectTypeString
(boolean useSeqOntology, boolean useFirstEffect) getEffectTypeString
(boolean useSeqOntology, boolean useFirstEffect, EffFormatVersion formatVersion) Get Effect Type as a stringgetError()
getExon()
Get exon (if any)Return functional class of this effect (i.e.getGene()
getGenes()
Get genotype stringgetHgvs()
Change in HGVS notationChange in HGVS (Dna) notationChange in HGVS (Protein) notationGet intron (if any)boolean
Do we have an associated marker with additional annotations?boolean
hasEffectImpact
(VariantEffect.EffectImpact effectImpact) boolean
hasEffectType
(EffectType effectType) boolean
hasError()
boolean
boolean
isCustom()
boolean
isExon()
boolean
boolean
isIntron()
boolean
isMotif()
boolean
boolean
boolean
boolean
boolean
boolean
boolean
isUtr3()
boolean
isUtr5()
void
set
(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message) void
Set codon change.void
setCodonsAround
(String codonsLeft, String codonsRight) Set values for codons around change.void
setDistance
(int distance) void
setEffect
(EffectType effectType) Set effect using default impactvoid
setEffectImpact
(VariantEffect.EffectImpact effectImpact) void
setEffectType
(EffectType effectType) void
Set marker.toStr()
toString()
toString
(boolean useSeqOntology, boolean useHgvs) toStringSimple
(boolean shortFormat) Get the simplest string describing the effect (this is mostly used for testcases)
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Field Details
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MAX_CODON_SEQUENCE_LEN
public static final int MAX_CODON_SEQUENCE_LEN- See Also:
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variant
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effectTypes
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effectType
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effectImpacts
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effectImpact
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marker
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error
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warning
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message
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codonsRef
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codonsAlt
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codonsAroundOld
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codonsAroundNew
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distance
protected int distance -
cDnaPos
protected int cDnaPos -
codonNum
protected int codonNum -
codonIndex
protected int codonIndex -
codonDegeneracy
protected int codonDegeneracy -
aaRef
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aaAlt
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aasAroundOld
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aasAroundNew
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Constructor Details
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VariantEffect
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VariantEffect
public VariantEffect(Variant variant, Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String codonsOld, String codonsNew, int codonNum, int codonIndex, int cDnaPos)
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Method Details
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addEffect
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addEffectImpact
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addEffectType
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addErrorMessage
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addErrorWarningInfo
Add an error or warning -
addInfoMessage
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addWarningMessge
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clone
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compareTo
- Specified by:
compareTo
in interfaceComparable<VariantEffect>
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effect
public String effect(boolean shortFormat, boolean showAaChange, boolean showBioType, boolean useSeqOntology, boolean useFirstEffect) Show a string with overall effect -
getAaAlt
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getAaChange
Amino acid change string (HGVS style) -
getAaChangeOld
Amino acid change string (old style) -
getAaLength
public int getAaLength()Amino acid length (negative if there is none)- Returns:
- Amino acid length (CDS length / 3 ) or '-1' if there is no CDS length
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getAaNetChange
Net AA change (InDels) -
getAaRef
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getBiotype
Get biotype -
getcDnaPos
public int getcDnaPos() -
getCdsLength
public int getCdsLength()CDS length (negative if there is none) -
getCodonChange
Codon change string -
getCodonChangeMax
Codon change string (if it's not too long) -
getCodonIndex
public int getCodonIndex() -
getCodonNum
public int getCodonNum() -
getCodonsAlt
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getCodonsRef
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getDistance
public int getDistance() -
setDistance
public void setDistance(int distance) -
getEffectImpact
Return impact of this effect -
setEffectImpact
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getEffectType
Highest effect type -
setEffectType
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getEffectTypes
Highest effect type -
getEffectTypeString
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getEffectTypeString
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getEffectTypeString
public String getEffectTypeString(boolean useSeqOntology, boolean useFirstEffect, EffFormatVersion formatVersion) Get Effect Type as a string -
getError
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getExon
Get exon (if any) -
getFunctionalClass
Return functional class of this effect (i.e. NONSENSE, MISSENSE, SILENT or NONE) -
getGene
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getGeneRegion
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getGenes
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getGenotype
Get genotype string -
getHgvs
Change in HGVS notation -
getHgvsDna
Change in HGVS (Dna) notation -
getHgvsProt
Change in HGVS (Protein) notation -
getIntron
Get intron (if any) -
getMarker
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setMarker
Set marker. Add some warnings if the marker relates to incomplete transcripts -
getTranscript
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getVariant
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getWarning
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hasAdditionalAnnotations
public boolean hasAdditionalAnnotations()Do we have an associated marker with additional annotations? -
hasEffectImpact
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hasEffectType
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hasError
public boolean hasError() -
hasWarning
public boolean hasWarning() -
isCustom
public boolean isCustom() -
isExon
public boolean isExon() -
isIntergenic
public boolean isIntergenic() -
isIntron
public boolean isIntron() -
isMotif
public boolean isMotif() -
isMultipleGenes
public boolean isMultipleGenes() -
isNextProt
public boolean isNextProt() -
isRegulation
public boolean isRegulation() -
isSpliceSite
public boolean isSpliceSite() -
isSpliceSiteCore
public boolean isSpliceSiteCore() -
isSpliceSiteRegion
public boolean isSpliceSiteRegion() -
isUtr3
public boolean isUtr3() -
isUtr5
public boolean isUtr5() -
set
public void set(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message) -
setCodons
Set codon change. Calculate effect type based on codon changes (for SNPs & MNPs) -
setCodonsAround
Set values for codons around change. -
setEffect
Set effect using default impact -
toStr
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toString
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toString
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toStringSimple
Get the simplest string describing the effect (this is mostly used for testcases)
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