Package org.snpeff.snpEffect

Class VariantEffect

  • All Implemented Interfaces:
    java.lang.Cloneable, java.lang.Comparable<VariantEffect>
    Direct Known Subclasses:
    VariantEffectStructural
    public class VariantEffect
extends java.lang.Object
implements java.lang.Cloneable, java.lang.Comparable<VariantEffect>
    Effect of a variant.
    Author:
    pcingola

    • Field Detail

      • variant

        protected Variant variant

      • effectTypes

        protected java.util.List<EffectType> effectTypes

      • marker

        protected Marker marker

      • error

        protected java.lang.String error

      • warning

        protected java.lang.String warning

      • message

        protected java.lang.String message

      • codonsRef

        protected java.lang.String codonsRef

      • codonsAlt

        protected java.lang.String codonsAlt

      • codonsAroundOld

        protected java.lang.String codonsAroundOld

      • codonsAroundNew

        protected java.lang.String codonsAroundNew

      • distance

        protected int distance

      • cDnaPos

        protected int cDnaPos

      • codonNum

        protected int codonNum

      • codonIndex

        protected int codonIndex

      • codonDegeneracy

        protected int codonDegeneracy

      • aaRef

        protected java.lang.String aaRef

      • aaAlt

        protected java.lang.String aaAlt

      • aasAroundOld

        protected java.lang.String aasAroundOld

      • aasAroundNew

        protected java.lang.String aasAroundNew

    • Constructor Detail

      • VariantEffect

        public VariantEffect​(Variant variant)

    • Method Detail

      • addEffect

        public void addEffect​(EffectType effectType)

      • addEffectType

        public void addEffectType​(EffectType effectType)

      • addErrorWarningInfo

        public void addErrorWarningInfo​(ErrorWarningType errwarn)
        Add an error or warning

      • clone

        public VariantEffect clone()
        Overrides:
        clone in class java.lang.Object

      • compareTo

        public int compareTo​(VariantEffect varEffOther)
        Specified by:
        compareTo in interface java.lang.Comparable<VariantEffect>

      • effect

        public java.lang.String effect​(boolean shortFormat,
                               boolean showAaChange,
                               boolean showBioType,
                               boolean useSeqOntology,
                               boolean useFirstEffect)
        Show a string with overall effect

      • getAaAlt

        public java.lang.String getAaAlt()

      • getAaChange

        public java.lang.String getAaChange()
        Amino acid change string (HGVS style)

      • getAaChangeOld

        public java.lang.String 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

      • getAaNetChange

        public java.lang.String getAaNetChange()
        Net AA change (InDels)

      • getAaRef

        public java.lang.String getAaRef()

      • getBiotype

        public BioType getBiotype()
        Get biotype

      • getcDnaPos

        public int getcDnaPos()

      • getCdsLength

        public int getCdsLength()
        CDS length (negative if there is none)

      • getCodonChange

        public java.lang.String getCodonChange()
        Codon change string

      • getCodonChangeMax

        public java.lang.String getCodonChangeMax()
        Codon change string (if it's not too long)

      • getCodonIndex

        public int getCodonIndex()

      • getCodonNum

        public int getCodonNum()

      • getCodonsAlt

        public java.lang.String getCodonsAlt()

      • getCodonsRef

        public java.lang.String getCodonsRef()

      • getDistance

        public int getDistance()

      • setDistance

        public void setDistance​(int distance)

      • getEffectType

        public EffectType getEffectType()
        Highest effect type

      • setEffectType

        public void setEffectType​(EffectType effectType)

      • getEffectTypes

        public java.util.List<EffectType> getEffectTypes()
        Highest effect type

      • getEffectTypeString

        public java.lang.String getEffectTypeString​(boolean useSeqOntology)

      • getEffectTypeString

        public java.lang.String getEffectTypeString​(boolean useSeqOntology,
                                            boolean useFirstEffect)

      • getEffectTypeString

        public java.lang.String getEffectTypeString​(boolean useSeqOntology,
                                            boolean useFirstEffect,
                                            EffFormatVersion formatVersion)
        Get Effect Type as a string

      • getError

        public java.lang.String getError()

      • getExon

        public Exon getExon()
        Get exon (if any)

      • getFunctionalClass

        public VariantEffect.FunctionalClass getFunctionalClass()
        Return functional class of this effect (i.e. NONSENSE, MISSENSE, SILENT or NONE)

      • getGene

        public Gene getGene()

      • getGeneRegion

        public java.lang.String getGeneRegion()

      • getGenes

        public java.util.List<Gene> getGenes()

      • getGenotype

        public java.lang.String getGenotype()
        Get genotype string

      • getHgvs

        public java.lang.String getHgvs()
        Change in HGVS notation

      • getHgvsDna

        public java.lang.String getHgvsDna()
        Change in HGVS (Dna) notation

      • getHgvsProt

        public java.lang.String getHgvsProt()
        Change in HGVS (Protein) notation

      • getIntron

        public Intron getIntron()
        Get intron (if any)

      • getMarker

        public Marker getMarker()

      • setMarker

        public void setMarker​(Marker marker)
        Set marker. Add some warnings if the marker relates to incomplete transcripts

      • getTranscript

        public Transcript getTranscript()

      • getVariant

        public Variant getVariant()

      • getWarning

        public java.lang.String getWarning()

      • hasAdditionalAnnotations

        public boolean hasAdditionalAnnotations()
        Do we have an associated marker with additional annotations?

      • hasEffectType

        public boolean hasEffectType​(EffectType effectType)

      • 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()

      • setCodons

        public void setCodons​(java.lang.String codonsOld,
                      java.lang.String codonsNew,
                      int codonNum,
                      int codonIndex)
        Set codon change. Calculate effect type based on codon changes (for SNPs & MNPs)

      • setCodonsAround

        public void setCodonsAround​(java.lang.String codonsLeft,
                            java.lang.String codonsRight)
        Set values for codons around change.

      • setEffect

        public void setEffect​(EffectType effectType)
        Set effect using default impact

      • toStr

        public java.lang.String toStr()

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • toString

        public java.lang.String toString​(boolean useSeqOntology,
                                 boolean useHgvs)

      • toStringSimple

        public java.lang.String toStringSimple​(boolean shortFormat)
        Get the simplest string describing the effect (this is mostly used for testcases)