Class VariantEffect

Method Details

• addEffect

  public void addEffect(EffectType effectType)

• addEffectImpact

  public void addEffectImpact(VariantEffect.EffectImpact effectImpact)

• addEffectType

  public void addEffectType(EffectType effectType)

• addErrorMessage

  public void addErrorMessage(ErrorWarningType errmsg)

• addErrorWarningInfo

  public void addErrorWarningInfo(ErrorWarningType errwarn)

  Add an error or warning

• addInfoMessage

  public void addInfoMessage(ErrorWarningType infomsg)

• addWarningMessge

  public void addWarningMessge(ErrorWarningType warnmsg)

• clone

  public VariantEffect clone()

  Overrides:

  clone in class Object

• compareTo

  public int compareTo(VariantEffect varEffOther)

  Specified by:

  compareTo in interface Comparable<VariantEffect>

• effect

  public String effect(boolean shortFormat, boolean showAaChange, boolean showBioType, boolean useSeqOntology, boolean useFirstEffect)

  Show a string with overall effect

• getAaAlt

  public String getAaAlt()

• getAaChange

  public String getAaChange()

  Amino acid change string (HGVS style)

• getAaChangeOld

  public 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 String getAaNetChange()

  Net AA change (InDels)

• getAaRef

  public 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 String getCodonChange()

  Codon change string

• getCodonChangeMax

  public String getCodonChangeMax()

  Codon change string (if it's not too long)

• getCodonIndex

  public int getCodonIndex()

• getCodonNum

  public int getCodonNum()

• getCodonsAlt

  public String getCodonsAlt()

• getCodonsRef

  public String getCodonsRef()

• getDistance

  public int getDistance()

• setDistance

  public void setDistance(int distance)

• getEffectImpact

  public VariantEffect.EffectImpact getEffectImpact()

  Return impact of this effect

• setEffectImpact

  public void setEffectImpact(VariantEffect.EffectImpact effectImpact)

• getEffectType

  public EffectType getEffectType()

  Highest effect type

• setEffectType

  public void setEffectType(EffectType effectType)

• getEffectTypes

  public List<EffectType> getEffectTypes()

  Highest effect type

• getEffectTypeString

  public String getEffectTypeString(boolean useSeqOntology)

• getEffectTypeString

  public String getEffectTypeString(boolean useSeqOntology, boolean useFirstEffect)

• getEffectTypeString

  public String getEffectTypeString(boolean useSeqOntology, boolean useFirstEffect, EffFormatVersion formatVersion)

  Get Effect Type as a string

• getError

  public 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 String getGeneRegion()

• getGenes

  public List<Gene> getGenes()

• getGenotype

  public String getGenotype()

  Get genotype string

• getHgvs

  public String getHgvs()

  Change in HGVS notation

• getHgvsDna

  public String getHgvsDna()

  Change in HGVS (Dna) notation

• getHgvsProt

  public 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 String getWarning()

• hasAdditionalAnnotations

  public boolean hasAdditionalAnnotations()

  Do we have an associated marker with additional annotations?

• hasEffectImpact

  public boolean hasEffectImpact(VariantEffect.EffectImpact effectImpact)

• 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()

• set

  public void set(Marker marker, EffectType effectType, VariantEffect.EffectImpact effectImpact, String message)

• setCodons

  public void setCodons(String codonsOld, String codonsNew, int codonNum, int codonIndex)

  Set codon change. Calculate effect type based on codon changes (for SNPs & MNPs)

• setCodonsAround

  public void setCodonsAround(String codonsLeft, String codonsRight)

  Set values for codons around change.

• setEffect

  public void setEffect(EffectType effectType)

  Set effect using default impact

• toStr

  public String toStr()

• toString

  public String toString()

  Overrides:

  toString in class Object

• toString

  public String toString(boolean useSeqOntology, boolean useHgvs)

• toStringSimple

  public String toStringSimple(boolean shortFormat)

  Get the simplest string describing the effect (this is mostly used for testcases)