Class VcfEffect


  • public class VcfEffect
    extends java.lang.Object
    An 'ANN' or 'EFF' entry in a VCF INFO field Note: 'EFF' is the old version that has been replaced by the standardized 'ANN' field (2014-12) *
    Author:
    pablocingolani
    • Field Detail

      • debug

        public static boolean debug
      • ANN_FIELD_NAMES

        public static java.lang.String[] ANN_FIELD_NAMES
      • EFF_FIELD_NAMES

        public static java.lang.String[] EFF_FIELD_NAMES
    • Constructor Detail

      • VcfEffect

        public VcfEffect​(java.lang.String effectString)
        Constructor: Guess format version
      • VcfEffect

        public VcfEffect​(java.lang.String effectString,
                         EffFormatVersion formatVersion)
        Constructor: Force format version
        Parameters:
        formatVersion - : If null, will try to guess it
      • VcfEffect

        public VcfEffect​(VariantEffect variantEffect,
                         EffFormatVersion formatVersion,
                         boolean useSequenceOntology,
                         boolean useFirstEffect)
    • Method Detail

      • infoFieldName

        public static java.lang.String infoFieldName​(EffFormatVersion formatVersion)
        Get info field name based on format version
      • addEffectType

        public void addEffectType​(EffectType effectType)
      • formatVersion

        public EffFormatVersion formatVersion()
        Guess effect format version
      • formatVersion

        protected EffFormatVersion formatVersion​(java.lang.String effectString)
        Guess format 'main' version (either 'ANN' of 'EFF') without trying to guess sub-version
      • getAa

        public java.lang.String getAa()
      • setAa

        public void setAa​(java.lang.String aa)
      • getAaLen

        public int getAaLen()
      • setAaLen

        public void setAaLen​(int aaLen)
      • getAaPos

        public int getAaPos()
      • getAllele

        public java.lang.String getAllele()
      • getBioType

        public BioType getBioType()
      • setBioType

        public void setBioType​(BioType bioType)
      • getcDnaLen

        public int getcDnaLen()
      • getcDnaPos

        public int getcDnaPos()
      • getCdsLen

        public int getCdsLen()
      • getCdsPos

        public int getCdsPos()
      • getCodon

        public java.lang.String getCodon()
      • setCodon

        public void setCodon​(java.lang.String codon)
      • getDistance

        public int getDistance()
      • getEffectDetails

        public java.lang.String getEffectDetails()
      • setEffectDetails

        public void setEffectDetails​(java.lang.String effectDetails)
      • getEffectsStr

        public java.lang.String getEffectsStr()
      • getEffectsStrSo

        public java.lang.String getEffectsStrSo()
      • getEffectType

        public EffectType getEffectType()
      • setEffectType

        public void setEffectType​(EffectType effect)
      • getEffectTypes

        public java.util.List<EffectType> getEffectTypes()
      • getEffectTypesStr

        public java.lang.String getEffectTypesStr()
      • getEffString

        public java.lang.String getEffString()
      • getErrorsWarning

        public java.lang.String getErrorsWarning()
      • getExonId

        public java.lang.String getExonId()
      • setExonId

        public void setExonId​(java.lang.String exonId)
      • getFeatureId

        public java.lang.String getFeatureId()
      • getFeatureType

        public java.lang.String getFeatureType()
      • getFieldByName

        public java.lang.String getFieldByName​(java.lang.String fieldName)
        Get a subfield by name
      • setFormatVersion

        public void setFormatVersion​(EffFormatVersion formatVersion)
      • getGeneId

        public java.lang.String getGeneId()
      • setGeneId

        public void setGeneId​(java.lang.String geneId)
      • getGeneName

        public java.lang.String getGeneName()
      • setGeneName

        public void setGeneName​(java.lang.String geneName)
      • getGenotype

        public java.lang.String getGenotype()
      • setGenotype

        public void setGenotype​(java.lang.String genotype)
      • getHgvsC

        public java.lang.String getHgvsC()
      • getHgvsDna

        public java.lang.String getHgvsDna()
      • getHgvsP

        public java.lang.String getHgvsP()
      • getHgvsProt

        public java.lang.String getHgvsProt()
      • getRank

        public int getRank()
      • getRankMax

        public int getRankMax()
      • getTranscriptId

        public java.lang.String getTranscriptId()
      • setTranscriptId

        public void setTranscriptId​(java.lang.String transcriptId)
      • getVcfFieldString

        public java.lang.String getVcfFieldString()
        String from VCF file (original, unparsed, string)
      • getVcfFieldString

        public java.lang.String getVcfFieldString​(int index)
        Get a subfield as an index
      • hasEffectType

        public boolean hasEffectType​(EffectType effType)
        Does it have 'effType' ?
      • setUseFirstEffect

        public void setUseFirstEffect​(boolean useFirstEffect)
      • setUseGeneId

        public void setUseGeneId​(boolean useGeneId)
      • setUseHgvs

        public void setUseHgvs​(boolean useHgvs)
      • split

        public java.lang.String[] split​(java.lang.String eff)
        Split a 'effect' string to an array of strings
      • toString

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