Class CodonChange

    • Field Detail

      • showCodonChange

        public static boolean showCodonChange
    • Method Detail

      • 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
      • cdsBaseNumber

        protected int cdsBaseNumber​(int pos)
        Calculate base number in a cds where 'pos' is
      • codonChange

        public void codonChange()
        Calculate a list of codon changes
      • codonChange

        protected boolean codonChange​(Exon exon)
        Calculate the effect on an exon
      • codonsAlt

        protected java.lang.String codonsAlt()
        Calculate new codons
      • codonsRef

        protected java.lang.String codonsRef()
        Calculate 'reference' codons
      • codonsRef

        protected java.lang.String codonsRef​(int numCodons)
        Calculate 'reference' codons
      • effect

        protected VariantEffect effect​(Marker marker,
                                       EffectType effectType,
                                       boolean allowReplace)
        Calculate variant effect
        Parameters:
        marker - : Genomic marker affected by this variant (e.g. exon, transcript, etc)
        effectType - : Effect type
        allowReplace - : Can another variant effect replace this one?
        Returns:
        A new VariantEffect object
      • intersectsExons

        protected boolean intersectsExons()
        Does the variant intersect any exons?
      • 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
      • toString

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