Class CodonChangeStructural

    • Field Detail

      • debug

        public static boolean debug
      • coding

        protected boolean coding
      • exonFull

        protected int exonFull
      • exonPartial

        protected int exonPartial
      • cdsAlt

        protected java.lang.String cdsAlt
      • cdsRef

        protected java.lang.String cdsRef
    • Method Detail

      • cdsDiff

        protected void cdsDiff()
        Differences between two CDSs after removing equal codons from the beginning and from the end of both strings
      • codonChange

        public void codonChange()
        Description copied from class: CodonChange
        Calculate a list of codon changes
        Overrides:
        codonChange in class CodonChange
      • codonChangeSuper

        protected void codonChangeSuper()
      • codonsRefAlt

        protected void codonsRefAlt()
        Calculate codons by applying the variant and calculating the differences in CDS sequences This is a slow method, makes sense only for complex variants
      • countAffectedExons

        protected void countAffectedExons()
        How many full / partial exons does the variant affect?
      • effectTranscript

        protected abstract void effectTranscript()
      • exons

        protected abstract void exons()
        Variant affect one or more exons
      • exonsCoding

        protected abstract void exonsCoding()
        Variant affect one or more coding exons
      • exonsNoncoding

        protected abstract void exonsNoncoding()
        Variant affect one or more non-coding exons
      • intron

        protected abstract void intron()
        Variant affect one intron