Class CodonChangeMnp

  • Direct Known Subclasses:
    CodonChangeMixed

    public class CodonChangeMnp
    extends CodonChange
    Calculate codon changes produced by a MNP
    Author:
    pcingola
    • Method Detail

      • codonChange

        public void codonChange()
        Calculate a list of codon changes
        Overrides:
        codonChange in class CodonChange
      • codonOldNew

        protected void codonOldNew()
        Calculate codons old / codons new
      • codonsAlt

        protected java.lang.String codonsAlt()
        Description copied from class: CodonChange
        Calculate new codons
        Overrides:
        codonsAlt in class CodonChange
      • codonsRef

        protected java.lang.String codonsRef()
        Calculate old codons
        Overrides:
        codonsRef in class CodonChange
      • 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
        Overrides:
        netCdsChange in class CodonChange
        Returns: