Class CodonChangeMnp

java.lang.Object
org.snpeff.interval.codonChange.CodonChange
org.snpeff.interval.codonChange.CodonChangeMnp
Direct Known Subclasses:
CodonChangeMixed

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

  • Method Details

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

      protected String codonsRef()
      Calculate old codons
      Overrides:
      codonsRef in class CodonChange
    • netCdsChange

      protected 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: