Package org.snpeff.interval.codonChange

Class CodonChangeStructural

java.lang.Object
org.snpeff.interval.codonChange.CodonChange
org.snpeff.interval.codonChange.CodonChangeStructural
Direct Known Subclasses:
CodonChangeDel, CodonChangeDup
public abstract class CodonChangeStructural extends CodonChange
Calculate codon changes produced by a duplication
Author:
pcingola

  • Field Details

    • debug

      public static boolean debug

    • coding

      protected boolean coding

    • exonFull

      protected int exonFull

    • exonPartial

      protected int exonPartial

    • cdsAlt

      protected String cdsAlt

    • cdsRef

      protected String cdsRef

  • Constructor Details

  • Method Details

    • 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