Class NeedlemanWunschOverlap

java.lang.Object
org.snpeff.align.NeedlemanWunschOverlap

public class NeedlemanWunschOverlap extends Object
Needleman-Wunsch algorithm for string alignment (short strings, since it's not memory optimized)
Author:
pcingola
  • Constructor Details

    • NeedlemanWunschOverlap

      public NeedlemanWunschOverlap(String a, String b)
  • Method Details

    • align

      public String align()
    • calcAlignment

      public String calcAlignment()
    • calcAlignmentScore

      public int calcAlignmentScore()
      Calculate score matrix
    • getAligmentScore

      public int getAligmentScore()
    • getAlignment

      public String getAlignment()
    • setDeletion

      public void setDeletion(int deletion)
    • setMatch

      public void setMatch(int match)
    • setMissMatch

      public void setMissMatch(int missMatch)
    • toString

      public String toString()
      Overrides:
      toString in class Object