Class NeedlemanWunschOverlap


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

      • NeedlemanWunschOverlap

        public NeedlemanWunschOverlap​(java.lang.String a,
                                      java.lang.String b)
    • Method Detail

      • align

        public java.lang.String align()
      • calcAlignment

        public java.lang.String calcAlignment()
      • calcAlignmentScore

        public int calcAlignmentScore()
        Calculate score matrix
      • getAligmentScore

        public int getAligmentScore()
      • getAlignment

        public java.lang.String getAlignment()
      • setDeletion

        public void setDeletion​(int deletion)
      • setMatch

        public void setMatch​(int match)
      • setMissMatch

        public void setMissMatch​(int missMatch)
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object