Class NeedlemanWunsch

  • Direct Known Subclasses:
    SmithWaterman, VcfRefAltAlign

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

      • NeedlemanWunsch

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

      • align

        public java.lang.String align()
      • getAlignment

        public java.lang.String getAlignment()
      • getAlignmentScore

        public int getAlignmentScore()
      • getOffset

        public int getOffset()
      • setDeletion

        public void setDeletion​(int deletion)
      • setMatch

        public void setMatch​(int match)
      • setMissMatch

        public void setMissMatch​(int missMatch)
      • setUseSpace

        public void setUseSpace​(boolean useSpace)
      • toString

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