Class SmithWatermanLinearSpace


  • public class SmithWatermanLinearSpace
    extends Align
    • Constructor Detail

      • SmithWatermanLinearSpace

        public SmithWatermanLinearSpace​(Scores sub,
                                        float d)
    • Method Detail

      • doAlignment

        public void doAlignment​(java.lang.String sq1,
                                java.lang.String sq2)
        Performs the alignment. Abstract.
        Parameters:
        sq1 -
        sq2 -
      • getScore

        public float getScore()
        Returns:
        the score of the best alignment
      • getMatch

        public java.lang.String[] getMatch()
        Overrides:
        getMatch in class Align
        Returns:
        two-element array containing an alignment with maximal score
      • prepareAlignment

        public void prepareAlignment​(java.lang.String sq1,
                                     java.lang.String sq2)
        Description copied from class: Align
        Initialises the matrices for the alignment.
      • printf

        public void printf​(Output out)
        Print matrix used to calculate this alignment.
        Parameters:
        out - Output to print to.
      • next

        public Traceback next​(Traceback tb)
        Get the next state in the traceback
        Overrides:
        next in class Align
        Parameters:
        tb - current Traceback
        Returns:
        next Traceback