Package jebl.evolution.align

Class NeedlemanWunschLinearSpace

  • public class NeedlemanWunschLinearSpace
extends Align
    Version:
    $Id: NeedlemanWunschLinearSpace.java 186 2006-01-24 00:41:22Z pepster $
    Author:
    Alexei Drummond

    • Constructor Detail

      • NeedlemanWunschLinearSpace

        public NeedlemanWunschLinearSpace​(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 -

      • getV

        public int getV()

      • getMatch

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

      • traceback

        public void traceback​(TracebackPlotter plotter,
                      int startx,
                      int starty,
                      java.lang.String sq1,
                      java.lang.String sq2)

      • getScore

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

      • 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