Class MaximalSegmentPair


  • public class MaximalSegmentPair
    extends Align
    Version:
    $Id: MaximalSegmentPair.java 185 2006-01-23 23:03:18Z rambaut $
    Author:
    Alexei Drummond
    • Constructor Detail

      • MaximalSegmentPair

        public MaximalSegmentPair​(Scores sub)
    • Method Detail

      • doAlignment

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

        public final Traceback next​(Traceback tb)
        Get the next state in the traceback
        Parameters:
        tb - current Traceback
        Returns:
        next Traceback
      • prepareAlignment

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

        public float getScore()
        Specified by:
        getScore in class Align
        Returns:
        the score of the best alignment
      • printf

        public void printf​(Output out)
        Print matrix used to calculate this alignment.
        Specified by:
        printf in class Align
        Parameters:
        out - Output to print to.