Class SmithWatermanLinearSpaceAffine


  • public class SmithWatermanLinearSpaceAffine
    extends Align
    Version:
    $Id: SmithWatermanLinearSpaceAffine.java 384 2006-07-17 07:17:39Z pepster $
    Author:
    Alexei Drummond
    • Constructor Detail

      • SmithWatermanLinearSpaceAffine

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

      • doAlignment

        public void doAlignment​(java.lang.String sq1,
                                java.lang.String sq2,
                                ProgressListener progress)
        Parameters:
        sq1 -
        sq2 -
      • doAlignment

        public void doAlignment​(java.lang.String sequence1,
                                java.lang.String sequence2)
        Performs the alignment. Abstract.
      • 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.
      • setGapExtend

        public void setGapExtend​(float e)
      • 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