Package jebl.evolution.align

Class SmithWatermanLinearSpaceAffine

java.lang.Object
jebl.evolution.align.Align
jebl.evolution.align.SmithWatermanLinearSpaceAffine
public class SmithWatermanLinearSpaceAffine extends Align
Version:
$Id: SmithWatermanLinearSpaceAffine.java 384 2006-07-17 07:17:39Z pepster $
Author:
Alexei Drummond

  • Constructor Details

    • SmithWatermanLinearSpaceAffine

      public SmithWatermanLinearSpaceAffine(Scores sub, float d, float e)

  • Method Details

    • doAlignment

      public void doAlignment(String sq1, String sq2, ProgressListener progress)
      Parameters:
      sq1 -
      sq2 -

    • doAlignment

      public void doAlignment(String sequence1, String sequence2)
      Performs the alignment. Abstract.
      Parameters:
      sequence1 -
      sequence2 -

    • getScore

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

    • getMatch

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

    • traceback

      public void traceback(TracebackPlotter plotter)
      Overrides:
      traceback in class Align

    • prepareAlignment

      public void prepareAlignment(String sq1, String sq2)
      Description copied from class: Align
      Initialises the matrices for the alignment.
      Parameters:
      sq1 -
      sq2 -

    • 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