Class SmithWaterman

java.lang.Object
jebl.evolution.align.Align
jebl.evolution.align.SmithWaterman
public class SmithWaterman extends Align

  • Constructor Details

    • SmithWaterman

      public SmithWaterman(Scores sub, float d)

  • Method Details

    • doAlignment

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

    • doAlignment

      public void doAlignment(String sq1, String sq2)
      Performs the alignment. Abstract.
      Parameters:
      sq1 -
      sq2 -

    • prepareAlignment

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

    • 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

    • 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.