Package jebl.evolution.align

Class NeedlemanWunschLinearSpace

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

  • Constructor Details

    • NeedlemanWunschLinearSpace

      public NeedlemanWunschLinearSpace(Scores sub, float d)

  • Method Details

    • doAlignment

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

    • getV

      public int getV()

    • 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

    • traceback

      public void traceback(TracebackPlotter plotter, int startx, int starty, String sq1, String sq2)

    • getScore

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

    • prepareAlignment

      public void prepareAlignment(String sq1, 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