Class SmithWatermanLinearSpace

Method Details

• doAlignment

  public void doAlignment(String sq1, String sq2)

  Performs the alignment. Abstract.

  Parameters:

  sq1 -

  sq2 -

• 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.

• 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