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

• traceback

  public void traceback​(TracebackPlotter plotter)

  Overrides:

  traceback in class Align

• 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