Constructor Detail

• OverlapAlign

  public OverlapAlign​(Scores sub,
                      float d)

Method Detail

• doAlignment

  public void doAlignment​(java.lang.String sq1,
                          java.lang.String sq2)

  Performs the alignment. Abstract.

  Parameters:

  sq1 -

  sq2 -

• prepareAlignment

  public void prepareAlignment​(java.lang.String sq1,
                               java.lang.String sq2)

  Description copied from class: Align
  Initialises the matrices for the alignment.

  Specified by:

  prepareAlignment in class Align

• 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.