Class PHYLIPFileBuilder

Method Details

• startFile

  public void startFile()

  Description copied from interface: PHYLIPFileListener

  About to start a new file.

  Specified by:

  startFile in interface PHYLIPFileListener

• endFile

  public void endFile() throws ParseException

  Description copied from interface: PHYLIPFileListener

  Finished reading a file.

  Specified by:

  endFile in interface PHYLIPFileListener

  Throws:

  ParseException

• setSequenceCount

  public void setSequenceCount(int count)

  Description copied from interface: PHYLIPFileListener

  Set the number of sequences in the alignment.

  Specified by:

  setSequenceCount in interface PHYLIPFileListener

  Parameters:

  count - the expected number of sequences

• setSitesCount

  public void setSitesCount(int count)

  Description copied from interface: PHYLIPFileListener

  Set the number of sites in the alignment

  Specified by:

  setSitesCount in interface PHYLIPFileListener

  Parameters:

  count - the expected number of sites

• setCurrentSequenceName

  public void setCurrentSequenceName(String name)

  Description copied from interface: PHYLIPFileListener

  Set the name of the sequence which is about to be received. If the name has already been seen, the sequence should be appended.

  Specified by:

  setCurrentSequenceName in interface PHYLIPFileListener

  Parameters:

  name - the label for the current sequence

• receiveSequence

  public void receiveSequence(String sequence)

  Description copied from interface: PHYLIPFileListener

  Receive sequence data for the current sequence.

  Specified by:

  receiveSequence in interface PHYLIPFileListener

  Parameters:

  sequence - sequence text for the current sequence

• getAlignment

  public Alignment getAlignment()