Package org.biojavax.bio.phylo.io.phylip

Interface PHYLIPFileListener

All Known Implementing Classes:
PHYLIPFileBuilder
public interface PHYLIPFileListener
Listens to events fired by the PHYLIP parser. Use these events to handle data directly or construct objects.
Since:
1.6
Author:
Richard Holland, Tobias Thierer, Jim Balhoff

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    endFile()
    Finished reading a file.
    void
    receiveSequence(String sequence)
    Receive sequence data for the current sequence.
    void
    setCurrentSequenceName(String name)
    Set the name of the sequence which is about to be received.
    void
    setSequenceCount(int count)
    Set the number of sequences in the alignment.
    void
    setSitesCount(int count)
    Set the number of sites in the alignment
    void
    startFile()
    About to start a new file.

  • Method Details

    • startFile

      void startFile()
      About to start a new file.

    • endFile

      void endFile() throws ParseException
      Finished reading a file.
      Throws:
      ParseException

    • setSequenceCount

      void setSequenceCount(int count)
      Set the number of sequences in the alignment.
      Parameters:
      count - the expected number of sequences

    • setSitesCount

      void setSitesCount(int count)
      Set the number of sites in the alignment
      Parameters:
      count - the expected number of sites

    • setCurrentSequenceName

      void setCurrentSequenceName(String name)
      Set the name of the sequence which is about to be received. If the name has already been seen, the sequence should be appended.
      Parameters:
      name - the label for the current sequence

    • receiveSequence

      void receiveSequence(String sequence)
      Receive sequence data for the current sequence.
      Parameters:
      sequence - sequence text for the current sequence