• public interface ParseListener

    Low-level event based parser callback.

    Since:
    1.8.2

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void appendQuality​(String quality)

      Notify this listener of a quality line.
      void appendSequence​(String sequence)

      Notify this parse listener of an additional sequence line.
      void complete()

      Notify this listener the FASTQ formatted sequence is complete.
      void description​(String description)

      Notify this parse listener of a description line.
      void quality​(String quality)

      Notify this listener of a quality line.
      void repeatDescription​(String repeatDescription)

      Notify this parse listener of a repeat description line.
      void sequence​(String sequence)

      Notify this parse listener of a sequence line.

    • Method Detail

      • description

        void description​(String description)
          throws IOException

        Notify this parse listener of a description line.

        Parameters:
        description - description line
        Throws:
        IOException - if an I/O error occurs

      • sequence

        void sequence​(String sequence)
       throws IOException

        Notify this parse listener of a sequence line.

        Note that the sequence in FASTQ format may contain end-of-line characters, so both this method and appendSequence(String) may be called per FASTQ formatted sequence.

        Parameters:
        sequence - sequence line
        Throws:
        IOException - if an I/O error occurs

      • appendSequence

        void appendSequence​(String sequence)
             throws IOException

        Notify this parse listener of an additional sequence line.

        Note that the sequence in FASTQ format may contain end-of-line characters, so this method may be called more than once per FASTQ formatted sequence.

        Parameters:
        sequence - additional sequence line
        Throws:
        IOException - if an I/O error occurs

      • repeatDescription

        void repeatDescription​(String repeatDescription)
                throws IOException

        Notify this parse listener of a repeat description line.

        Parameters:
        repeatDescription - repeat description line
        Throws:
        IOException - if an I/O error occurs

      • quality

        void quality​(String quality)
      throws IOException

        Notify this listener of a quality line.

        Note that the quality scores in FASTQ format may contain end-of-line characters, so both this method and appendQuality(String) may be called per FASTQ formatted sequence.

        Parameters:
        quality - quality line
        Throws:
        IOException - if an I/O error occurs

      • appendQuality

        void appendQuality​(String quality)
            throws IOException

        Notify this listener of a quality line.

        Note that the quality scores in FASTQ format may contain end-of-line characters, so this method may be called more than once per FASTQ formatted sequence.

        Parameters:
        quality - additional quality line
        Throws:
        IOException - if an I/O error occurs

      • complete

        void complete()
       throws IOException

        Notify this listener the FASTQ formatted sequence is complete.

        Throws:
        IOException - if an I/O error occurs