Package org.biojava.nbio.sequencing.io.fastq

Interface ParseListener

  • public interface ParseListener
    Low-level event based parser callback.
    Since:
    3.0.3

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      void appendQuality​(java.lang.String quality)
      Notify this listener of a quality line.
      void appendSequence​(java.lang.String sequence)
      Notify this parse listener of an additional sequence line.
      void complete()
      Notify this listener the FASTQ formatted sequence is complete.
      void description​(java.lang.String description)
      Notify this parse listener of a description line.
      void quality​(java.lang.String quality)
      Notify this listener of a quality line.
      void repeatDescription​(java.lang.String repeatDescription)
      Notify this parse listener of a repeat description line.
      void sequence​(java.lang.String sequence)
      Notify this parse listener of a sequence line.

    • Method Detail

      • description

        void description​(java.lang.String description)
          throws java.io.IOException
        Notify this parse listener of a description line.
        Parameters:
        description - description line
        Throws:
        java.io.IOException - if an I/O error occurs

      • sequence

        void sequence​(java.lang.String sequence)
       throws java.io.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:
        java.io.IOException - if an I/O error occurs

      • appendSequence

        void appendSequence​(java.lang.String sequence)
             throws java.io.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:
        java.io.IOException - if an I/O error occurs

      • repeatDescription

        void repeatDescription​(java.lang.String repeatDescription)
                throws java.io.IOException
        Notify this parse listener of a repeat description line.
        Parameters:
        repeatDescription - repeat description line
        Throws:
        java.io.IOException - if an I/O error occurs

      • quality

        void quality​(java.lang.String quality)
      throws java.io.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:
        java.io.IOException - if an I/O error occurs

      • appendQuality

        void appendQuality​(java.lang.String quality)
            throws java.io.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:
        java.io.IOException - if an I/O error occurs

      • complete

        void complete()
       throws java.io.IOException
        Notify this listener the FASTQ formatted sequence is complete.
        Throws:
        java.io.IOException - if an I/O error occurs