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

Interface ParseListener

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

  • Method Summary

    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 Details

    • 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