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