org.biojava3.sequencing.io.fastq
Interface ParseListener


public interface ParseListener

Low-level event based parser callback.

Since:
3.0.3

Method Summary
 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