org.biojava.nbio.sequencing.io.fastq

Interface ParseListener

public interface ParseListener

Low-level event based parser callback.

Since:

3.0.3

Method Summary

Methods

Modifier and Type	Method and 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