org.biojava3.sequencing.io.fastq
Interface FastqReader

All Known Implementing Classes:

IlluminaFastqReader, SangerFastqReader, SolexaFastqReader

public interface FastqReader

Reader for FASTQ formatted sequences.

Since:

3.0.3

Method Summary

<R extends java.lang.Readable & java.io.Closeable> void	parse( supplier, ParseListener listener) Parse the specified input supplier.
java.lang.Iterable<Fastq>	read(java.io.File file) Read zero or more FASTQ formatted sequences from the specified file.
java.lang.Iterable<Fastq>	read(java.io.InputStream inputStream) Read zero or more FASTQ formatted sequences from the specified input stream.
java.lang.Iterable<Fastq>	read(java.net.URL url) Read zero or more FASTQ formatted sequences from the specified url.
<R extends java.lang.Readable & java.io.Closeable> void	stream( supplier, StreamListener listener) Stream the specified input supplier.

Method Detail

parse

<R extends java.lang.Readable & java.io.Closeable> void parse( supplier,
                                                             ParseListener listener)
           throws java.io.IOException

Parse the specified input supplier.

Parameters:

supplier - input supplier, must not be null

listener - low-level event based parser callback, must not be null

Throws:

java.io.IOException - if an I/O error occurs

stream

<R extends java.lang.Readable & java.io.Closeable> void stream( supplier,
                                                              StreamListener listener)
            throws java.io.IOException

Stream the specified input supplier.

Parameters:

supplier - input supplier, must not be null

listener - event based reader callback, must not be null

Throws:

java.io.IOException - if an I/O error occurs

read

java.lang.Iterable<Fastq> read(java.io.File file)
                               throws java.io.IOException

Read zero or more FASTQ formatted sequences from the specified file.

Parameters:

file - file to read from, must not be null

Returns:

zero or more FASTQ formatted sequences read from the specified file

Throws:

java.io.IOException - if an I/O error occurs

read

java.lang.Iterable<Fastq> read(java.net.URL url)
                               throws java.io.IOException

Read zero or more FASTQ formatted sequences from the specified url.

Parameters:

url - URL to read from, must not be null

Returns:

zero or more FASTQ formatted sequences read from the specified url

Throws:

java.io.IOException - if an I/O error occurs

read

java.lang.Iterable<Fastq> read(java.io.InputStream inputStream)
                               throws java.io.IOException

Read zero or more FASTQ formatted sequences from the specified input stream.

Parameters:

inputStream - input stream to read from, must not be null

Returns:

zero or more FASTQ formatted sequences read from the specified input stream

Throws:

java.io.IOException - if an I/O error occurs