org.biojava.bio.program.fastq
Interface FastqReader

All Known Implementing Classes:

IlluminaFastqReader, SangerFastqReader, SolexaFastqReader

public interface FastqReader

Reader for FASTQ formatted sequences.

Method Summary

Iterable<Fastq>	read(File file) Read zero or more FASTQ formatted sequences from the specified file.
Iterable<Fastq>	read(InputStream inputStream) Read zero or more FASTQ formatted sequences from the specified input stream.
Iterable<Fastq>	read(URL url) Read zero or more FASTQ formatted sequences from the specified url.

Method Detail

read

Iterable<Fastq> read(File file)
                     throws 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:

IOException - if an IO error occurs

read

Iterable<Fastq> read(URL url)
                     throws 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:

IOException - if an IO error occurs

read

Iterable<Fastq> read(InputStream inputStream)
                     throws 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:

IOException - if an IO error occurs