org.biojava.bio.program.fastq

Interface FastqReader

All Known Implementing Classes:

IlluminaFastqReader, SangerFastqReader, SolexaFastqReader

public interface FastqReader

Reader for FASTQ formatted sequences.

Method Summary

Modifier and Type	Method and Description
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.

Method Detail

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 IO 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 IO 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 IO error occurs