Package org.biojava.bio.program.fastq

Interface FastqReader

All Known Implementing Classes:

IlluminaFastqReader, SangerFastqReader, SolexaFastqReader

public interface FastqReader

Reader for FASTQ formatted sequences.

Since:

1.7.1

Method Summary

Modifier and Type	Method	Description
void	parse(Readable readable, ParseListener listener)	Parse the specified readable.
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.
void	stream(Readable readable, StreamListener listener)	Stream the specified readable.

Method Detail

parse

void parse(Readable readable,
           ParseListener listener)
    throws IOException

Parse the specified readable.

Parameters:

readable - readable, must not be null

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

Throws:

IOException - if an I/O error occurs

Since:

1.9.1

stream

void stream(Readable readable,
            StreamListener listener)
     throws IOException

Stream the specified readable.

Parameters:

readable - readable, must not be null

listener - event based reader callback, must not be null

Throws:

IOException - if an I/O error occurs

Since:

1.9.1

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 I/O 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 I/O 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 I/O error occurs