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 Readable & Closeable>
void
parse( supplier, ParseListener listener)
          Parse the specified input supplier.
 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.
<R extends Readable & Closeable>
void
stream( supplier, StreamListener listener)
          Stream the specified input supplier.
 

Method Detail

parse

<R extends Readable & Closeable> void parse( supplier,
                                           ParseListener listener)
           throws 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:
IOException - if an I/O error occurs

stream

<R extends Readable & Closeable> void stream( supplier,
                                            StreamListener listener)
            throws IOException
Stream the specified input supplier.

Parameters:
supplier - input supplier, must not be null
listener - event based reader callback, must not be null
Throws:
IOException - if an I/O error occurs

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