org.biojava3.sequencing.io.fastq
Class SolexaFastqReader

java.lang.Object
  extended by org.biojava3.sequencing.io.fastq.SolexaFastqReader
All Implemented Interfaces:
FastqReader

public final class SolexaFastqReader
extends Object

Reader for FastqVariant.FASTQ_SOLEXA formatted sequences.

Since:
3.0.3

Constructor Summary
SolexaFastqReader()
           
 
Method Summary
protected  FastqVariant getVariant()
          Return the FASTQ sequence format variant for this reader.
<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.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SolexaFastqReader

public SolexaFastqReader()
Method Detail

getVariant

protected FastqVariant getVariant()
Return the FASTQ sequence format variant for this reader.

Returns:
the FASTQ sequence format variant for this reader

parse

public final <R extends Readable & Closeable> void parse( supplier,
                                                        ParseListener listener)
                 throws IOException
Parse the specified input supplier.

Specified by:
parse in interface FastqReader
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

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

Specified by:
stream in interface FastqReader
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

public final Iterable<Fastq> read(File file)
                           throws IOException
Read zero or more FASTQ formatted sequences from the specified file.

Specified by:
read in interface FastqReader
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

public final Iterable<Fastq> read(URL url)
                           throws IOException
Read zero or more FASTQ formatted sequences from the specified url.

Specified by:
read in interface FastqReader
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

public final Iterable<Fastq> read(InputStream inputStream)
                           throws IOException
Read zero or more FASTQ formatted sequences from the specified input stream.

Specified by:
read in interface FastqReader
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