org.biojava.bio.program.fastq
Interface FastqReader

All Known Implementing Classes:
IlluminaFastqReader, SangerFastqReader, SolexaFastqReader

public interface FastqReader

Reader for FASTQ formatted sequences.


Method Summary
 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