org.biojava.nbio.genome.io.fastq.FastqReader Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of biojava-genome Show documentation
The newest version!
/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.genome.io.fastq;

import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;

/**
 * Reader for FASTQ formatted sequences.
 *
 * @since 3.0.3
 */
public interface FastqReader
{

	/**
	 * Parse the specified readable.
	 *
	 * @param readable readable, must not be null
	 * @param listener low-level event based parser callback, must not be null
	 * @throws IOException if an I/O error occurs
	 */
	void parse(Readable readable, ParseListener listener) throws IOException;

	/**
	 * Stream the specified readable.
	 *
	 * @param readable readable, must not be null
	 * @param listener event based reader callback, must not be null
	 * @throws IOException if an I/O error occurs
	 */
	void stream(Readable readable, StreamListener listener) throws IOException;

	/**
	 * Read zero or more FASTQ formatted sequences from the specified file.
	 *
	 * @param file file to read from, must not be null
	 * @return zero or more FASTQ formatted sequences read from the specified file
	 * @throws IOException if an I/O error occurs
	 */
	Iterable read(File file) throws IOException;

	/**
	 * Read zero or more FASTQ formatted sequences from the specified url.
	 *
	 * @param url URL to read from, must not be null
	 * @return zero or more FASTQ formatted sequences read from the specified url
	 * @throws IOException if an I/O error occurs
	 */
	Iterable read(URL url) throws IOException;

	/**
	 * Read zero or more FASTQ formatted sequences from the specified input stream.
	 *
	 * @param inputStream input stream to read from, must not be null
	 * @return zero or more FASTQ formatted sequences read from the specified input stream
	 * @throws IOException if an I/O error occurs
	 */
	Iterable read(InputStream inputStream) throws IOException;
}