org.biojava.nbio.genome.io.fastq.FastqWriter 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.OutputStream;

/**
 * Writer for FASTQ formatted sequences.
 *
 * @since 3.0.3
 */
public interface FastqWriter
{

	/**
	 * Append the specified FASTQ formatted sequences to the specified appendable.
	 *
	 * @param  extends Appendable
	 * @param appendable appendable to append the specified FASTQ formatted sequences to, must not be null
	 * @param fastq variable number of FASTQ formatted sequences to append, must not be null
	 * @return the specified appendable with the specified FASTQ formatted sequences appended
	 * @throws IOException if an I/O error occurs
	 */
	 T append(T appendable, Fastq... fastq) throws IOException;

	/**
	 * Append the specified FASTQ formatted sequences to the specified appendable.
	 *
	 * @param  extends Appendable
	 * @param appendable appendable to append the specified FASTQ formatted sequences to, must not be null
	 * @param fastq zero or more FASTQ formatted sequences to append, must not be null
	 * @return the specified appendable with the specified FASTQ formatted sequences appended
	 * @throws IOException if an I/O error occurs
	 */
	 T append(T appendable, Iterable fastq) throws IOException;

	/**
	 * Write the specified FASTQ formatted sequences to the specified file.
	 *
	 * @param file file to write to, must not be null
	 * @param fastq variable number of FASTQ formatted sequences to write, must not be null
	 * @throws IOException if an I/O error occurs
	 */
	void write(File file, Fastq... fastq) throws IOException;

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

	/**
	 * Write the specified FASTQ formatted sequences to the specified output stream.
	 *
	 * @param outputStream output stream to write to, must not be null
	 * @param fastq variable number of FASTQ formatted sequences to write, must not be null
	 * @throws IOException if an I/O error occurs
	 */
	void write(OutputStream outputStream, Fastq... fastq) throws IOException;

	/**
	 * Write the specified FASTQ formatted sequences to the specified output stream.
	 *
	 * @param outputStream output stream to write to, must not be null
	 * @param fastq zero or more FASTQ formatted sequences to write, must not be null
	 * @throws IOException if an I/O error occurs
	 */
	void write(OutputStream outputStream, Iterable fastq) throws IOException;
}