001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021package org.biojava.nbio.sequencing.io.fastq;
022
023import java.io.File;
024import java.io.IOException;
025import java.io.OutputStream;
026
027/**
028 * Writer for FASTQ formatted sequences.
029 *
030 * @since 3.0.3
031 */
032public interface FastqWriter
033{
034
035        /**
036         * Append the specified FASTQ formatted sequences to the specified appendable.
037         *
038         * @param <T> extends Appendable
039         * @param appendable appendable to append the specified FASTQ formatted sequences to, must not be null
040         * @param fastq variable number of FASTQ formatted sequences to append, must not be null
041         * @return the specified appendable with the specified FASTQ formatted sequences appended
042         * @throws IOException if an I/O error occurs
043         */
044        <T extends Appendable> T append(T appendable, Fastq... fastq) throws IOException;
045
046        /**
047         * Append the specified FASTQ formatted sequences to the specified appendable.
048         *
049         * @param <T> extends Appendable
050         * @param appendable appendable to append the specified FASTQ formatted sequences to, must not be null
051         * @param fastq zero or more FASTQ formatted sequences to append, must not be null
052         * @return the specified appendable with the specified FASTQ formatted sequences appended
053         * @throws IOException if an I/O error occurs
054         */
055        <T extends Appendable> T append(T appendable, Iterable<Fastq> fastq) throws IOException;
056
057        /**
058         * Write the specified FASTQ formatted sequences to the specified file.
059         *
060         * @param file file to write to, must not be null
061         * @param fastq variable number of FASTQ formatted sequences to write, must not be null
062         * @throws IOException if an I/O error occurs
063         */
064        void write(File file, Fastq... fastq) throws IOException;
065
066        /**
067         * Write the specified FASTQ formatted sequences to the specified file.
068         *
069         * @param file file to write to, must not be null
070         * @param fastq zero or more FASTQ formatted sequences to write, must not be null
071         * @throws IOException if an I/O error occurs
072         */
073        void write(File file, Iterable<Fastq> fastq) throws IOException;
074
075        /**
076         * Write the specified FASTQ formatted sequences to the specified output stream.
077         *
078         * @param outputStream output stream to write to, must not be null
079         * @param fastq variable number of FASTQ formatted sequences to write, must not be null
080         * @throws IOException if an I/O error occurs
081         */
082        void write(OutputStream outputStream, Fastq... fastq) throws IOException;
083
084        /**
085         * Write the specified FASTQ formatted sequences to the specified output stream.
086         *
087         * @param outputStream output stream to write to, must not be null
088         * @param fastq zero or more FASTQ formatted sequences to write, must not be null
089         * @throws IOException if an I/O error occurs
090         */
091        void write(OutputStream outputStream, Iterable<Fastq> fastq) throws IOException;
092}