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.genome.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}