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.bio.program.fastq; 022 023import java.io.IOException; 024 025/** 026 * Low-level event based parser callback. 027 * 028 * @since 1.8.2 029 */ 030public interface ParseListener 031{ 032 /** 033 * Notify this parse listener of a description line. 034 * 035 * @param description description line 036 * @throws IOException if an I/O error occurs 037 */ 038 void description(String description) throws IOException; 039 040 /** 041 * Notify this parse listener of a sequence line. 042 * 043 * <p> 044 * Note that the sequence in FASTQ format may contain end-of-line characters, 045 * so both this method and <code>appendSequence(String)</code> may be called per FASTQ 046 * formatted sequence. 047 * </p> 048 * 049 * @param sequence sequence line 050 * @throws IOException if an I/O error occurs 051 */ 052 void sequence(String sequence) throws IOException; 053 054 /** 055 * Notify this parse listener of an additional sequence line. 056 * 057 * <p> 058 * Note that the sequence in FASTQ format may contain end-of-line characters, 059 * so this method may be called more than once per FASTQ formatted sequence. 060 * </p> 061 * 062 * @param sequence additional sequence line 063 * @throws IOException if an I/O error occurs 064 */ 065 void appendSequence(String sequence) throws IOException; 066 067 /** 068 * Notify this parse listener of a repeat description line. 069 * 070 * @param repeatDescription repeat description line 071 * @throws IOException if an I/O error occurs 072 */ 073 void repeatDescription(String repeatDescription) throws IOException; 074 075 /** 076 * Notify this listener of a quality line. 077 * 078 * <p> 079 * Note that the quality scores in FASTQ format may contain end-of-line characters, 080 * so both this method and <code>appendQuality(String)</code> may be called per FASTQ 081 * formatted sequence. 082 * </p> 083 * 084 * @param quality quality line 085 * @throws IOException if an I/O error occurs 086 */ 087 void quality(String quality) throws IOException; 088 089 /** 090 * Notify this listener of a quality line. 091 * 092 * <p> 093 * Note that the quality scores in FASTQ format may contain end-of-line characters, 094 * so this method may be called more than once per FASTQ formatted sequence. 095 * </p> 096 * 097 * @param quality additional quality line 098 * @throws IOException if an I/O error occurs 099 */ 100 void appendQuality(String quality) throws IOException; 101 102 /** 103 * Notify this listener the FASTQ formatted sequence is complete. 104 * 105 * @throws IOException if an I/O error occurs 106 */ 107 void complete() throws IOException; 108}