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 */ 021 022package org.biojava.bio.seq.io; 023 024import org.biojava.bio.seq.Feature; 025import org.biojava.bio.symbol.Alphabet; 026import org.biojava.bio.symbol.IllegalAlphabetException; 027import org.biojava.bio.symbol.Symbol; 028 029/** 030 * Notification interface for objects which listen to a sequence stream 031 * parser. 032 * More functionality is offered by the 033 * {@link org.biojavax.bio.seq.io.RichSeqIOListener RichSeqIOListener}. 034 * @author Thomas Down 035 * @author Matthew Pocock 036 * @since 1.1 037 * @see org.biojavax.bio.seq.io.RichSeqIOListener 038 */ 039 040public interface SeqIOListener { 041 /** 042 * Start the processing of a sequence. This method exists primarily 043 * to enforce the life-cycles of SeqIOListener objects. 044 */ 045 046 public void startSequence() throws ParseException; 047 048 /** 049 * Notify the listener that processing of the sequence is complete. 050 */ 051 052 public void endSequence() throws ParseException; 053 054 /** 055 * Notify the listener that the current sequence is generally known 056 * by a particular name. 057 * 058 * @param name the String that should be returned by getName for the sequence 059 * being parsed 060 */ 061 062 public void setName(String name) throws ParseException; 063 064 /** 065 * Notify the listener of a URI identifying the current sequence. 066 */ 067 068 public void setURI(String uri) throws ParseException; 069 070 /** 071 * Notify the listener of symbol data. All symbols passed to 072 * this method are guarenteed to be contained within the 073 * specified alphabet. Generally all calls to a given Listener 074 * should have the same alphabet -- if not, the listener implementation 075 * is likely to throw an exception 076 * 077 * @param alpha The alphabet of the symbol data 078 * @param syms An array containing symbols 079 * @param start The start offset of valid data within the array 080 * @param length The number of valid symbols in the array 081 * 082 * @throws IllegalAlphabetException if we can't cope with this 083 * alphabet. 084 */ 085 086 public void addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) 087 throws IllegalAlphabetException; 088 089 /** 090 * Notify the listener of a sequence-wide property. This might 091 * be stored as an entry in the sequence's annotation bundle. 092 */ 093 094 public void addSequenceProperty(Object key, Object value) throws ParseException; 095 096 /** 097 * Notify the listener that a new feature object is starting. 098 * Every call to startFeature should have a corresponding call 099 * to endFeature. If the listener is concerned with a hierarchy 100 * of features, it should maintain a stack of `open' features. 101 */ 102 103 public void startFeature(Feature.Template templ) throws ParseException; 104 105 /** 106 * Mark the end of data associated with one specific feature. 107 */ 108 109 public void endFeature() throws ParseException; 110 111 /** 112 * Notify the listener of a feature property. 113 */ 114 115 public void addFeatureProperty(Object key, Object value) throws ParseException; 116}