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.biojavax.bio.seq.io; 023 024import java.io.BufferedInputStream; 025import java.io.IOException; 026import java.io.InputStream; 027 028import org.biojava.bio.seq.Feature.Template; 029import org.biojava.bio.seq.io.ParseException; 030import org.biojava.bio.symbol.Alphabet; 031import org.biojava.bio.symbol.IllegalAlphabetException; 032import org.biojava.bio.symbol.Symbol; 033import org.biojavax.Namespace; 034import org.biojavax.RankedCrossRef; 035import org.biojavax.RankedDocRef; 036import org.biojavax.bio.BioEntryRelationship; 037import org.biojavax.bio.seq.RichFeature; 038import org.biojavax.bio.taxa.NCBITaxon; 039 040/** 041 * This is purely for debugging purposes. Use it to wrap an input stream 042 * then pass it as a parameter to some format to listen for 043 * sequence generation events. It will dump out char-by-char what it reads, 044 * followed event-by-event the events it receives from the format. 045 * @author Richard Holland 046 * @author Mark Schreiber 047 * @author Michael Heuer 048 * @since 1.5 049 */ 050public class DebuggingRichSeqIOListener extends BufferedInputStream implements 051 RichSeqIOListener { 052 053 private RichFeature currentFeature; 054 055 public DebuggingRichSeqIOListener(InputStream inputStream) { 056 super(inputStream); 057 this.message("Beginning debug session."); 058 } 059 060 /** 061 * {@inheritDoc} 062 * <p> 063 * Echoes everything that is read to stdout. 064 */ 065 public int read() throws IOException { 066 int ch = super.read(); 067 System.out.print(ch); 068 return ch; 069 } 070 071 public void setAccession(String accession) throws ParseException { 072 this.message("setAccession: "+accession); 073 } 074 075 public void setIdentifier(String identifier) throws ParseException { 076 this.message("setIdentifier: "+identifier); 077 } 078 079 public void setDivision(String division) throws ParseException { 080 this.message("setDivision: "+division); 081 } 082 083 public void setDescription(String description) throws ParseException { 084 this.message("setDescription: "+description); 085 } 086 087 public void setVersion(int version) throws ParseException { 088 this.message("setVersion: "+version); 089 } 090 091 public void setSeqVersion(String version) throws ParseException { 092 this.message("setSeqVersion: "+version); 093 } 094 095 public void setComment(String comment) throws ParseException { 096 this.message("setComment: "+comment); 097 } 098 099 public void setRankedDocRef(RankedDocRef ref) throws ParseException { 100 this.message("setRankedDocRef: "+ref); 101 } 102 103 public void setTaxon(NCBITaxon taxon) throws ParseException { 104 this.message("setTaxon: "+taxon); 105 } 106 107 public void setNamespace(Namespace namespace) throws ParseException { 108 this.message("setNamespace: "+namespace); 109 } 110 111 public void setRelationship(BioEntryRelationship relationship) 112 throws ParseException { 113 this.message("setRelationship: "+relationship); 114 } 115 116 public void setRankedCrossRef(RankedCrossRef crossRef) 117 throws ParseException { 118 this.message("setRankedCrossRef: "+crossRef); 119 } 120 121 public void setURI(String uri) throws ParseException { 122 this.message("setURI: "+uri); 123 } 124 125 public RichFeature getCurrentFeature() throws ParseException { 126 this.message("Current feature requested."); 127 return this.currentFeature; 128 } 129 130 public void setCircular(boolean circular) throws ParseException { 131 this.message("setCircular: "+circular); 132 } 133 134 public void startSequence() throws ParseException { 135 this.message("startSequence"); 136 } 137 138 public void endSequence() throws ParseException { 139 this.message("endSequence"); 140 } 141 142 public void setName(String name) throws ParseException { 143 this.message("setName: "+name); 144 } 145 146 public void addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) 147 throws IllegalAlphabetException { 148 this.message("addSymbols: (alpha) "+alpha 149 +" (syms) "+syms 150 +" (start) "+start 151 +" (length) "+length); 152 } 153 154 public void addSequenceProperty(Object key, Object value) 155 throws ParseException { 156 this.message("addSequenceProperty: (key) "+key+" (value) "+value); 157 } 158 159 public void startFeature(Template templ) throws ParseException { 160 this.message("startFeature: (templ) "+templ); 161 this.currentFeature = RichFeature.Tools.makeEmptyFeature(); 162 } 163 164 public void endFeature() throws ParseException { 165 this.message("endFeature"); 166 } 167 168 public void addFeatureProperty(Object key, Object value) 169 throws ParseException { 170 this.message("addFeatureProperty: (key) "+key+" (value) "+value); 171 } 172 173 private void message(String message) { 174 System.out.println("\n\n#####\n"+message+"\n#####\n\n"); 175 System.out.println("##### READING... #####\n\n"); 176 } 177}