Source code

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.ontology;
023
024import java.util.Arrays;
025import java.util.Set;
026import java.util.TreeSet;
027
028import org.biojava.bio.Annotatable;
029import org.biojava.bio.Annotation;
030import org.biojava.bio.SmallAnnotation;
031import org.biojava.utils.ChangeType;
032
033/**
034 * A term in an ontology. This has an {@link org.biojava.bio.Annotation Annotation}
035 * which can be used for storing additional human-displayable information. It
036 * is strongly recommended that the Annotation is not used for any machine-readable
037 * data -- this should be represented by relations in the ontology instead.
038 *
039 * <p>
040 * Terms are things that represent things. They are the same sort of thing as a
041 * Java object or a prolog atom. A sub-set of terms are themselves relations.
042 * This means that they are used to describe associations between pairs of terms.
043 * Since all terms can be described, it is possible (and indeed encouraged) to
044 * describe relations. As a minimum, you should consider saying if they are
045 * identity or partial order relations, or if they are transitive, reflexive,
046 * symmetrical, anti-symmetrical or anything else you know about them. This gives
047 * the inference engine some chance of working out what is going on.
048 * </p>
049 *
050 * @author Thomas Down
051 * @author Matthew Pocock
052 * @since 1.4
053 * @see org.biojavax.ontology.ComparableTerm
054 */
055
056public interface Term extends Annotatable {
057 /**
058 * ChangeType which indicates that this term's ontology has been
059 * altered
060 */
061
062 public static final ChangeType ONTOLOGY = new ChangeType(
063 "This term's ontology has been changed",
064 "org.biojava.ontology.Term",
065 "ONTOLOGY"
066 );
067
068 /**
069 * Return the name of this term.
070 * @return the name of the term
071 */
072
073 public String getName();
074
075 /**
076 * Return a human-readable description of this term, or the empty string if
077 * none is available.
078 * @return the description of the term
079 */
080
081 public String getDescription();
082 
083 /** set the description of the term;
084 * 
085 * @param description
086 * 
087 */
088 public void setDescription(String description);
089
090 /**
091 * Return the ontology in which this term exists.
092 * @return the ontology
093 */
094
095 public Ontology getOntology();
096
097 /**
098 * Return the synonyms for this term.
099 * @return the synonyms
100 */
101
102 public Object[] getSynonyms();
103
104 /**
105 * Add a synonym for this term.
106 * @param synonym the synonym
107 */
108
109 public void addSynonym(Object synonym);
110
111 /**
112 * Remove a synonym for this term.
113 * @param synonym 
114 */
115
116 public void removeSynonym(Object synonym);
117 
118 /**
119 * Simple in-memory implementation of an ontology term.
120 * @see org.biojavax.ontology.SimpleComparableTerm
121 * This can be used to implement Ontology.createTerm
122 */
123
124 public static class Impl
125 extends AbstractTerm
126 implements Term, java.io.Serializable {
127 /**
128 * 
129 */
130 private static final long serialVersionUID = 6561668917514377417L;
131
132 private final String name;
133 
134 private final Ontology ontology;
135 private Annotation annotation;
136 private Set<Object> synonyms;
137
138 public Impl(Ontology ontology, String name) {
139 this(ontology,name,null,null);
140 }
141 
142 public Impl(Ontology ontology, String name, String description) {
143 this(ontology,name,description,null);
144 }
145 
146 public Impl(Ontology ontology, String name, String description, Object[] synonyms) {
147 if (name == null) {
148 throw new NullPointerException("Name must not be null");
149 }
150 // by AP - description can change from now on...
151 //if (description == null) {
152 // throw new NullPointerException("Description must not be null");
153 //}
154 if (ontology == null) {
155 throw new NullPointerException("Ontology must not be null");
156 }
157
158 this.name = name;
159 this.description = description;
160 this.ontology = ontology;
161
162 this.synonyms = new TreeSet<Object>();
163 if (synonyms!=null) this.synonyms.addAll(Arrays.asList(synonyms));
164 }
165
166 public void addSynonym(Object synonym) {
167 this.synonyms.add(synonym);
168 }
169 
170 public void removeSynonym(Object synonym) {
171 this.synonyms.remove(synonym);
172 }
173 
174 public Object[] getSynonyms() {
175 return this.synonyms.toArray();
176 }
177
178 public String getName() {
179 return name;
180 } 
181
182 public void setAnnotation(Annotation annotation) {
183 this.annotation = annotation;
184 }
185
186 public void setSynonyms(Set<Object> synonyms) {
187 this.synonyms = synonyms;
188 }
189
190 public String getDescription() {
191 return description;
192 }
193
194 public Ontology getOntology() {
195 return ontology;
196 }
197
198 public String toString() {
199 return name;
200 }
201
202 public Annotation getAnnotation() {
203 if (annotation == null) {
204 annotation = new SmallAnnotation();
205 }
206 return annotation;
207 }
208
209 public int hashCode() {
210 int value = 17;
211 if(getName() != null)
212 value *= 31 * getName().hashCode();
213 return 17 * value;
214 }
215
216 public boolean equals(Object obj)
217 {
218 if(obj == this) return true;
219 if(!(obj instanceof Term)) return false;
220
221 Term that = (Term) obj;
222
223 return this.getOntology() == that.getOntology() &&
224 this.getName() == that.getName();
225 }
226 }
227}