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.Annotation;
029
030/**
031 * A term in another ontology.
032 *
033 * <p>
034 * This is how you allow one ontology to refer to terms in another one. Since
035 * these ontologies are designed to be modular and self-contained, it is
036 * expected that you would not copy terms from one ontology into another. The
037 * best-practice way to represent terms from another ontology in your one is to
038 * use RemoteTerm instances. Ontology has a method importTerm that does this
039 * for you. By default, imported terms will have names composed from the source
040 * ontology and the imported term name. However, this should be over-rideable.
041 * </p>
042 *
043 * <p>
044 * The imported term will have the same name as the original term. They are
045 * implicitly identical to each other. The most common use of imports will be
046 * to slurp in the "core" ontology so that operations such as <code>is-a</code>
047 * and <code>has-a</code> are available.
048 * </p>
049 *
050 * @author Thomas Down
051 * @author Matthew Pocock
052 * @since 1.4
053 */
054
055public interface RemoteTerm extends Term {
056 /**
057 * Return the imported term
058 * @return the term
059 */
060
061 public Term getRemoteTerm();
062
063 /**
064 * Simple in-memory implementation of a remote ontology term.
065 *
066 * This can be used to implement Ontology.importTerm
067 */
068
069 public final static class Impl
070 extends AbstractTerm
071 implements RemoteTerm, java.io.Serializable {
072 /**
073 * 
074 */
075 private static final long serialVersionUID = 922700041939183676L;
076 private final Ontology ontology;
077 private final Term remoteTerm;
078 private final String name;
079 private Set synonyms;
080
081 public Impl(Ontology ontology, Term remoteTerm, String name) {
082 this(ontology, remoteTerm, name, null);
083 }
084 
085 public Impl(Ontology ontology, Term remoteTerm, String name, Object[] synonyms) {
086 if (ontology == null) {
087 throw new NullPointerException("Ontology must not be null");
088 }
089 if (remoteTerm == null) {
090 throw new NullPointerException("RemoteTerm must not be null");
091 }
092 if(name == null) {
093 name = remoteTerm.getOntology().getName() + "." + remoteTerm.getName();
094 }
095
096 this.ontology = ontology;
097 this.remoteTerm = remoteTerm;
098 this.name = name;
099 
100 this.synonyms = new TreeSet();
101 if (synonyms!=null) this.synonyms.addAll(Arrays.asList(synonyms));
102 }
103
104 public void addSynonym(Object synonym) {
105 this.synonyms.add(synonym);
106 }
107 
108 public void removeSynonym(Object synonym) {
109 this.synonyms.remove(synonym);
110 }
111 
112 public Object[] getSynonyms() {
113 return this.synonyms.toArray();
114 }
115
116 public String getName() {
117 return getOntology().getName() + ":" + remoteTerm.getName();
118 }
119
120 public String getDescription() {
121 return remoteTerm.getDescription();
122 }
123
124 public Ontology getOntology() {
125 return ontology;
126 }
127
128 public Term getRemoteTerm() {
129 return remoteTerm;
130 }
131
132 public String toString() {
133 return name;
134 }
135
136 public Annotation getAnnotation() {
137 return remoteTerm.getAnnotation();
138 }
139 }
140}