/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */

package org.biojava.ontology;

import java.util.Arrays;
import java.util.Set;
import java.util.TreeSet;

import org.biojava.bio.Annotation;

/**
 * A term in another ontology.
 *
 * <p>
 * This is how you allow one ontology to refer to terms in another one. Since
 * these ontologies are designed to be modular and self-contained, it is
 * expected that you would not copy terms from one ontology into another. The
 * best-practice way to represent terms from another ontology in your one is to
 * use RemoteTerm instances. Ontology has a method importTerm that does this
 * for you. By default, imported terms will have names composed from the source
 * ontology and the imported term name. However, this should be over-rideable.
 * </p>
 *
 * <p>
 * The imported term will have the same name as the original term. They are
 * implicitly identical to each other. The most common use of imports will be
 * to slurp in the "core" ontology so that operations such as <code>is-a</code>
 * and <code>has-a</code> are available.
 * </p>
 *
 * @author Thomas Down
 * @author Matthew Pocock
 * @since 1.4
 */

public interface RemoteTerm extends Term {
    /**
     * Return the imported term
     * @return the term
     */

    public Term getRemoteTerm();

    /**
     * Simple in-memory implementation of a remote ontology term.
     *
     * This can be used to implement Ontology.importTerm
     */

    public final static class Impl
    extends AbstractTerm
    implements RemoteTerm, java.io.Serializable {
        /**
		 * 
		 */
		private static final long serialVersionUID = 922700041939183676L;
		private final Ontology ontology;
        private final Term remoteTerm;
        private final String name;
        private Set synonyms;

        public Impl(Ontology ontology, Term remoteTerm, String name) {
            this(ontology, remoteTerm, name, null);
        }
         
        public Impl(Ontology ontology, Term remoteTerm, String name, Object[] synonyms) {
            if (ontology == null) {
                throw new NullPointerException("Ontology must not be null");
            }
            if (remoteTerm == null) {
                throw new NullPointerException("RemoteTerm must not be null");
            }
            if(name == null) {
              name = remoteTerm.getOntology().getName() + "." + remoteTerm.getName();
            }

            this.ontology = ontology;
            this.remoteTerm = remoteTerm;
            this.name = name;
            
            this.synonyms = new TreeSet();
            if (synonyms!=null) this.synonyms.addAll(Arrays.asList(synonyms));
        }

        public void addSynonym(Object synonym) {
            this.synonyms.add(synonym);
        }
        
        public void removeSynonym(Object synonym) {
            this.synonyms.remove(synonym);
        }
        
        public Object[] getSynonyms() {
            return this.synonyms.toArray();
        }

        public String getName() {
            return getOntology().getName() + ":" + remoteTerm.getName();
        }

        public String getDescription() {
            return remoteTerm.getDescription();
        }

        public Ontology getOntology() {
            return ontology;
        }

        public Term getRemoteTerm() {
            return remoteTerm;
        }

        public String toString() {
            return name;
        }

        public Annotation getAnnotation() {
            return remoteTerm.getAnnotation();
        }
    }
}