/*
 *                    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.nbio.ontology;

import org.biojava.nbio.ontology.utils.Annotation;

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


/**
 * A term in an ontology which identifies another ontology.
 *
 * <p>
 * This Term type has an associated ontology. It is meant to represent that
 * ontology so that you can reason over them. For example, you could add
 * information to an Ontology containing an OntologyTerm stating how the
 * OntologyTerm's Ontology relates to other entities. This allows
 * classifications of Ontologies to be built. You could say that GO is a
 * biological ontology, as is SO or perhaps declare something about the source
 * of the information.
 * </p>
 *
 * @author Thomas Down
 * @author Matthew Pocock
 * @since 1.4
 */

public interface OntologyTerm extends Term {
	/**
	 * Get the remote ontology referenced by this term
	 */

	@Override
	public Ontology getOntology();

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

	public final static class Impl

	implements OntologyTerm, java.io.Serializable {

		private static final long serialVersionUID = 1L;
		private final Ontology ontology;
		private final Ontology target;

		private Set synonyms;

		public Impl(Ontology ontology, Ontology target) {
			this(ontology, target, null);
		}

		public Impl(Ontology ontology, Ontology target, Object[] synonyms) {
			if (ontology == null) {
				throw new NullPointerException("The ontology may not be null");
			}
			if (target == null) {
				throw new NullPointerException("The targetted ontology may not be null");
			}
			this.ontology = ontology;
			this.target = target;

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

		@Override
		public void addSynonym(Object synonym) {
			this.synonyms.add(synonym);
		}

		@Override
		public void removeSynonym(Object synonym) {
			this.synonyms.remove(synonym);
		}

		@Override
		public Object[] getSynonyms() {
			return this.synonyms.toArray();
		}

		@Override
		public String getName() {
			return target.getName();
		}

		@Override
		public String getDescription() {
			return target.getDescription();
		}
		@Override
		public void setDescription(String description) {
			 target.setDescription(description);
		}

		@Override
		public Ontology getOntology() {
			return ontology;
		}

		public Ontology getTargetOntology() {
			return target;
		}

		@Override
		public String toString() {
			return "Remote ontology: " + getName();
		}

		@Override
		public Annotation getAnnotation() {
			return Annotation.EMPTY_ANNOTATION;
		}


	}
}