org.openscience.cdk.Mapping Maven / Gradle / Ivy

/* Copyright (C) 2003-2007  Egon Willighagen 
 *
 * Contact: [email protected]
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
 *
 */
package org.openscience.cdk;

import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IMapping;

import java.util.Iterator;

/**
 * A Mapping is an relation between two ChemObjects in a non-chemical
 * entity. It is not a Bond, nor a Association, merely a relation.
 * An example of such a mapping, is the mapping between corresponding atoms
 * in a Reaction.
 *
 * @cdk.module data
 * @cdk.githash
 *
 * @cdk.keyword reaction, atom mapping
 *
 * @author  Egon Willighagen
 * @cdk.created 2003-08-16
 */
public class Mapping extends ChemObject implements java.io.Serializable, Cloneable, IMapping {

    /**
     * Determines if a de-serialized object is compatible with this class.
     *
     * This value must only be changed if and only if the new version
     * of this class is incompatible with the old version. See Sun docs
     * for details.
     */
    private static final long serialVersionUID = -6541914644492043503L;

    private IChemObject[]     relation;

    /**
     * Constructs an unconnected lone pair.
     *
     * @param objectOne The first IChemObject of the mapping
     * @param objectTwo The second IChemObject of the mapping
     */
    public Mapping(IChemObject objectOne, IChemObject objectTwo) {
        relation = new IChemObject[2];
        relation[0] = objectOne;
        relation[1] = objectTwo;
    }

    /**
     * Returns an Iterable to the two IChemObjects.
     * Iterable.remove() is not implemented.
     *
     * @return An Iterable to two IChemObjects that define the mapping
     */
    @Override
    public Iterable relatedChemObjects() {
        return new Iterable() {

            @Override
            public Iterator iterator() {
                return new ChemObjectIterator();
            }
        };
    }

    /**
     * The inner Iterator class.
     *
     */
    private class ChemObjectIterator implements Iterator {

        private int pointer = 0;

        @Override
        public boolean hasNext() {
            return pointer < 2;
        }

        @Override
        public IChemObject next() {
            return relation[pointer++];
        }

        @Override
        public void remove() {}

    }

    /**
     * Retrieves the first or second of the related IChemObjects.
     *
     * @param   pos  The position of the IChemObject.
     * @return  The IChemObject to retrieve.
     */
    @Override
    public IChemObject getChemObject(int pos) {
        return relation[pos];
    }

    /**
     * Clones this Mapping and the mapped IChemObjects.
     *
     * @return  The cloned object
     */
    @Override
    public Object clone() throws CloneNotSupportedException {
        Mapping clone = (Mapping) super.clone();
        // clone the related IChemObject's
        if (relation != null) {
            clone.relation = new IChemObject[relation.length];
            for (int f = 0; f < relation.length; f++) {
                if (relation[f] != null) {
                    clone.relation[f] = (IChemObject) relation[f].clone();
                }
            }
        }
        return clone;
    }
}