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

/* Copyright (C) 2006-2007  Miguel Rojas 
 *
 *  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 java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
import java.util.Map;

import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IReactionScheme;

/**
 * Classes that extends the definition of reaction to a scheme.
 * This is designed to contain a set of reactions which are linked in
 * some way but without hard coded semantics.
 *
 * @author miguelrojasch <[email protected]>
 * @cdk.module  data
 * @cdk.keyword reaction
 * @cdk.githash
 */
public class ReactionScheme extends ReactionSet implements IReactionScheme {

    /** A List of reaction schemes*/
    private List reactionScheme;
    /**
     * 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 = -3676327644698347260L;

    /**  Constructs an empty ReactionScheme.
     */
    public ReactionScheme() {
        reactionScheme = new ArrayList();
    }

    /**
     * Add a Scheme of Reactions.
     *
     * @param scheme The IReactionScheme to include
     */
    @Override
    public void add(IReactionScheme scheme) {
        reactionScheme.add(scheme);
    }

    /**
     *  Returns an Iterable for looping over all IMolecularScheme
     *   in this ReactionScheme.
     *
     * @return    An Iterable with the IMolecularScheme in this ReactionScheme
     */
    @Override
    public Iterable reactionSchemes() {
        return reactionScheme;
    }

    /**
     * Returns the number of ReactionScheme in this Scheme.
     *
     * @return     The number of ReactionScheme in this Scheme
     */
    @Override
    public int getReactionSchemeCount() {
        return reactionScheme.size();
    }

    /**
     * Removes all IReactionScheme from this chemObject.
     */
    @Override
    public void removeAllReactionSchemes() {
        reactionScheme.clear();
    }

    /**
     * Removes an IReactionScheme from this chemObject.
     *
     * @param  scheme  The IReactionScheme to be removed from this chemObject
     */
    @Override
    public void removeReactionScheme(IReactionScheme scheme) {
        reactionScheme.remove(scheme);
    }

    /**
     * Clones this ReactionScheme object and its content.
     *
     * @return    The cloned object
     */
    @Override
    public Object clone() throws CloneNotSupportedException {

        IReactionScheme clone = new ReactionScheme();
        for (IReactionScheme scheme : this.reactionSchemes()) {
            clone.add((IReactionScheme) scheme.clone());
        }

        for (IReaction reaction : reactions()) {
            clone.addReaction((IReaction) reaction.clone());
        }
        // clone the properties
        if (getProperties() != null) {
            Map properties = getProperties();
            Map clonedHashtable = new HashMap();
            Iterator