ReactionScheme.java

/*
 *  $RCSfile$
 *  $Author$
 *  $Date$
 *  $Revision$
 *
 *  Copyright (C) 2006-2007  Miguel Rojas <miguelrojasch@yahoo.es>
 *
 *  Contact: cdk-devel@lists.sourceforge.net
 *
 *  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.List;

import org.openscience.cdk.annotations.TestMethod;
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 <miguelrojasch@yahoo.es>
 * @cdk.module  data
 * @cdk.keyword reaction
 */
public class ReactionScheme extends ReactionSet implements IReactionScheme{
	
	/** A List of reaction schemes*/
	private List<IReactionScheme> 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 <a href=http://java.sun.com/products/jdk/1.1/docs/guide
     * /serialization/spec/version.doc.html>details</a>.
	 */
	private static final long serialVersionUID = -3676327644698347260L;
	
	/**  Constructs an empty ReactionScheme.
	 */
	public ReactionScheme() {
		reactionScheme = new ArrayList<IReactionScheme>();
	}
	
	/**
	 * Add a Scheme of Reactions.
	 * 
	 * @param scheme The IReactionScheme to include
	 */
	@TestMethod("testAdd_IReactionScheme")
	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
	 */
    @TestMethod("testReactionSchemes")
	public Iterable<IReactionScheme> reactionSchemes() {
		return reactionScheme;
	}
    
    /**
	 * Returns the number of ReactionScheme in this Scheme.
	 *
	 * @return     The number of ReactionScheme in this Scheme
	 */
    @TestMethod("testGetReactionSchemeCount")
	public int getReactionSchemeCount(){
    	return reactionScheme.size();
    }
    
    /**
	 * Removes all IReactionScheme from this chemObject.
	 */
    @TestMethod("testRemoveAllReactionSchemes")
    public void removeAllReactionSchemes() {
    	reactionScheme.clear();
    }

    /**
	 * Removes an IReactionScheme from this chemObject.
	 *
	 * @param  scheme  The IReactionScheme to be removed from this chemObject
	 */
    @TestMethod("testRemoveReactionScheme_IReactionScheme")
    public void removeReactionScheme(IReactionScheme scheme) {
    	reactionScheme.remove(scheme);
    }
    /**
	 * Clones this ReactionScheme object and its content.
	 *
	 * @return    The cloned object
	 */
    @TestMethod("testClone")
	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());
		}
		
		return clone;
	}
}