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/* Copyright (C) 2009  Gilleain Torrance 
 *
 * 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.
 * All we ask is that proper credit is given for our work, which includes
 * - but is not limited to - adding the above copyright notice to the beginning
 * of your source code files, and to any copyright notice that you may distribute
 * with programs based on this work.
 *
 * 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.graph;

import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;

/**
 * This class allows the user to iterate through the set of all possible
 * permutations of the bond order in a given atom container. This provides a
 * means to check the dependency of an algorithm's results on the bond order of
 * the input atom container.
 *
 * Typical use:
 * AtomContainerBondPermutor permutor = new AtomContainerBondPermutor(container);
 * while (permutor.hasNext()) {
 *   IAtomContainer permutedContainer = permutor.next();
 *   ...
 * }
 *
 *
 * @author         maclean
 * @cdk.githash
 * @cdk.created    2009-09-09
 * @cdk.keyword    permutation
 * @cdk.module     standard
 */
public class AtomContainerBondPermutor extends AtomContainerPermutor {

    /**
     * A permutor wraps the original atom container, and produces cloned
     * (and permuted!) copies on demand.
     *
     * @param atomContainer the atom container to permute
     */
    public AtomContainerBondPermutor(IAtomContainer atomContainer) {
        super(atomContainer.getBondCount(), atomContainer);
    }

    /*
     * (non-Javadoc)
     * @see
     * org.openscience.cdk.graph.AtomContainerPermutor#containerFromPermutation
     * (int[])
     */
    @Override
    public IAtomContainer containerFromPermutation(int[] permutation) {
        try {
            IAtomContainer permutedContainer = (IAtomContainer) super.atomContainer.clone();
            int n = permutedContainer.getBondCount();
            IBond[] permutedBonds = new IBond[n];
            for (int i = 0; i < n; i++) {
                permutedBonds[i] = permutedContainer.getBond(permutation[i]);
            }
            permutedContainer.setBonds(permutedBonds);
            return permutedContainer;
        } catch (CloneNotSupportedException cne) {
            return null;
        }
    }

}