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/*
 * Copyright (c) 2013 John May 
 *
 * 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 U
 */

package org.openscience.cdk.hash;

import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.ringsearch.RingSearch;

import java.util.Collections;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import java.util.TreeMap;

/**
 * Finds the smallest set of equivalent values are members of a ring. If there
 * are multiple smallest sets then the set with the lowest invariant value is
 * returned. This class is intended to drive the systematic perturbation of the
 * {@link org.openscience.cdk.hash.PerturbedAtomHashGenerator}.
 *
 * This method will not distinguish all possible molecules but represents a good
 * enough approximation to quickly narrow down an identity search. At the time
 * of writing (Feb, 2013) there are only 128 molecules (64 false positives) in
 * PubChem-Compound (46E6 molecules) which are not separated. In many data sets
 * this method will suffice however the exact {@link AllEquivalentCyclicSet} is
 * provided. 

 *
 * This method is currently the default used by the {@link
 * org.openscience.cdk.hash.HashGeneratorMaker} but can also be explicitly
 * specified. 
 *  * MoleculeHashGenerator generator =
 *   new HashGeneratorMaker().depth(6)
 *                           .elemental()
 *                           .perturbed() // use this class by default
 *                           .molecular();
 *
 * // explicitly specify the method
 * MoleculeHashGenerator generator =
 *   new HashGeneratorMaker().depth(6)
 *                           .elemental()
 *                           .perturbWith(new MinimumEquivalentCyclicSet())
 *                           .molecular();
 * 
 * 
 *
 * @author John May
 * @cdk.module hash
 * @see org.openscience.cdk.hash.PerturbedAtomHashGenerator
 * @see MinimumEquivalentCyclicSetUnion
 * @see AllEquivalentCyclicSet
 * @see org.openscience.cdk.hash.HashGeneratorMaker
 * @cdk.githash
 */
final class MinimumEquivalentCyclicSet extends EquivalentSetFinder {

    /**
     *{@inheritDoc}
     */
    @Override
    Set find(long[] invariants, IAtomContainer container, int[][] graph) {

        int n = invariants.length;

        // find cyclic vertices using DFS
        RingSearch ringSearch = new RingSearch(container, graph);

        // ordered map of the set of vertices for each value
        Map> equivalent = new TreeMap>();

        // divide the invariants into equivalent indexed and ordered sets
        for (int i = 0; i < invariants.length; i++) {

            Long invariant = invariants[i];
            Set set = equivalent.get(invariant);

            if (set == null) {
                if (ringSearch.cyclic(i)) {
                    set = new HashSet(n / 2);
                    set.add(i);
                    equivalent.put(invariant, set);
                }
            } else {
                set.add(i);
            }
        }

        // find the smallest set of equivalent cyclic vertices
        int minSize = Integer.MAX_VALUE;
        Set min = Collections.emptySet();
        for (Map.Entry> e : equivalent.entrySet()) {
            Set vertices = e.getValue();
            if (vertices.size() < minSize && vertices.size() > 1) {
                min = vertices;
                minSize = vertices.size();
            }
        }

        return min;
    }

}