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/* Copyright (C) 2002-2007  Christoph Steinbeck 
 *
 * 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.fingerprint;

import java.util.ArrayList;
import java.util.BitSet;
import java.util.List;
import java.util.Map;
import java.util.Random;
import java.util.Set;
import java.util.TreeMap;
import java.util.TreeSet;

import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

/**
 * Tool with helper methods for IFingerprint.
 *
 * @author         steinbeck
 * @cdk.created    2002-02-24
 * @cdk.keyword    fingerprint
 * @cdk.module     standard
 * @cdk.githash
 */
public class FingerprinterTool {

    private final static ILoggingTool LOGGER = LoggingToolFactory.createLoggingTool(FingerprinterTool.class);

    /**
     *  Checks whether all the positive bits in BitSet bs2 occur in BitSet bs1. If
     *  so, the molecular structure from which bs2 was generated is a possible
     *  substructure of bs1. 
     *
     *  Example: 
     *  Molecule mol = MoleculeFactory.makeIndole();
     *  BitSet bs = Fingerprinter.getBitFingerprint(mol);
     *  Molecule frag1 = MoleculeFactory.makePyrrole();
     *  BitSet bs1 = Fingerprinter.getBitFingerprint(frag1);
     *  if (Fingerprinter.isSubset(bs, bs1)) {
     *      System.out.println("Pyrrole is subset of Indole.");
     *  }
     *  
     *
     *@param  bs1     The reference BitSet
     *@param  bs2     The BitSet which is compared with bs1
     *@return         True, if bs2 is a subset of bs1
     *@cdk.keyword    substructure search
     */
    public static boolean isSubset(BitSet bs1, BitSet bs2) {
        BitSet clone = (BitSet) bs1.clone();
        clone.and(bs2);
        if (clone.equals(bs2)) {
            return true;
        }
        return false;
    }

    /**
     * This lists all bits set in bs2 and not in bs2 (other way round not considered) in a list and to logger.
     * See. {@link #differences(java.util.BitSet, java.util.BitSet)} for a method to list all differences,
     * including those missing present in bs2 but not bs1.
     *
     * @param bs1 First bitset
     * @param bs2 Second bitset
     * @return An arrayList of Integers
     * @see #differences(java.util.BitSet, java.util.BitSet)
     */
    public static List listDifferences(BitSet bs1, BitSet bs2) {
        List l = new ArrayList();
        LOGGER.debug("Listing bit positions set in bs2 but not in bs1");
        for (int f = 0; f < bs2.size(); f++) {
            if (bs2.get(f) && !bs1.get(f)) {
                l.add(f);
                LOGGER.debug("Bit " + f + " not set in bs1");
            }
        }
        return l;
    }

    /**
     * List all differences between the two bit vectors. Unlike {@link
     * #listDifferences(java.util.BitSet, java.util.BitSet)} which only list
     * those which are set in s but not in t.
     *
     * @param s a bit vector
     * @param t another bit vector
     * @return all differences between s and t
     */
    public static Set differences(BitSet s, BitSet t) {
        BitSet u = (BitSet) s.clone();
        u.xor(t);

        Set differences = new TreeSet();

        for (int i = u.nextSetBit(0); i >= 0; i = u.nextSetBit(i + 1)) {
            differences.add(i);
        }

        return differences;
    }

    /**
     * Convert a mapping of features and their counts to a 1024-bit binary fingerprint. A single 
     * bit is set for each pattern.
     *
     * @param features features to include
     * @return the continuous fingerprint
     * @see #makeBitFingerprint(java.util.Map, int, int)
     */
    public static IBitFingerprint makeBitFingerprint(final Map features) {
        return makeBitFingerprint(features, 1024, 1);
    }

    /**
     * Convert a mapping of features and their counts to a binary fingerprint. A single bit is
     * set for each pattern.
     *
     * @param features features to include
     * @param len fingerprint length
     * @return the continuous fingerprint
     * @see #makeBitFingerprint(java.util.Map, int, int) 
     */
    public static IBitFingerprint makeBitFingerprint(final Map features, int len) {
        return makeBitFingerprint(features, len, 1);
    }

    /**
     * Convert a mapping of features and their counts to a binary fingerprint. Each feature
     * can set 1-n hashes, the amount is modified by the {@code bits} operand.
     *
     * @param features features to include
     * @param len fingerprint length
     * @param bits number of bits to set for each pattern            
     * @return the continuous fingerprint
     */
    public static IBitFingerprint makeBitFingerprint(final Map features, int len, int bits) {
        final BitSetFingerprint fingerprint = new BitSetFingerprint(len);
        final Random rand = new Random();
        for (String feature : features.keySet()) {
            int hash = feature.hashCode();
            fingerprint.set(Math.abs(hash % len));
            for (int i = 1; i < bits; i++) {
                rand.setSeed(hash);
                fingerprint.set(hash = rand.nextInt(len));
            }
        }
        return fingerprint;
    }

    /**
     * Wrap a mapping of features and their counts to a continuous (count based) fingerprint.
     * 
     * @param features features to include
     * @return the continuous fingerprint
     */
    public static ICountFingerprint makeCountFingerprint(final Map features) {
        return new IntArrayCountFingerprint(features);
    }

}