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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.interfaces.IBond;

import java.util.Arrays;

/**
 * An abstract hash function providing several utility methods to be used by
 * other hashing functions.
 *
 * @author John May
 * @cdk.module hash
 * @cdk.githash
 */
class AbstractHashGenerator {

    /* pseudorandom number generator */
    private final Pseudorandom pseudorandom;

    /**
     * Construct an abstract hash function providing the pseudorandom number
     * generator.
     *
     * @param pseudorandom a pseudorandom number generator
     * @throws NullPointerException the pseudorandom number generator was null
     */
    public AbstractHashGenerator(Pseudorandom pseudorandom) {
        if (pseudorandom == null) throw new NullPointerException("null pseduorandom number generator provided");
        this.pseudorandom = pseudorandom;
    }

    /**
     * Create a copy of the array of long values.
     *
     * @param src original values
     * @return copy of the original values
     * @see Arrays#copyOf(long[], int)
     */
    static long[] copy(long[] src) {
        return Arrays.copyOf(src, src.length);
    }

    /**
     * Copy the values from the source (src) array to the destination (dest).
     *
     * @param src  source values
     * @param dest destination of the source copy
     * @see System#arraycopy(Object, int, Object, int, int);
     */
    static void copy(long[] src, long[] dest) {
        System.arraycopy(src, 0, dest, 0, dest.length);
    }

    /**
     * Generate the next random number.
     *
     * @param seed a {@literal long} value to seed a pseudorandom number
     *             generator
     * @return next pseudorandom number
     */
    long rotate(long seed) {
        return pseudorandom.next(seed);
    }

    /**
     * Rotate a value, n times. The rotation uses a pseudorandom
     * number generator to sequentially generate values seed on the previous
     * value.
     *
     * @param value the {@literal long} value to rotate
     * @param n     the number of times to rotate the value
     * @return the {@literal long} value rotated the specified number of times
     */
    long rotate(long value, int n) {
        while (n-- > 0)
            value = pseudorandom.next(value);
        return value;
    }

    /**
     * Returns the value of the lowest three bits. This value is between 0 and 7
     * inclusive.
     *
     * @param value a {@literal long} value
     * @return the {@literal int} value of the lowest three bits.
     */
    static int lowestThreeBits(long value) {
        return (int) (value & 0x7);
    }

    /**
     * Distribute the provided value across the set of {@literal long} values.
     *
     * @param value a {@literal long} value to distribute
     * @return the {@literal long} value distributed a set amount
     */
    long distribute(long value) {
        // rotate 1-8 times
        return rotate(value, 1 + lowestThreeBits(value));
    }

    /**
     * Convert an IAtomContainer to an adjacency list.
     *
     * @param container the container to convert
     * @return adjacency list representation
     */
    static int[][] toAdjList(IAtomContainer container) {

        if (container == null) throw new IllegalArgumentException("atom container was null");

        int n = container.getAtomCount();

        int[][] graph = new int[n][16];
        int[] degree = new int[n];

        for (IBond bond : container.bonds()) {

            int v = container.getAtomNumber(bond.getAtom(0));
            int w = container.getAtomNumber(bond.getAtom(1));

            if (v < 0 || w < 0)
                throw new IllegalArgumentException("bond at index " + container.getBondNumber(bond)
                        + " contained an atom not pressent in molecule");

            graph[v][degree[v]++] = w;
            graph[w][degree[w]++] = v;

            // if the vertex degree of v or w reaches capacity, double the size
            if (degree[v] == graph[v].length) graph[v] = Arrays.copyOf(graph[v], degree[v] * 2);
            if (degree[w] == graph[w].length) graph[w] = Arrays.copyOf(graph[w], degree[w] * 2);
        }

        for (int v = 0; v < n; v++) {
            graph[v] = Arrays.copyOf(graph[v], degree[v]);
        }

        return graph;

    }
}