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/*
 * Copyright (c) 1997 - 2016
 * Actelion Pharmaceuticals Ltd.
 * Gewerbestrasse 16
 * CH-4123 Allschwil, Switzerland
 *
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice, this
 *    list of conditions and the following disclaimer.
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 * 3. Neither the name of the the copyright holder nor the
 *    names of its contributors may be used to endorse or promote products
 *    derived from this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
 * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
 * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
 * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
 * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * @author Thomas Sander
 */

package com.actelion.research.calc;

import com.actelion.research.chem.SSSearcherWithIndex;

import java.awt.*;
import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Random;

public class BinarySOM extends SelfOrganizedMap {
    private static final int KEY_COUNT = SSSearcherWithIndex.getNoOfKeys();
    private static final int MASK_COUNT = (SSSearcherWithIndex.getNoOfKeys()+31)/32;
	private double[]	mKeyFrequency;
	private int			mMaxKeyCount;
	private int[]		mMask;
	private int[][]		mKeyMaskMap;
	private ArrayList	mRandomizedKeyIndexList;
	private byte[]		mBitCount;
	private Random		mRandom;

	public BinarySOM() {
			// constructor to be used if SOM interna are read from a SOM file with read()
		init();
		}
	
	public BinarySOM(int nx, int ny, int mode) {
		super(nx, ny, mode);
		init();
		}

	private void init() {
		mRandom = new Random();

		mMask = new int[32];
		mMask[0] = 0x80000000;
		for (int i=0; i<31; i++)
		    mMask[i+1] = mMask[i] >>> 1;

		mRandomizedKeyIndexList = new ArrayList();
		for (int i=0; i");
		writer.newLine();
		}

	public void read(BufferedReader reader) throws Exception {
		super.read(reader);

		String theLine = reader.readLine();
		boolean error = !theLine.startsWith(">> 16];
	        allKeys += mBitCount[0xFFFF & ak] + mBitCount[ak >>> 16];
	    	}
	    return 1.0 - (double)sharedKeys/(double)allKeys;

//	    return 1.0 - SSSearcherWithIndex.getSimilarityTanimoto((int[])vector1, (int[])vector2);
		}

	protected void updateReference(Object inputVector, Object referenceVector, double influence) {
	    int[] mask = mKeyMaskMap[(int)influence];

	    int[] inputKeyList = (int[])inputVector;
	    int[] referenceKeyList = (int[])referenceVector;
		for (int i=0; i> 5] |= mMask[keyIndex & 0x1F];
            if (mKeyMaskMap[keyCount] != null)
                for (int i=0; i




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