com.actelion.research.calc.BinarySOM Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of openchemlib Show documentation
Open Source Chemistry Library
There is a newer version: 2024.12.1
/*
 * Copyright 2017 Idorsia Pharmaceuticals Ltd., Hegenheimermattweg 91, CH-4123 Allschwil, Switzerland
 *
 * This file is part of DataWarrior.
 * 
 * DataWarrior is free software: you can redistribute it and/or modify it under the terms of the
 * GNU General Public License as published by the Free Software Foundation, either version 3 of
 * the License, or (at your option) any later version.
 * 
 * DataWarrior 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 General Public License for more details.
 * You should have received a copy of the GNU General Public License along with DataWarrior.
 * If not, see http://www.gnu.org/licenses/.
 *
 * @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