content: /*
   * Copyright (c) 1997 - 2022
   * Idorsia Pharmaceuticals Ltd.
   * Hegenheimermattweg 91
   * 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 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.chem.prediction;
  
  import com.actelion.research.chem.SSSearcherWithIndex;
  import com.actelion.research.chem.descriptor.DescriptorHandlerLongFFP512;
  
  import java.io.BufferedReader;
  import java.io.InputStreamReader;
  import java.nio.charset.StandardCharsets;
  import java.util.ArrayList;
  
  public class IncrementTableWithIndex {
  	private static final String cHeader = "<index version "+SSSearcherWithIndex.cIndexVersion+">";
  
      ArrayList<IncrementTableRecordWithIndex>	mRecords;
  
  	protected IncrementTableWithIndex() {
  		mRecords = new ArrayList<IncrementTableRecordWithIndex>();
  		}
  
  
  	protected IncrementTableWithIndex(String filename) throws Exception {
  		BufferedReader theReader = new BufferedReader(new InputStreamReader(this.getClass().getResourceAsStream(filename), StandardCharsets.UTF_8));
  
  		String header = theReader.readLine();
  		if (!header.equals(cHeader))
  			throw new Exception("index version mismatch");
  
          DescriptorHandlerLongFFP512 descriptorHandler = new DescriptorHandlerLongFFP512();
  		mRecords = new ArrayList<IncrementTableRecordWithIndex>();
  		while (true) {
  			String theLine = theReader.readLine();
  			if (theLine == null)
  				break;
  
  			int firstTab = theLine.indexOf('\t');
  			if (firstTab == -1)
  				throw new Exception("line without TAB");
  			int secondTab = theLine.indexOf('\t', firstTab+1);
  			if (secondTab == -1)
  				throw new Exception("line without second TAB");
  
              long[] index = (long[])descriptorHandler.decode(theLine.substring(0, firstTab));
  			String idcode = theLine.substring(firstTab+1, secondTab);
  			double increment = Double.valueOf(theLine.substring(secondTab+1)).doubleValue();
  
  			mRecords.add(new IncrementTableRecordWithIndex(idcode, index, increment));
  			}
  		theReader.close();
  		}
  
  
  	protected void addElement(String idcode, long[] index, double increment) {
  		mRecords.add(new IncrementTableRecordWithIndex(idcode, index, increment));
  		}
  
  
  	protected int getSize() {
  		return mRecords.size();
  		}
  
  
  	protected String getFragment(int i) {
  		return mRecords.get(i).mIDCode;
  		}
  
  
  	protected long[] getIndex(int i) {
  		return mRecords.get(i).mIndex;
  		}
  
  
  	protected double getIncrement(int i) {
  		return mRecords.get(i).mIncrement;
  		}
  	}
  
  
  class IncrementTableRecordWithIndex {
  	String				mIDCode;
  	long[]				mIndex;
  	double				mIncrement;
  
  	protected IncrementTableRecordWithIndex(String idcode, long[] index, double increment) {
  		mIDCode = idcode;
  		mIndex = index;
  		mIncrement = increment;
  		}
  	}