content: /*
   * 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.chem.descriptor;
  
  import java.nio.charset.StandardCharsets;
  
  /**
   * This is a descriptor handler, where the input object is an integer array
   * that typically represents counts of some sort. This class may be used
   * if input objects are more complex and the descriptors derived from them
   * can be represented as integer vectors.<br>
   * This class provides similarity calculation and descriptor en- and decoding.
   */
  
  public class DescriptorHandlerIntVector<U extends Object> implements DescriptorHandler<int[], U> {
      protected static final int[] FAILED_OBJECT = new int[0];
      private static final double CORRECTION_FACTOR = 0.42;
  
      private double correctionFactor;
  
  	public DescriptorHandlerIntVector() {
  		correctionFactor = CORRECTION_FACTOR;
  	}
  
  	public void setCorrectionFactor(double correctionFactor) {
  		this.correctionFactor = correctionFactor;
  	}
  
  	@Override
  	public float getSimilarity(int[] d1, int[] d2) {
          if (d1 == null || d2 == null)
              return Float.NaN;
  
          int total = 0;
          int matching = 0;
          for (int i=0; i<d1.length; i++) {
              total += Math.max(d1[i], d2[i]);
              matching += Math.min(d1[i], d2[i]);
              }
  
          return normalizeValue((float)matching/(float)total);
  		}
  
  	private float normalizeValue(double value) {
  		return value <= 0.0f ? 0.0f
  			 : value >= 1.0f ? 1.0f
  			 : (float)(1.0-Math.pow(1-Math.pow(value, correctionFactor) ,1.0/correctionFactor));
  		}
  
  	@Override
  	public DescriptorInfo getInfo() {
          return DescriptorConstants.DESCRIPTOR_IntegerVector;
  		}
  
  	@Override
  	public String getVersion() {
  		return DescriptorConstants.DESCRIPTOR_IntegerVector.version;
  		}
  
  	@Override
  	public String encode(int[] d) {
          return calculationFailed(d) ? FAILED_STRING : new String(new DescriptorEncoder().encodeIntArray(d), StandardCharsets.UTF_8);
  		}
  
  	@Override
  	public int[] decode(String s) {
  		return s == null ? null : new DescriptorEncoder().decodeIntArray(s);
  		}
  
  	@Override
  	public int[] decode(byte[] bytes) {
  		return bytes == null ? null : new DescriptorEncoder().decodeIntArray(bytes);
  		}
  
  	@Override
  	public int[] createDescriptor(U o) {
  		return (int[])o;	// the object is the descriptor
  		}
  
  	@Override
  	public boolean calculationFailed(int[] d) {
          return d==null || d.length==0;
  		}
  
  	@Override
  	public DescriptorHandler<int[], U> getThreadSafeCopy() {
  		return this;
  		}
  	}
  