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;
  
  import java.util.Arrays;
  
  public class CanonizerBaseValue implements Comparable<CanonizerBaseValue> {
      public long[] mValue;
      private int mAtom;
      private int mIndex;
      private int mAvailableBits;
  
      /**
       * @param size depends on the maximum number of non-H neighbors
       *             and whether bond query features are present
       */
      public CanonizerBaseValue(int size) {
          mValue = new long[size];
          }
  
      public void init(int atom) {
          mAtom = atom;
          mIndex = 0;
          mAvailableBits = 63;
          Arrays.fill(mValue, 0);
          }
  
      public void add(long data) {
          mValue[mIndex] += data;
          }
  
      public void add(int bits, long data) {
          if (mAvailableBits == 0) {
              mIndex++;
              mAvailableBits = 63;
              }
          if (mAvailableBits == 63) {
              mValue[mIndex] |= data;
              mAvailableBits -= bits;
              }
          else {
              if (mAvailableBits >= bits) {
                  mValue[mIndex] <<= bits;
                  mValue[mIndex] |= data;
                  mAvailableBits -= bits;
                  }
              else {
                  mValue[mIndex] <<= mAvailableBits;
                  mValue[mIndex] |= (data >> (bits - mAvailableBits));
                  bits -= mAvailableBits;
                  mIndex++;
                  mAvailableBits = 63 - bits;
                  mValue[mIndex] |= (data & ((1 << bits) - 1));
                  }
              }
          }
  
      public int getAtom() {
          return mAtom;
          }
  
      public int compareTo(CanonizerBaseValue b) {
          assert(mIndex == b.mIndex);
          for (int i=0; i<mIndex; i++)
              if (mValue[i] != b.mValue[i])
                  return (mValue[i] < b.mValue[i]) ? -1 : 1;
          return (mValue[mIndex] == b.mValue[mIndex]) ? 0
               : (mValue[mIndex] < b.mValue[mIndex]) ? -1 : 1;
          }
      }
  