content: package com.actelion.research.chem.mcs;
  
  import com.actelion.research.chem.Molecule;
  import com.actelion.research.chem.StereoMolecule;
  import com.actelion.research.chem.properties.complexity.FragmentDefinedByBondsIdCode;
  import com.actelion.research.chem.properties.complexity.IBitArray;
  import com.actelion.research.util.Pipeline;
  
  import java.util.concurrent.atomic.AtomicBoolean;
  import java.util.concurrent.atomic.AtomicInteger;
  
  /*
  * 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.
  *
  */
  public class RunBondVector2IdCode implements Runnable {
  
      private static final long SLEEP = 10;
  
      private int id;
  
      private Pipeline<IBitArray> pipeInputFragIndexListsFromEFG;
  
      private Pipeline<FragmentDefinedByBondsIdCode> pipeOutputFragmentDefinedByBondsIdCode;
  
      private AtomicBoolean endOfRunReached;
  
      private BondVector2IdCode bondVector2IdCode;
  
      private AtomicInteger processedFragments;
  
      public RunBondVector2IdCode(int id, Pipeline<IBitArray> pipeInputFragIndexListsFromEFG, Pipeline<FragmentDefinedByBondsIdCode> pipeOutputFragmentDefinedByBondsIdCode) {
  
          this.id = id;
  
          this.pipeInputFragIndexListsFromEFG = pipeInputFragIndexListsFromEFG;
  
          this.pipeOutputFragmentDefinedByBondsIdCode = pipeOutputFragmentDefinedByBondsIdCode;
  
          endOfRunReached = new AtomicBoolean(false);
      }
  
      public void init(StereoMolecule mol){
          StereoMolecule molCopy = new StereoMolecule(mol);
          molCopy.ensureHelperArrays(Molecule.cHelperCIP);
          bondVector2IdCode = new BondVector2IdCode(molCopy);
          processedFragments = new AtomicInteger();
      }
  
  
      public void run() {
  
          try {
  
              while(!pipeInputFragIndexListsFromEFG.wereAllDataFetched()){
                  IBitArray livIndexBond = pipeInputFragIndexListsFromEFG.pollData();
                  if(livIndexBond == null){
                      try {Thread.sleep(SLEEP);} catch (InterruptedException e) {e.printStackTrace();}
                      continue;
                  }
  
                  try {
                      FragmentDefinedByBondsIdCode livIdCode = new FragmentDefinedByBondsIdCode(livIndexBond);
                      String idcodeFrag = bondVector2IdCode.getFragmentIdCode(livIndexBond);
                      livIdCode.setIdCode(idcodeFrag);
                      pipeOutputFragmentDefinedByBondsIdCode.addData(livIdCode);
  
                  } catch (Throwable e) {
                      e.printStackTrace();
                  } finally {
                      processedFragments.incrementAndGet();
                  }
  
              } // End while
  
          } catch (Exception e){
            e.printStackTrace();
          } finally {
              // System.out.println("RunBondVector2IdCode finally reached.");
              endOfRunReached.set(true);
          }
  
      } // End run()
  
      public boolean isEndOfRunReached() {
          return endOfRunReached.get();
      }
  
  }
  
  
  
  
  