Molecule.h

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/***************************************************************************
                          Molecule.h  -  description
                             -------------------
    begin                : ven jun 08 2003
    copyright            : (C) 2003 by Michel Dubois, Yann Le Guyadec
    email                : Michel.Dubois@univ-ubs.fr, Yann.Le-Guyadec@univ-ubs.fr
 ***************************************************************************/

/***************************************************************************
 *                                                                         *
 *   This program 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 2 of the License, or     *
 *   (at your option) any later version.                                   *
 *                                                                         *
 ***************************************************************************/


// Modele statique
/*
  * changes :
  *  - 08/06/03 MD Creation !
  */


#ifndef __MOLECULE__
#define __MOLECULE__


// Include files
#include "nommgr.h"
#include <vector>
#include "mmgr.h"
#include "Atom.h"
#include <RigidBodyEntity.h>
#include "SimMolecule.h"
#include "Link.h"

class SimMolecule;

namespace API {
  class Atom;
  class Link;

  class Molecule
  {
    class Util;
    friend class Util;
    friend class Atom;
    friend class Leg;

    public:

      class Util {
        friend class Molecule;
        private:
          Molecule * molecule;
          SimMolecule * simmolecule;

          Util(Molecule * molecule);
          ~Util();
        public:
          void          printAtoms() const;

          void          printLinks() const;
          void          printAdjacencyMatrix() const;
          void          printConnectedComponentID() const;

          void          print() const;

          SimMolecule * getSimulatedObject();

      };

      Util * util;
    
      unsigned int  getID();

      unsigned int  getAtomCount() const;

      Atom *        getAtom(unsigned int index) const;

      int           getAtomIndex (Atom * anAtom) const;

      unsigned int  getLinkCount() const;

      unsigned int  getLinkCount(unsigned int atomIndex1,unsigned int atomIndex2) const;

      Link *        getLink(unsigned int atomIndex1,unsigned int atomIndex2, unsigned linkIndex=0) const;


      Link *        getLink(unsigned int index) const;

      int           getLinkIndex (Link * aLink) const;

      void          atomize();
      void          stop();
      unsigned int  getNextSyncIndex();

      unsigned int  getSyncIndexCount();

      unsigned int  getSyncIndex(unsigned int index);
            
      void          releaseSyncIndex(unsigned int index);

      bool          isFinished(unsigned int index);

    protected:
      Molecule ();

      ~Molecule();
            
      void          setID      (int aMoleculeID);

      void          addAtom    (Atom *   atom);

      void          removeAtom (Atom *   atom);

      void          insertLink    (Link*   link);

      void          removeLink (Link*   link);

private :
      void          computeConnectedComponent();
      void          computeConnectedComponent(unsigned int atomIndex);
      void          setBaseConnectedComponent(unsigned int atomIndex);
      unsigned int  getConnectedComponentCount() const;
      bool          isConnected(unsigned int atomIndex, unsigned int anotherAtomIndex) const;
      unsigned int  getConnectedComponentCard(unsigned int index) const;
      void          adjItInit(unsigned int atomIndex) ;
      int           adjItBeg() ;
      int           adjItNext() ;

      bool          adjItEnd() const;
          std::vector<Atom *> atoms;
          unsigned int atomCount;
          std::vector<std::vector <Link *> > adj;
          unsigned int linkCount;
      std::vector<int> connectedComponentID;
      std::vector<unsigned int> syncIndexes;
      int connectedComponentCount;
      int ID;
      int adjItPos;
      int adjItAtom;
  };// END CLASS DEFINITION Molecule
}

#endif // __MOLECULE__

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