/****************************************************************************
 * Copyright (C) 2015 EPAM Systems
 *
 * This file is part of Indigo toolkit.
 *
 * This file may be distributed and/or modified under the terms of the
 * GNU General Public License version 3 as published by the Free Software
 * Foundation and appearing in the file LICENSE.GPL included in the
 * packaging of this file.
 *
 * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
 * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
 ***************************************************************************/

#ifndef __molecule_cdx_loader__
#define __molecule_cdx_loader__

#include "base_cpp/exception.h"
#include "base_cpp/obj.h"
#include "molecule/base_molecule.h"
#include "molecule/molecule_stereocenter_options.h"

typedef unsigned short int UINT16;
typedef int INT32;
typedef unsigned int UINT32;
#include "molecule/CDXConstants.h"

#ifdef _WIN32
#pragma warning(push)
#pragma warning(disable:4251)
#endif

namespace indigo
{

class Scanner;
class Molecule;

class DLLEXPORT MoleculeCdxLoader
{
public:

   DECL_ERROR;

   explicit MoleculeCdxLoader (Scanner &scanner);

   void loadMolecule (Molecule &mol);

   StereocentersOptions stereochemistry_options;

   const float COORD_COEF;

   CP_DECL;
   TL_CP_DECL(RedBlackStringObjMap< Array<char> >, properties);

protected:

   struct _ExtConnection
   {
      int bond_id;
      int point_id;
      int atom_id;
   };

   struct _NodeDesc
   {
      int id;
      int type;
      int label;
      int isotope;
      int charge;
      int radical;
      int valence; 
      int hydrogens; 
      int stereo;
      int enchanced_stereo;
      int stereo_group;
      int x;
      int y;
      int z;
      int index;
      Array<_ExtConnection> connections;
   };

   struct _BondDesc
   {
      int id;
      int beg;
      int end;
      int type;
      int stereo;
      int dir;
      int index;
      bool swap_bond;
   };

   Scanner *_scanner;

   TL_CP_DECL(Array<_NodeDesc>, _nodes);
   TL_CP_DECL(Array<_BondDesc>, _bonds);

   TL_CP_DECL(Array<int>, _stereo_care_atoms);
   TL_CP_DECL(Array<int>, _stereo_care_bonds);
   TL_CP_DECL(Array<int>, _stereocenter_types);
   TL_CP_DECL(Array<int>, _stereocenter_groups);
   TL_CP_DECL(Array<int>, _sensible_bond_directions);
   TL_CP_DECL(Array<int>, _ignore_cistrans);

   void _checkHeader ();
   void _loadMolecule ();
   void _updateConnectionPoint (int point_id, int atom_id);
   void _postLoad ();
   void _readFragment (UINT32 fragmment_id);
   void _readNode (UINT32 node_id);
   void _readBond (UINT32 bond_id);
   void _skipObject ();
   void _read2DPosition (int &x, int &y);
   void _read3DPosition (int &x, int &y, int &z);
   int _getElement ();
   int _getCharge (int size);
   int _getRadical ();
   int _getBondType ();
   int _getBondDirection (bool &swap_bond);
   void _getBondOrdering (int size, Array<_ExtConnection> &cons);
   void _getConnectionOrder (int size, Array<_ExtConnection> &cons);

   Molecule      *_mol;
   BaseMolecule  *_bmol;

private:
   MoleculeCdxLoader (const MoleculeCdxLoader &); // no implicit copy
};


}

#ifdef _WIN32
#pragma warning(pop)
#endif

#endif