/****************************************************************************
 * Copyright (C) 2009-2015 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 __base_reaction__substructure_matcher__
#define __base_reaction__substructure_matcher__

#include "base_cpp/red_black.h"
#include "base_cpp/tlscont.h"
#include "base_cpp/auto_ptr.h"
#include "base_cpp/obj.h"
#include "graph/embedding_enumerator.h"
#include "molecule/molecule_arom_match.h"

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

namespace indigo {

class Reaction;
class ReactionAtomNeighbourhoodCounters;
class BaseReaction;
class Graph;
class BaseMolecule;
class Molecule;

typedef RedBlackMap<int, int> RedBlackIntMap;

class DLLEXPORT BaseReactionSubstructureMatcher
{
protected:
   class _Matcher;
   
public:
   BaseReactionSubstructureMatcher (Reaction &target);

   void setQuery (BaseReaction &query);
   void setNeiCounters (const ReactionAtomNeighbourhoodCounters *query_counters,
      const ReactionAtomNeighbourhoodCounters *target_counters);

   bool highlight;
   bool use_aromaticity_matcher;

   AromaticityOptions arom_options;

   bool find ();

   int getTargetMoleculeIndex (int query_molecule_idx);
   const int * getQueryMoleculeMapping (int query_mol_idx);

   DECL_ERROR;

   bool (*match_atoms) (BaseReaction &query_, Reaction &target,
                        int sub_mol_idx, int sub_atom_idx, int super_mol_idx, int super_atom_idx, void *context);

   bool (*match_bonds) (BaseReaction &query_, Reaction &target,
                        int sub_mol_idx, int sub_atom_idx, int super_mol_idx, int super_atom_idx,
                        AromaticityMatcher *am, void *context);

   void (*remove_atom) (BaseMolecule &submol, int sub_idx, AromaticityMatcher *am);

   void (*add_bond) (BaseMolecule &submol, Molecule &supermol,
                      int sub_idx, int super_idx, AromaticityMatcher *am);

   bool (*prepare) (BaseReaction &query_, Reaction &target, void *context);

   bool (*prepare_ee) (EmbeddingEnumerator &ee, BaseMolecule &submol, Molecule &supermol,
                       void *context);

   void *context;

protected:

   void _initMap (BaseReaction &reaction, int side, RedBlackMap<int, int> &aam_map);
   virtual bool _checkAAM ();
   void _highlight ();
   bool _match_stereo;

   enum
   {
      _FIRST_SIDE,
      _SECOND_SIDE,
      _SECOND_SIDE_REST,
      _CONTINUE,
      _NO_WAY,
      _RETURN
   };

   class _Matcher
   {
   public:
      _Matcher (BaseReactionSubstructureMatcher &context);
      _Matcher (const _Matcher &other);

      int  nextPair ();
      void setMode (int mode) { _mode = mode; }
      int  getMode () { return _mode; }
      bool addPair (int mol1_idx, int mol2_idx, const Array<int> &core1, const Array<int> &core2, bool from_first_side);
      void restore ();

      bool match_stereo;

      int _current_molecule_1, _current_molecule_2;

      CP_DECL;
      TL_CP_DECL(Array<int>, _current_core_1);
      TL_CP_DECL(Array<int>, _current_core_2);

   protected:
      int _nextPair ();

      bool _initEnumerator (BaseMolecule &mol_1, Molecule &mol_2);

      static int _embedding (Graph &subgraph, Graph &supergraph, int *core_sub, int *core_super, void *userdata);
      static bool _matchAtoms (Graph &subgraph, Graph &supergraph, const int *core_sub, int sub_idx, int super_idx, void *userdata);
      static bool _matchBonds (Graph &subgraph, Graph &supergraph, int sub_idx, int super_idx, void *userdata);
      static void _removeAtom (Graph &subgraph, int sub_idx, void *userdata);
      static void _addBond (Graph &subgraph, Graph &supergraph, int sub_idx, int super_idx, void *userdata);

      BaseReactionSubstructureMatcher &_context;
      AutoPtr<AromaticityMatcher> _am;

      Obj<EmbeddingEnumerator> _enumerator;
      int _mode;
      int _selected_molecule_1;
      int _selected_molecule_2;
      TL_CP_DECL(Array<int>, _mapped_aams);
   };

   Reaction &_target;

   CP_DECL;
   TL_CP_DECL(PtrArray<_Matcher>, _matchers);
   TL_CP_DECL(RedBlackIntMap, _aam_to_second_side_1);
   TL_CP_DECL(RedBlackIntMap, _aam_to_second_side_2);
   TL_CP_DECL(Array<int>, _molecule_core_1);
   TL_CP_DECL(Array<int>, _molecule_core_2);
   TL_CP_DECL(RedBlackIntMap, _aam_core_first_side);

   int _first_side;
   int _second_side;

   BaseReaction *_query;

   const ReactionAtomNeighbourhoodCounters
      *_query_nei_counters, *_target_nei_counters;
};

}

#ifdef _WIN32
#pragma warning(pop)
#endif

#endif
