#ifndef __bingo_object__
#define __bingo_object__

//#include "base_c/defs.h"
#include "base_cpp/output.h"
#include "base_cpp/scanner.h"

#include "reaction/reaction.h"
#include "reaction/query_reaction.h"
#include "reaction/crf_saver.h"
#include "reaction/crf_loader.h"
#include "reaction/reaction_fingerprint.h"
#include "reaction/reaction_substructure_matcher.h"

#include "molecule/molecule.h"
#include "molecule/cmf_saver.h"
#include "molecule/cmf_loader.h"
#include "molecule/molecule_fingerprint.h"
#include "molecule/molecule_substructure_matcher.h"

using namespace indigo;
namespace bingo
{
   class QueryObject
   {
   public:
      virtual bool buildFingerprint (const MoleculeFingerprintParameters &fp_params, Array<byte> *sub_fp, Array<byte> *sim_fp)/* const */ = 0;
      virtual ~QueryObject () {};
   };

   //////////////////////////
   // Molecule query objects
   //////////////////////////

   class BaseMoleculeQuery : public QueryObject
   {
   private:
      BaseMolecule &_base_mol;
      
      bool _needs_query_fingerprint;

   public:
      BaseMoleculeQuery (BaseMolecule &mol, bool needs_query_fingerprint);

      virtual bool buildFingerprint (const MoleculeFingerprintParameters &fp_params, Array<byte> *sub_fp, Array<byte> *sim_fp) /*const*/;
      
      const BaseMolecule &getMolecule ();
   };

   class SubstructureMoleculeQuery : public BaseMoleculeQuery
   {
   private:
      QueryMolecule _mol;
      
   public:
      SubstructureMoleculeQuery (/* const */ QueryMolecule &mol);
   };

   class SimilarityMoleculeQuery : public BaseMoleculeQuery
   {
   private:
      Molecule _mol;
      
   public:
      SimilarityMoleculeQuery (/* const */ Molecule &mol);
   };

   class GrossQuery : public QueryObject
   {
   private:
      Array<char> _gross_str;

      virtual bool buildFingerprint (const MoleculeFingerprintParameters &fp_params, Array<byte> *sub_fp, Array<byte> *sim_fp) /*const*/;
      
   public:
      GrossQuery (/* const */ Array<char> &str);

      Array<char> &getGrossString();
   };

   //////////////////////////
   // Reaction query objects
   //////////////////////////

   class BaseReactionQuery : public QueryObject
   {
   private:
      BaseReaction &_base_rxn;
      
   public:
      BaseReactionQuery (BaseReaction &rxn);

      virtual bool buildFingerprint (const MoleculeFingerprintParameters &fp_params, Array<byte> *sub_fp, Array<byte> *sim_fp) /*const*/;

      const BaseReaction &getReaction ();
   };

   class SubstructureReactionQuery : public BaseReactionQuery
   {
   public:
      SubstructureReactionQuery (/* const */ QueryReaction &rxn);

   private:
      QueryReaction _rxn;
   };

   class SimilarityReactionQuery : public BaseReactionQuery
   {
   public:
      SimilarityReactionQuery (/* const */ Reaction &rxn);

   private:
      Reaction _rxn;
   };
   
   class IndexObject
   {
   public:
      virtual bool buildFingerprint (const MoleculeFingerprintParameters &fp_params, Array<byte> *sub_fp, Array<byte> *sim_fp) /* const */ = 0;

      virtual bool buildGrossString (Array<char> &cf)/* const */ = 0;

      virtual bool buildCfString (Array<char> &cf)/* const */ = 0;

      virtual bool buildHash (dword &hash)/* const */ = 0;

      virtual ~IndexObject () {};
   };

   class IndexMolecule : public IndexObject
   {
   protected:
      Molecule _mol;

   public:
      IndexMolecule (/* const */ Molecule &mol);

      virtual bool buildFingerprint (const MoleculeFingerprintParameters &fp_params, Array<byte> *sub_fp, Array<byte> *sim_fp) /*const*/;

      virtual bool buildGrossString (Array<char> &gross_string)/* const */;

      virtual bool buildCfString (Array<char> &cf) /*const*/;

      virtual bool buildHash (dword &hash)/* const */;
   };

   class IndexReaction : public IndexObject
   {
   protected:
      Reaction _rxn;

   public:
      IndexReaction (/* const */ Reaction &rxn);

      virtual bool buildFingerprint (const MoleculeFingerprintParameters &fp_params, Array<byte> *sub_fp, Array<byte> *sim_fp) /*const*/;

      virtual bool buildGrossString (Array<char> &gross_string)/* const */;

      virtual bool buildCfString (Array<char> &cf) /*const*/;

      virtual bool buildHash (dword &hash)/* const */;
   };
};

#endif //__bingo_object__