/******************************************************************************
 *
 * Copyright (C) 2020 by
 * The Salk Institute for Biological Studies
 *
 * Use of this source code is governed by an MIT-style
 * license that can be found in the LICENSE file or at
 * https://opensource.org/licenses/MIT.
 *
******************************************************************************/

#ifndef API_SUBSYSTEM_H
#define API_SUBSYSTEM_H

#include <functional>

#include "generated/gen_subsystem.h"
#include "api/api_common.h"
#include "api/api_utils.h"
#include "api/species.h"
#include "api/surface_class.h"
#include "api/reaction_rule.h"

namespace BNG {
class ElemMolType;
class RxnRule;
class Cplx;
}

namespace MCell {
namespace API {

class Complex;

class Subsystem: public GenSubsystem {
public:
  SUBSYSTEM_CTOR()

  // from generated template
  void add_species(std::shared_ptr<Species> s) override {
    append_to_vec_canonical_name(species, s);
  }

  std::shared_ptr<Species> find_species(const std::string& name) override {
    return vec_find_by_name(species, name);
  }

  void add_reaction_rule(std::shared_ptr<ReactionRule> r) override {
    // reactions don't have to have name
    append_to_vec_canonical_name(reaction_rules, r);
  }

  std::shared_ptr<ReactionRule> find_reaction_rule(const std::string& name) override {
    return vec_find_by_name(reaction_rules, name);
  }

  void add_surface_class(std::shared_ptr<SurfaceClass> sc) override {
    append_to_vec(surface_classes, sc);
  }

  std::shared_ptr<SurfaceClass> find_surface_class(const std::string& name) override {
    return vec_find_by_name(surface_classes, name);
  }

  void add_elementary_molecule_type(std::shared_ptr<ElementaryMoleculeType> mt) override {
    append_to_vec_canonical_name(elementary_molecule_types, mt);
  }

  std::shared_ptr<ElementaryMoleculeType> find_elementary_molecule_type(const std::string& name) override {
    return vec_find_by_name(elementary_molecule_types, name);
  }


  void load_bngl_molecule_types_and_reaction_rules(
      const std::string& file_name,
      const std::map<std::string, double>& parameter_overrides = std::map<std::string, double>()
  ) override;

  // added manually

  // may return nullptr
  std::shared_ptr<Species> get_species_with_id(const species_id_t id);

  // go through all species and make sure that
  // 1) all identical elementary molecule type objects exist only once and
  // 2) all are also in the elementary_molecule_types array
  void unify_and_register_elementary_molecule_types();

  void dump() const;

protected:
  void convert_bng_data_to_subsystem_data(const BNG::BNGData& bng_data);

private:
  void convert_reaction_rule(const BNG::BNGData& bng_data, const BNG::RxnRule& bng_rr);
};

} // namespace API
} // namespace MCell

#endif // API_SUBSYSTEM_H