SECompartmentManager.h

/**************************************************************************************
Copyright 2015 Applied Research Associates, Inc.
Licensed under the Apache License, Version 2.0 (the "License"); you may not use
this file except in compliance with the License. You may obtain a copy of the License
at:
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under
the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
CONDITIONS OF ANY KIND, either express or implied. See the License for the
specific language governing permissions and limitations under the License.
**************************************************************************************/

#pragma once
#include <string>
#include <vector>
#include <map>

#include <biogears/exports.h>

#include <biogears/cdm/CommonDataModel.h>
#include <biogears/cdm/circuit/SECircuitManager.h>
#include <biogears/cdm/compartment/fluid/SEGasCompartmentGraph.h>
#include <biogears/cdm/compartment/fluid/SELiquidCompartmentGraph.h>
#include <biogears/cdm/compartment/thermal/SEThermalCompartment.h>
#include <biogears/cdm/compartment/thermal/SEThermalCompartmentLink.h>
#include <biogears/cdm/compartment/tissue/SETissueCompartment.h>
#include <biogears/schema/cdm/Compartment.hxx>

CDM_BIND_DECL(CompartmentManagerData)

namespace biogears {
class BIOGEARS_API SECompartmentManager : public Loggable {
public:
  SECompartmentManager(SESubstanceManager& subMgr);
  virtual ~SECompartmentManager();

  virtual void Clear(); //clear memory

  virtual bool Load(const CDM::CompartmentManagerData& in, SECircuitManager* circuits = nullptr);
  virtual CDM::CompartmentManagerData* Unload() const;

protected:
  void Unload(CDM::CompartmentManagerData& data) const;

public:
  virtual void StateChange(); // Identify leaves and other bookkeeping
  virtual void UpdateLinks();
  virtual void UpdateLinks(SEGasCompartmentGraph& graph);
  virtual void UpdateLinks(SELiquidCompartmentGraph& graph);

  virtual bool HasCompartment(CDM::enumCompartmentType::value type, const char* name) const;
  virtual bool HasCompartment(CDM::enumCompartmentType::value type, const std::string& name) const;
  virtual SECompartment* GetCompartment(CDM::enumCompartmentType::value type, const char* name);
  virtual SECompartment* GetCompartment(CDM::enumCompartmentType::value type, const std::string& name);
  virtual const SECompartment* GetCompartment(CDM::enumCompartmentType::value type, const char* name) const;
  virtual const SECompartment* GetCompartment(CDM::enumCompartmentType::value type, const std::string& name) const;

  virtual SEGasCompartment& CreateGasCompartment(const char* name);
  virtual SEGasCompartment& CreateGasCompartment(const std::string& name);
  virtual void DeleteGasCompartment(const char* name);
  virtual void DeleteGasCompartment(const std::string& name);
  virtual bool HasGasCompartment(const char* name) const;
  virtual bool HasGasCompartment(const std::string& name) const;
  virtual SEGasCompartment* GetGasCompartment(const char* name); 
  virtual SEGasCompartment* GetGasCompartment(const std::string& name);
  virtual const SEGasCompartment* GetGasCompartment(const char* name) const;
  virtual const SEGasCompartment* GetGasCompartment(const std::string& name) const;
  virtual const std::vector<SEGasCompartment*>& GetGasCompartments();
  virtual const std::vector<SEGasCompartment*>& GetGasLeafCompartments();
  virtual SEGasCompartmentLink& CreateGasLink(SEGasCompartment& src, SEGasCompartment& tgt, const char* name);
  virtual SEGasCompartmentLink& CreateGasLink(SEGasCompartment& src, SEGasCompartment& tgt, const std::string& name);
  virtual void DeleteGasLink(const char* name);
  virtual void DeleteGasLink(const std::string& name);
  virtual bool HasGasLink(const char* name) const;
  virtual bool HasGasLink(const std::string& name) const;
  virtual SEGasCompartmentLink* GetGasLink(const char* name);
  virtual SEGasCompartmentLink* GetGasLink(const std::string& name);
  virtual const SEGasCompartmentLink* GetGasLink(const char* name) const;
  virtual const SEGasCompartmentLink* GetGasLink(const std::string& name) const;
  virtual const std::vector<SEGasCompartmentLink*>& GetGasLinks();
  virtual SEGasCompartmentGraph& CreateGasGraph(const char* name);
  virtual SEGasCompartmentGraph& CreateGasGraph(const std::string& name);
  virtual void DeleteGasGraph(const char* name);
  virtual void DeleteGasGraph(const std::string& name);
  virtual bool HasGasGraph(const char* name) const;
  virtual bool HasGasGraph(const std::string& name) const;
  virtual SEGasCompartmentGraph* GetGasGraph(const char* name);
  virtual SEGasCompartmentGraph* GetGasGraph(const std::string& name);
  virtual const SEGasCompartmentGraph* GetGasGraph(const char* name) const;
  virtual const SEGasCompartmentGraph* GetGasGraph(const std::string& name) const;
  virtual const std::vector<SEGasCompartmentGraph*>& GetGasGraphs();
  virtual void AddGasCompartmentSubstance(SESubstance& sub);
  virtual const std::vector<SESubstance*>& GetGasCompartmentSubstances() const;

  virtual SELiquidCompartment& CreateLiquidCompartment(const char* name);
  virtual SELiquidCompartment& CreateLiquidCompartment(const std::string& name);
  virtual void DeleteLiquidCompartment(const char* name);
  virtual void DeleteLiquidCompartment(const std::string& name);
  virtual bool HasLiquidCompartment(const char* name) const;
  virtual bool HasLiquidCompartment(const std::string& name) const;
  virtual SELiquidCompartment* GetLiquidCompartment(const char* name);
  virtual SELiquidCompartment* GetLiquidCompartment(const std::string& name);
  virtual const SELiquidCompartment* GetLiquidCompartment(const char* name) const;
  virtual const SELiquidCompartment* GetLiquidCompartment(const std::string& name) const;
  virtual const std::vector<SELiquidCompartment*>& GetLiquidCompartments();
  virtual const std::vector<SELiquidCompartment*>& GetLiquidLeafCompartments();
  virtual SELiquidCompartmentLink& CreateLiquidLink(SELiquidCompartment& src, SELiquidCompartment& tgt, const char* name);
  virtual SELiquidCompartmentLink& CreateLiquidLink(SELiquidCompartment& src, SELiquidCompartment& tgt, const std::string& name);
  virtual void DeleteLiquidLink(const char* name);
  virtual void DeleteLiquidLink(const std::string& name);
  virtual bool HasLiquidLink(const char* name) const;
  virtual bool HasLiquidLink(const std::string& name) const;
  virtual SELiquidCompartmentLink* GetLiquidLink(const char* name);
  virtual SELiquidCompartmentLink* GetLiquidLink(const std::string& name);
  virtual const SELiquidCompartmentLink* GetLiquidLink(const char* name) const;
  virtual const SELiquidCompartmentLink* GetLiquidLink(const std::string& name) const;
  virtual const std::vector<SELiquidCompartmentLink*>& GetLiquidLinks();
  virtual SELiquidCompartmentGraph& CreateLiquidGraph(const char* name);
  virtual SELiquidCompartmentGraph& CreateLiquidGraph(const std::string& name);
  virtual void DeleteLiquidGraph(const char* name);
  virtual void DeleteLiquidGraph(const std::string& name);
  virtual bool HasLiquidGraph(const char* name) const;
  virtual bool HasLiquidGraph(const std::string& name) const;
  virtual SELiquidCompartmentGraph* GetLiquidGraph(const char* name);
  virtual SELiquidCompartmentGraph* GetLiquidGraph(const std::string& name);
  virtual const SELiquidCompartmentGraph* GetLiquidGraph(const char* name) const;
  virtual const SELiquidCompartmentGraph* GetLiquidGraph(const std::string& name) const;
  virtual const std::vector<SELiquidCompartmentGraph*>& GetLiquidGraphs();
  virtual void AddLiquidCompartmentSubstance(SESubstance& sub);
  virtual const std::vector<SESubstance*>& GetLiquidCompartmentSubstances() const;

  virtual SEThermalCompartment& CreateThermalCompartment(const char* name);
  virtual SEThermalCompartment& CreateThermalCompartment(const std::string& name);
  virtual void DeleteThermalCompartment(const char* name);
  virtual void DeleteThermalCompartment(const std::string& name);
  virtual bool HasThermalCompartment(const char* name) const;
  virtual bool HasThermalCompartment(const std::string& name) const;
  virtual SEThermalCompartment* GetThermalCompartment(const char* name);
  virtual SEThermalCompartment* GetThermalCompartment(const std::string& name);
  virtual const SEThermalCompartment* GetThermalCompartment(const char* name) const;
  virtual const SEThermalCompartment* GetThermalCompartment(const std::string& name) const;
  virtual const std::vector<SEThermalCompartment*>& GetThermalCompartments();
  virtual const std::vector<SEThermalCompartment*>& GetThermalLeafCompartments();
  virtual SEThermalCompartmentLink& CreateThermalLink(SEThermalCompartment& src, SEThermalCompartment& tgt, const char* name);
  virtual SEThermalCompartmentLink& CreateThermalLink(SEThermalCompartment& src, SEThermalCompartment& tgt, const std::string& name);
  virtual void DeleteThermalLink(const char* name);
  virtual void DeleteThermalLink(const std::string& name);
  virtual bool HasThermalLink(const char* name) const;
  virtual bool HasThermalLink(const std::string& name) const;
  virtual SEThermalCompartmentLink* GetThermalLink(const char* name);
  virtual SEThermalCompartmentLink* GetThermalLink(const std::string& name);
  virtual const SEThermalCompartmentLink* GetThermalLink(const char* name) const;
  virtual const SEThermalCompartmentLink* GetThermalLink(const std::string& name) const;
  virtual const std::vector<SEThermalCompartmentLink*>& GetThermalLinks();

  virtual bool HasTissueCompartment(const char* name) const;
  virtual bool HasTissueCompartment(const std::string& name) const;
  virtual void DeleteTissueCompartment(const char* name);
  virtual void DeleteTissueCompartment(const std::string& name);
  virtual SETissueCompartment& CreateTissueCompartment(const char* name);
  virtual SETissueCompartment& CreateTissueCompartment(const std::string& name);
  virtual SETissueCompartment* GetTissueCompartment(const char* name);
  virtual SETissueCompartment* GetTissueCompartment(const std::string& name);
  virtual const SETissueCompartment* GetTissueCompartment(const char* name) const;
  virtual const SETissueCompartment* GetTissueCompartment(const std::string& name) const;
  virtual const std::vector<SETissueCompartment*>& GetTissueCompartments();
  virtual const std::vector<SETissueCompartment*>& GetTissueLeafCompartments();

protected:
  std::vector<SEGasCompartment*> m_GasCompartments;
  std::vector<SEGasCompartment*> m_GasLeafCompartments;
  std::map<std::string, SEGasCompartment*> m_GasName2Compartments;
  std::vector<SEGasCompartmentLink*> m_GasLinks;
  std::map<std::string, SEGasCompartmentLink*> m_GasName2Links;
  std::vector<SEGasCompartmentGraph*> m_GasGraphs;
  std::map<std::string, SEGasCompartmentGraph*> m_GasName2Graphs;
  std::vector<SESubstance*> m_GasSubstances;

  std::vector<SELiquidCompartment*> m_LiquidCompartments;
  std::vector<SELiquidCompartment*> m_LiquidLeafCompartments;
  std::map<std::string, SELiquidCompartment*> m_LiquidName2Compartments;
  std::vector<SELiquidCompartmentLink*> m_LiquidLinks;
  std::map<std::string, SELiquidCompartmentLink*> m_LiquidName2Links;
  std::vector<SELiquidCompartmentGraph*> m_LiquidGraphs;
  std::map<std::string, SELiquidCompartmentGraph*> m_LiquidName2Graphs;
  std::vector<SESubstance*> m_LiquidSubstances;

  std::vector<SEThermalCompartment*> m_ThermalCompartments;
  std::vector<SEThermalCompartment*> m_ThermalLeafCompartments;
  std::map<std::string, SEThermalCompartment*> m_ThermalName2Compartments;
  std::vector<SEThermalCompartmentLink*> m_ThermalLinks;
  std::map<std::string, SEThermalCompartmentLink*> m_ThermalName2Links;

  std::vector<SETissueCompartment*> m_TissueCompartments;
  std::vector<SETissueCompartment*> m_TissueLeafCompartments;
  std::map<std::string, SETissueCompartment*> m_TissueName2Compartments;

  template <typename CompartmentType, typename LinkType>
  void UpdateLinks(const std::vector<CompartmentType*>& compartments, const std::vector<LinkType*>& links) const;

  template <typename CompartmentType, typename LinkType>
  void GetChildLinks(CompartmentType* pnt, CompartmentType* child) const;

  template <typename CompartmentType>
  void FindLeaves(CompartmentType* cmpt, std::vector<CompartmentType*>& leaves) const;

  template <typename CompartmentType>
  CompartmentType& CreateCompartment(const std::string& name, std::map<std::string, CompartmentType*>& name2cmpt, std::vector<SESubstance*>* substances);

  template <typename CompartmentType>
  bool HasCompartment(const std::string& name, const std::map<std::string, CompartmentType*>& name2cmpt) const;

  template <typename CompartmentType>
  CompartmentType* GetCompartment(const std::string& name, std::map<std::string, CompartmentType*>& name2cmpt) const;

  template <typename CompartmentType>
  const CompartmentType* GetCompartment(const std::string& name, const std::map<std::string, CompartmentType*>& name2cmpt) const;

  template <typename LinkType, typename CompartmentType>
  LinkType& CreateLink(CompartmentType& src, CompartmentType& tgt, const std::string& name, std::map<std::string, LinkType*>& name2link) const;

  template <typename LinkType>
  bool HasLink(const std::string& name, const std::map<std::string, LinkType*>& name2link) const;

  template <typename LinkType>
  LinkType* GetLink(const std::string& name, std::map<std::string, LinkType*>& name2link) const;

  template <typename LinkType>
  const LinkType* GetLink(const std::string& name, const std::map<std::string, LinkType*>& name2link) const;

  template <typename CompartmentType>
  void SetSubstances(CompartmentType& cmpt, std::vector<SESubstance*>& substances) const;

  template <typename CompartmentType>
  void AddSubstance(SESubstance& s, CompartmentType& cmpt) const;

  // By default, every compartment gets every substance. Override these if you want to discritize better who gets what
  virtual bool AllowGasSubstance(SESubstance& s, SEGasCompartment& cmpt) const { return true; }
  virtual bool AllowLiquidSubstance(SESubstance& s, SELiquidCompartment& cmpt) const { return true; }

  SESubstance* m_O2;
  SESubstance* m_CO2;
  SESubstance* m_CO;
  SESubstance* m_Hb;
  SESubstance* m_HbO2;
  SESubstance* m_HbCO2;
  SESubstance* m_HbO2CO2;
  SESubstance* m_HbCO;
  SESubstanceManager& m_subMgr;
};
}