| AddGasCompartmentSubstance(SESubstance &sub) | biogears::SECompartmentManager | virtual |
| AddLiquidCompartmentSubstance(SESubstance &sub) | biogears::SECompartmentManager | virtual |
| AddSubstance(SESubstance &s, CompartmentType &cmpt) const | biogears::SECompartmentManager | protected |
| AllowGasSubstance(SESubstance &s, SEGasCompartment &cmpt) const | biogears::SECompartmentManager | inlineprotectedvirtual |
| AllowLiquidSubstance(SESubstance &s, SELiquidCompartment &cmpt) const | biogears::SECompartmentManager | inlineprotectedvirtual |
| Clear() | biogears::SECompartmentManager | virtual |
| CreateCompartment(const std::string &name, std::map< std::string, CompartmentType * > &name2cmpt, std::vector< SESubstance * > *substances) | biogears::SECompartmentManager | protected |
| CreateGasCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| CreateGasCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| CreateGasGraph(const char *name) | biogears::SECompartmentManager | virtual |
| CreateGasGraph(const std::string &name) | biogears::SECompartmentManager | virtual |
| CreateGasLink(SEGasCompartment &src, SEGasCompartment &tgt, const char *name) | biogears::SECompartmentManager | virtual |
| CreateGasLink(SEGasCompartment &src, SEGasCompartment &tgt, const std::string &name) | biogears::SECompartmentManager | virtual |
| CreateLink(CompartmentType &src, CompartmentType &tgt, const std::string &name, std::map< std::string, LinkType * > &name2link) const | biogears::SECompartmentManager | protected |
| CreateLiquidCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| CreateLiquidCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| CreateLiquidGraph(const char *name) | biogears::SECompartmentManager | virtual |
| CreateLiquidGraph(const std::string &name) | biogears::SECompartmentManager | virtual |
| CreateLiquidLink(SELiquidCompartment &src, SELiquidCompartment &tgt, const char *name) | biogears::SECompartmentManager | virtual |
| CreateLiquidLink(SELiquidCompartment &src, SELiquidCompartment &tgt, const std::string &name) | biogears::SECompartmentManager | virtual |
| CreateThermalCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| CreateThermalCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| CreateThermalLink(SEThermalCompartment &src, SEThermalCompartment &tgt, const char *name) | biogears::SECompartmentManager | virtual |
| CreateThermalLink(SEThermalCompartment &src, SEThermalCompartment &tgt, const std::string &name) | biogears::SECompartmentManager | virtual |
| CreateTissueCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| CreateTissueCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| Debug(const char *msg, const char *origin="") const | biogears::Loggable | protectedvirtual |
| Debug(const std::string &msg, const std::string &origin=empty) const | biogears::Loggable | protectedvirtual |
| Debug(std::ostream &msg, const std::string &origin=empty) const | biogears::Loggable | protectedvirtual |
| DeleteGasCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| DeleteGasCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| DeleteGasGraph(const char *name) | biogears::SECompartmentManager | virtual |
| DeleteGasGraph(const std::string &name) | biogears::SECompartmentManager | virtual |
| DeleteGasLink(const char *name) | biogears::SECompartmentManager | virtual |
| DeleteGasLink(const std::string &name) | biogears::SECompartmentManager | virtual |
| DeleteLiquidCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| DeleteLiquidCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| DeleteLiquidGraph(const char *name) | biogears::SECompartmentManager | virtual |
| DeleteLiquidGraph(const std::string &name) | biogears::SECompartmentManager | virtual |
| DeleteLiquidLink(const char *name) | biogears::SECompartmentManager | virtual |
| DeleteLiquidLink(const std::string &name) | biogears::SECompartmentManager | virtual |
| DeleteThermalCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| DeleteThermalCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| DeleteThermalLink(const char *name) | biogears::SECompartmentManager | virtual |
| DeleteThermalLink(const std::string &name) | biogears::SECompartmentManager | virtual |
| DeleteTissueCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| DeleteTissueCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| empty | biogears::Loggable | static |
| empty_cStr | biogears::Loggable | static |
| Error(const char *msg, const char *origin="") const | biogears::Loggable | protectedvirtual |
| Error(const std::string msg, const std::string origin=empty) const | biogears::Loggable | protectedvirtual |
| Error(std::ostream &msg, const std::string &origin=empty) const | biogears::Loggable | protectedvirtual |
| Fatal(const char *msg, const char *origin="") const | biogears::Loggable | protectedvirtual |
| Fatal(const std::string &msg, const std::string &origin=empty) const | biogears::Loggable | protectedvirtual |
| Fatal(std::ostream &msg, const std::string &origin=empty) const | biogears::Loggable | protectedvirtual |
| FindLeaves(CompartmentType *cmpt, std::vector< CompartmentType * > &leaves) const | biogears::SECompartmentManager | protected |
| GetChildLinks(CompartmentType *pnt, CompartmentType *child) const | biogears::SECompartmentManager | protected |
| GetCompartment(CDM::enumCompartmentType::value type, const char *name) | biogears::SECompartmentManager | virtual |
| GetCompartment(CDM::enumCompartmentType::value type, const std::string &name) | biogears::SECompartmentManager | virtual |
| GetCompartment(CDM::enumCompartmentType::value type, const char *name) const | biogears::SECompartmentManager | virtual |
| GetCompartment(CDM::enumCompartmentType::value type, const std::string &name) const | biogears::SECompartmentManager | virtual |
| GetCompartment(const std::string &name, std::map< std::string, CompartmentType * > &name2cmpt) const | biogears::SECompartmentManager | protected |
| GetCompartment(const std::string &name, const std::map< std::string, CompartmentType * > &name2cmpt) const | biogears::SECompartmentManager | protected |
| GetGasCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| GetGasCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| GetGasCompartment(const char *name) const | biogears::SECompartmentManager | virtual |
| GetGasCompartment(const std::string &name) const | biogears::SECompartmentManager | virtual |
| GetGasCompartments() | biogears::SECompartmentManager | virtual |
| GetGasCompartmentSubstances() const | biogears::SECompartmentManager | virtual |
| GetGasGraph(const char *name) | biogears::SECompartmentManager | virtual |
| GetGasGraph(const std::string &name) | biogears::SECompartmentManager | virtual |
| GetGasGraph(const char *name) const | biogears::SECompartmentManager | virtual |
| GetGasGraph(const std::string &name) const | biogears::SECompartmentManager | virtual |
| GetGasGraphs() | biogears::SECompartmentManager | virtual |
| GetGasLeafCompartments() | biogears::SECompartmentManager | virtual |
| GetGasLink(const char *name) | biogears::SECompartmentManager | virtual |
| GetGasLink(const std::string &name) | biogears::SECompartmentManager | virtual |
| GetGasLink(const char *name) const | biogears::SECompartmentManager | virtual |
| GetGasLink(const std::string &name) const | biogears::SECompartmentManager | virtual |
| GetGasLinks() | biogears::SECompartmentManager | virtual |
| GetLink(const std::string &name, std::map< std::string, LinkType * > &name2link) const | biogears::SECompartmentManager | protected |
| GetLink(const std::string &name, const std::map< std::string, LinkType * > &name2link) const | biogears::SECompartmentManager | protected |
| GetLiquidCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| GetLiquidCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| GetLiquidCompartment(const char *name) const | biogears::SECompartmentManager | virtual |
| GetLiquidCompartment(const std::string &name) const | biogears::SECompartmentManager | virtual |
| GetLiquidCompartments() | biogears::SECompartmentManager | virtual |
| GetLiquidCompartmentSubstances() const | biogears::SECompartmentManager | virtual |
| GetLiquidGraph(const char *name) | biogears::SECompartmentManager | virtual |
| GetLiquidGraph(const std::string &name) | biogears::SECompartmentManager | virtual |
| GetLiquidGraph(const char *name) const | biogears::SECompartmentManager | virtual |
| GetLiquidGraph(const std::string &name) const | biogears::SECompartmentManager | virtual |
| GetLiquidGraphs() | biogears::SECompartmentManager | virtual |
| GetLiquidLeafCompartments() | biogears::SECompartmentManager | virtual |
| GetLiquidLink(const char *name) | biogears::SECompartmentManager | virtual |
| GetLiquidLink(const std::string &name) | biogears::SECompartmentManager | virtual |
| GetLiquidLink(const char *name) const | biogears::SECompartmentManager | virtual |
| GetLiquidLink(const std::string &name) const | biogears::SECompartmentManager | virtual |
| GetLiquidLinks() | biogears::SECompartmentManager | virtual |
| GetLogger() const | biogears::Loggable | virtual |
| GetThermalCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| GetThermalCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| GetThermalCompartment(const char *name) const | biogears::SECompartmentManager | virtual |
| GetThermalCompartment(const std::string &name) const | biogears::SECompartmentManager | virtual |
| GetThermalCompartments() | biogears::SECompartmentManager | virtual |
| GetThermalLeafCompartments() | biogears::SECompartmentManager | virtual |
| GetThermalLink(const char *name) | biogears::SECompartmentManager | virtual |
| GetThermalLink(const std::string &name) | biogears::SECompartmentManager | virtual |
| GetThermalLink(const char *name) const | biogears::SECompartmentManager | virtual |
| GetThermalLink(const std::string &name) const | biogears::SECompartmentManager | virtual |
| GetThermalLinks() | biogears::SECompartmentManager | virtual |
| GetTissueCompartment(const char *name) | biogears::SECompartmentManager | virtual |
| GetTissueCompartment(const std::string &name) | biogears::SECompartmentManager | virtual |
| GetTissueCompartment(const char *name) const | biogears::SECompartmentManager | virtual |
| GetTissueCompartment(const std::string &name) const | biogears::SECompartmentManager | virtual |
| GetTissueCompartments() | biogears::SECompartmentManager | virtual |
| GetTissueLeafCompartments() | biogears::SECompartmentManager | virtual |
| HasCompartment(CDM::enumCompartmentType::value type, const char *name) const | biogears::SECompartmentManager | virtual |
| HasCompartment(CDM::enumCompartmentType::value type, const std::string &name) const | biogears::SECompartmentManager | virtual |
| HasCompartment(const std::string &name, const std::map< std::string, CompartmentType * > &name2cmpt) const | biogears::SECompartmentManager | protected |
| HasGasCompartment(const char *name) const | biogears::SECompartmentManager | virtual |
| HasGasCompartment(const std::string &name) const | biogears::SECompartmentManager | virtual |
| HasGasGraph(const char *name) const | biogears::SECompartmentManager | virtual |
| HasGasGraph(const std::string &name) const | biogears::SECompartmentManager | virtual |
| HasGasLink(const char *name) const | biogears::SECompartmentManager | virtual |
| HasGasLink(const std::string &name) const | biogears::SECompartmentManager | virtual |
| HasLink(const std::string &name, const std::map< std::string, LinkType * > &name2link) const | biogears::SECompartmentManager | protected |
| HasLiquidCompartment(const char *name) const | biogears::SECompartmentManager | virtual |
| HasLiquidCompartment(const std::string &name) const | biogears::SECompartmentManager | virtual |
| HasLiquidGraph(const char *name) const | biogears::SECompartmentManager | virtual |
| HasLiquidGraph(const std::string &name) const | biogears::SECompartmentManager | virtual |
| HasLiquidLink(const char *name) const | biogears::SECompartmentManager | virtual |
| HasLiquidLink(const std::string &name) const | biogears::SECompartmentManager | virtual |
| HasThermalCompartment(const char *name) const | biogears::SECompartmentManager | virtual |
| HasThermalCompartment(const std::string &name) const | biogears::SECompartmentManager | virtual |
| HasThermalLink(const char *name) const | biogears::SECompartmentManager | virtual |
| HasThermalLink(const std::string &name) const | biogears::SECompartmentManager | virtual |
| HasTissueCompartment(const char *name) const | biogears::SECompartmentManager | virtual |
| HasTissueCompartment(const std::string &name) const | biogears::SECompartmentManager | virtual |
| Info(const char *msg, const char *origin="") const | biogears::Loggable | protectedvirtual |
| Info(const std::string &msg, const std::string &origin=empty) const | biogears::Loggable | protectedvirtual |
| Info(std::ostream &msg, const std::string &origin=empty) const | biogears::Loggable | protectedvirtual |
| Load(const CDM::CompartmentManagerData &in, SECircuitManager *circuits=nullptr) | biogears::SECompartmentManager | virtual |
| Loggable() | biogears::Loggable | |
| Loggable(Logger *log) | biogears::Loggable | |
| m_CO | biogears::SECompartmentManager | protected |
| m_CO2 | biogears::SECompartmentManager | protected |
| m_GasCompartments | biogears::SECompartmentManager | protected |
| m_GasGraphs | biogears::SECompartmentManager | protected |
| m_GasLeafCompartments | biogears::SECompartmentManager | protected |
| m_GasLinks | biogears::SECompartmentManager | protected |
| m_GasName2Compartments | biogears::SECompartmentManager | protected |
| m_GasName2Graphs | biogears::SECompartmentManager | protected |
| m_GasName2Links | biogears::SECompartmentManager | protected |
| m_GasSubstances | biogears::SECompartmentManager | protected |
| m_Hb | biogears::SECompartmentManager | protected |
| m_HbCO | biogears::SECompartmentManager | protected |
| m_HbCO2 | biogears::SECompartmentManager | protected |
| m_HbO2 | biogears::SECompartmentManager | protected |
| m_HbO2CO2 | biogears::SECompartmentManager | protected |
| m_LiquidCompartments | biogears::SECompartmentManager | protected |
| m_LiquidGraphs | biogears::SECompartmentManager | protected |
| m_LiquidLeafCompartments | biogears::SECompartmentManager | protected |
| m_LiquidLinks | biogears::SECompartmentManager | protected |
| m_LiquidName2Compartments | biogears::SECompartmentManager | protected |
| m_LiquidName2Graphs | biogears::SECompartmentManager | protected |
| m_LiquidName2Links | biogears::SECompartmentManager | protected |
| m_LiquidSubstances | biogears::SECompartmentManager | protected |
| m_Logger | biogears::Loggable | protected |
| m_O2 | biogears::SECompartmentManager | protected |
| m_subMgr | biogears::SECompartmentManager | protected |
| m_ThermalCompartments | biogears::SECompartmentManager | protected |
| m_ThermalLeafCompartments | biogears::SECompartmentManager | protected |
| m_ThermalLinks | biogears::SECompartmentManager | protected |
| m_ThermalName2Compartments | biogears::SECompartmentManager | protected |
| m_ThermalName2Links | biogears::SECompartmentManager | protected |
| m_TissueCompartments | biogears::SECompartmentManager | protected |
| m_TissueLeafCompartments | biogears::SECompartmentManager | protected |
| m_TissueName2Compartments | biogears::SECompartmentManager | protected |
| SECompartmentManager(SESubstanceManager &subMgr) | biogears::SECompartmentManager | |
| SetSubstances(CompartmentType &cmpt, std::vector< SESubstance * > &substances) const | biogears::SECompartmentManager | protected |
| StateChange() | biogears::SECompartmentManager | virtual |
| Unload() const | biogears::SECompartmentManager | virtual |
| Unload(CDM::CompartmentManagerData &data) const | biogears::SECompartmentManager | protected |
| UpdateLinks() | biogears::SECompartmentManager | virtual |
| UpdateLinks(SEGasCompartmentGraph &graph) | biogears::SECompartmentManager | virtual |
| UpdateLinks(SELiquidCompartmentGraph &graph) | biogears::SECompartmentManager | virtual |
| UpdateLinks(const std::vector< CompartmentType * > &compartments, const std::vector< LinkType * > &links) const | biogears::SECompartmentManager | protected |
| Warning(const char *msg, const char *origin="") const | biogears::Loggable | protectedvirtual |
| Warning(const std::string &msg, const std::string &origin=empty) const | biogears::Loggable | protectedvirtual |
| Warning(std::ostream &msg, const std::string &origin=empty) const | biogears::Loggable | protectedvirtual |
| ~Loggable() | biogears::Loggable | virtual |
| ~SECompartmentManager() | biogears::SECompartmentManager | virtual |
