| applyEvents(double timeEnd, const unsigned char *previousEventState, const double *initialState, double *finalState) | rrllvm::LLVMExecutableModel | virtual |
| assignEvent(size_t eventId, double *data) | rrllvm::LLVMExecutableModel | inline |
| computeAllRatesOfChange() | rr::ExecutableModel | inline |
| copyCachedModel(a_type *src, b_type *dst) | rrllvm::LLVMExecutableModel | friend |
| evalInitialConditions(uint32_t flags=0) | rrllvm::LLVMExecutableModel | |
| ExecutableModel() | rr::ExecutableModel | |
| ExecutableModelFlags enum name | rr::ExecutableModel | |
| getAssignmentRuleIds(std::list< std::string > &out) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getBoundarySpeciesAmounts(size_t len, int const *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getBoundarySpeciesConcentrations(size_t len, int const *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getBoundarySpeciesId(size_t index) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getBoundarySpeciesIndex(const std::string &) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getBoundarySpeciesInitAmounts(size_t size_t, const int *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getBoundarySpeciesInitConcentrations(size_t len, const int *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getCompartmentId(size_t) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getCompartmentIndex(const std::string &) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getCompartmentIndexForBoundarySpecies(size_t index) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getCompartmentIndexForFloatingSpecies(size_t index) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getCompartmentInitVolumes(size_t len, const int *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getCompartmentVolumes(size_t len, int const *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getConservedMoietyId(size_t index) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getConservedMoietyIndex(const std::string &name) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getConservedMoietyValues(size_t len, int const *indx, double *values) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getEventBufferSize(size_t event) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | inline |
| getEventData(size_t eventId, double *data) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | inline |
| getEventDelay(size_t event) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | inline |
| getEventId(size_t index) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getEventIds(std::list< std::string > &out) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getEventIndex(const std::string &eid) | rrllvm::LLVMExecutableModel | virtual |
| getEventInitialValue(size_t event) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | inline |
| getEventListener(size_t index) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getEventPersistent(size_t event) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | inline |
| getEventPriority(size_t event) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | inline |
| getEventRoots(double time, const double *y, double *gdot) | rrllvm::LLVMExecutableModel | virtual |
| getEventTieBreak(size_t eventA, size_t eventB) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | |
| getEventTrigger(size_t event) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | |
| getEventTriggers(size_t len, const int *indx, unsigned char *eventState) | rrllvm::LLVMExecutableModel | virtual |
| getEventUseValuesFromTriggerTime(size_t event) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | inline |
| getExecutableModelDesc() const | rrllvm::LLVMExecutableModel | inlinevirtual |
| getFlags() const | rrllvm::LLVMExecutableModel | inlinevirtual |
| getFloatingSpeciesAmountRate(size_t index, const double *reactionRates) | rrllvm::LLVMExecutableModel | virtual |
| getFloatingSpeciesAmountRates(size_t len, int const *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getFloatingSpeciesAmounts(size_t len, int const *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getFloatingSpeciesConcentrationRates(size_t len, int const *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getFloatingSpeciesConcentrations(size_t len, int const *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getFloatingSpeciesId(size_t index) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getFloatingSpeciesIndex(const std::string &) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getFloatingSpeciesInitAmounts(size_t size_t, const int *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getFloatingSpeciesInitConcentrations(size_t len, const int *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getGlobalParameterId(size_t) | rrllvm::LLVMExecutableModel | virtual |
| getGlobalParameterIndex(const std::string &) | rrllvm::LLVMExecutableModel | virtual |
| getGlobalParameterInitValues(size_t len, const int *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getGlobalParameterValues(size_t len, int const *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getIds(int types, std::list< std::string > &ids) | rrllvm::LLVMExecutableModel | virtual |
| getInfo() (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getInitialAssignmentIds(std::list< std::string > &out) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getModelName() | rrllvm::LLVMExecutableModel | virtual |
| getNextPendingEventTime(bool pop) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getNumBoundarySpecies() | rrllvm::LLVMExecutableModel | virtual |
| getNumCompartments() (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getNumConservedMoieties() (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getNumDepFloatingSpecies() | rrllvm::LLVMExecutableModel | virtual |
| getNumEvents() (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getNumFloatingSpecies() | rrllvm::LLVMExecutableModel | virtual |
| getNumGlobalParameters() | rrllvm::LLVMExecutableModel | virtual |
| getNumIndFloatingSpecies() | rrllvm::LLVMExecutableModel | virtual |
| getNumPiecewiseTriggers() | rrllvm::LLVMExecutableModel | virtual |
| getNumRateRules() (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getNumReactions() | rrllvm::LLVMExecutableModel | virtual |
| getPendingEventSize() (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getPiecewiseTriggerRoots(double time, const double *y, double *gdot) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getRandom() | rrllvm::LLVMExecutableModel | virtual |
| getRandomSeed() | rrllvm::LLVMExecutableModel | virtual |
| getRateRuleIds(std::list< std::string > &out) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getRateRuleRates(size_t len, int const *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getRateRuleSymbols() const | rrllvm::LLVMExecutableModel | virtual |
| getRateRuleValues(double *rateRuleValues) | rrllvm::LLVMExecutableModel | virtual |
| getReactionId(size_t) | rrllvm::LLVMExecutableModel | virtual |
| getReactionIndex(const std::string &) | rrllvm::LLVMExecutableModel | virtual |
| getReactionRates(size_t len, int const *indx, double *values) | rrllvm::LLVMExecutableModel | virtual |
| getStateVector(double *stateVector) | rrllvm::LLVMExecutableModel | virtual |
| getStateVectorId(size_t index) | rrllvm::LLVMExecutableModel | virtual |
| getStateVectorRate(double time, const double *y, double *dydt=0) | rrllvm::LLVMExecutableModel | virtual |
| getStoichiometry(int index) | rrllvm::LLVMExecutableModel | virtual |
| getStoichiometry(int speciesIndex, int reactionIndex) | rrllvm::LLVMExecutableModel | virtual |
| getStoichiometryId(size_t) | rrllvm::LLVMExecutableModel | virtual |
| getStoichiometryIndex(const std::string &) | rrllvm::LLVMExecutableModel | virtual |
| getStoichiometryIndex(const std::string &speciesId, const std::string &reactionId) | rrllvm::LLVMExecutableModel | virtual |
| getSupportedIdTypes() | rrllvm::LLVMExecutableModel | virtual |
| getTime() (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| getValue(const std::string &id) | rrllvm::LLVMExecutableModel | virtual |
| INTEGRATION enum value | rr::ExecutableModel | |
| LLVMExecutableModel() | rrllvm::LLVMExecutableModel | |
| LLVMExecutableModel(const std::shared_ptr< ModelResources > &resources, LLVMModelData *modelData) | rrllvm::LLVMExecutableModel | |
| LLVMExecutableModel(std::istream &in, uint modelGeneratorOpt) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | |
| LLVMModelGenerator (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | friend |
| mIntegrationStartTime (defined in rr::ExecutableModel) | rr::ExecutableModel | protected |
| OPTIMIZE_REACTION_RATE_SELECTION enum value | rr::ExecutableModel | |
| print(std::ostream &stream) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| reset() | rrllvm::LLVMExecutableModel | virtual |
| reset(int options) | rrllvm::LLVMExecutableModel | virtual |
| resetEvents() (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| saveState(std::ostream &out) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setBoundarySpeciesAmounts(size_t len, int const *indx, double const *values) | rrllvm::LLVMExecutableModel | virtual |
| setBoundarySpeciesAmounts(size_t len, int const *indx, double const *values, bool strict) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setBoundarySpeciesConcentrations(size_t len, int const *indx, double const *values) | rrllvm::LLVMExecutableModel | virtual |
| setBoundarySpeciesInitAmounts(size_t len, const int *indx, double const *values) | rrllvm::LLVMExecutableModel | virtual |
| setBoundarySpeciesInitConcentrations(size_t len, const int *indx, double const *values) | rrllvm::LLVMExecutableModel | virtual |
| setCompartmentInitVolumes(size_t len, const int *indx, double const *values) | rrllvm::LLVMExecutableModel | virtual |
| setCompartmentVolumes(size_t len, int const *indx, const double *values) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setCompartmentVolumes(size_t len, int const *indx, const double *values, bool strict) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setConservedMoietyValues(size_t len, int const *indx, const double *values) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setEventListener(size_t index, rr::EventListenerPtr eventHandler) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setFlags(uint32_t val) | rrllvm::LLVMExecutableModel | inlinevirtual |
| setFloatingSpeciesAmounts(size_t len, int const *indx, const double *values) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setFloatingSpeciesAmounts(size_t len, int const *indx, const double *values, bool strict) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setFloatingSpeciesConcentrations(size_t len, int const *indx, double const *values) | rrllvm::LLVMExecutableModel | virtual |
| setFloatingSpeciesInitAmounts(size_t len, const int *indx, double const *values) | rrllvm::LLVMExecutableModel | virtual |
| setFloatingSpeciesInitConcentrations(size_t len, const int *indx, double const *values) | rrllvm::LLVMExecutableModel | virtual |
| setGlobalParameterInitValues(size_t len, const int *indx, double const *values) | rrllvm::LLVMExecutableModel | virtual |
| setGlobalParameterValues(size_t len, int const *indx, const double *values) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setGlobalParameterValues(size_t len, int const *indx, const double *values, bool strict) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setIntegration(bool value) | rr::ExecutableModel | inlineprotected |
| setIntegrationStartTime(double time) (defined in rr::ExecutableModel) | rr::ExecutableModel | virtual |
| setRandomSeed(int64_t) | rrllvm::LLVMExecutableModel | virtual |
| setStateVector(const double *stateVector) | rrllvm::LLVMExecutableModel | virtual |
| setStoichiometries(size_t len, int const *indx, const double *values) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setStoichiometries(size_t len, int const *indx, const double *values, bool strict) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setStoichiometry(int index, double value) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setStoichiometry(int speciesIndex, int reactionIndex, double value) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setTime(double _time) (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| setValue(const std::string &id, double value) | rrllvm::LLVMExecutableModel | virtual |
| testConstraints() (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
| ~ExecutableModel() | rr::ExecutableModel | inlinevirtual |
| ~LLVMExecutableModel() (defined in rrllvm::LLVMExecutableModel) | rrllvm::LLVMExecutableModel | virtual |
