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 |