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virtual std::string | getExecutableModelDesc () const |
| Returns a human-readable description of the code generation backend, e.g. LLVM, legacy C, etc. More...
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| CompiledExecutableModel (const ModelSymbols &symbols, ModelSharedLibrary *dll) |
| makes a copy of the ModelSymbols and keeps it. More...
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virtual bool | getConservedSumChanged () |
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virtual void | setConservedSumChanged (bool) |
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virtual std::string | getModelName () |
| get the name of the model
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virtual void | setTime (double _time) |
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virtual double | getTime () |
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virtual void | evalInitialConditions () |
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virtual void | reset () |
| reset the model to its original state
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virtual void | reset (int options) |
| reset the model accordign to a bitfield specified by the SelectionRecord::SelectionType values.
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virtual int | pushState (unsigned options=0) |
| A ExecutableModel holds a stack of states, the entire state of this model is pushed onto the saved state stack, and the current state remains unchanged. More...
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virtual int | popState (unsigned options=0) |
| restore the state from a previously saved state, if the state stack is empty, this has no effect. More...
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virtual int | getNumIndFloatingSpecies () |
| independent species do are not defined by rules, they typically participate in reactions and can have thier values set at any time.
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virtual int | getNumDepFloatingSpecies () |
| dependent species are defined by rules and the only way to change them is by changing the values on which they depend.
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virtual int | getNumFloatingSpecies () |
| total number of floating species.
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virtual int | getFloatingSpeciesIndex (const std::string &name) |
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virtual std::string | getFloatingSpeciesId (int index) |
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virtual int | getNumBoundarySpecies () |
| get the number of boundary species.
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virtual int | getBoundarySpeciesIndex (const std::string &name) |
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virtual std::string | getBoundarySpeciesId (int index) |
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virtual int | getBoundarySpeciesCompartmentIndex (int index) |
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virtual int | getFloatingSpeciesAmounts (int len, int const *indx, double *values) |
| get the floating species amounts More...
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virtual int | setFloatingSpeciesAmounts (int len, int const *indx, const double *values) |
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virtual int | getFloatingSpeciesConcentrations (int len, int const *indx, double *values) |
| get the floating species concentrations More...
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virtual int | setFloatingSpeciesConcentrations (int len, int const *indx, double const *values) |
| set the floating species concentrations More...
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virtual int | getFloatingSpeciesAmountRates (int len, int const *indx, double *values) |
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virtual int | getFloatingSpeciesConcentrationRates (int len, int const *indx, double *values) |
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virtual int | getBoundarySpeciesAmounts (int len, int const *indx, double *values) |
| get the boundary species amounts More...
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virtual int | getBoundarySpeciesConcentrations (int len, int const *indx, double *values) |
| get the boundary species concentrations More...
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virtual int | setBoundarySpeciesConcentrations (int len, int const *indx, double const *values) |
| set the boundary species concentrations More...
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virtual int | getNumGlobalParameters () |
| get the number of global parameters
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virtual int | getGlobalParameterIndex (const std::string &name) |
| index of the global parameter id, -1 if it does not exist.
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virtual std::string | getGlobalParameterId (int index) |
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virtual int | getGlobalParameterValues (int len, int const *indx, double *values) |
| get the global parameter values More...
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virtual int | setGlobalParameterValues (int len, int const *indx, const double *values) |
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virtual int | getNumCompartments () |
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virtual int | getCompartmentIndex (const std::string &name) |
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virtual std::string | getCompartmentId (int index) |
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virtual int | getCompartmentVolumes (int len, int const *indx, double *values) |
| get the compartment volumes More...
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virtual int | getNumRateRules () |
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virtual int | getNumReactions () |
| get the number of reactions the model has
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virtual int | getReactionRates (int len, const int *indx, double *values) |
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virtual int | getReactionIndex (const std::string &reactionName) |
| get the index of a named reaction More...
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virtual std::string | getReactionId (int index) |
| get the name of the specified reaction
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virtual int | getNumEvents () |
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virtual void | computeEventPriorites () |
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void | setConcentration (int index, double value) |
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virtual void | evalReactionRates () |
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virtual void | setCompartmentVolumes () |
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virtual int | getNumLocalParameters (int reactionId) |
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virtual void | computeRules () |
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virtual void | initializeInitialConditions () |
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virtual void | setParameterValues () |
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virtual void | setBoundaryConditions () |
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virtual void | setInitialConditions () |
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virtual void | evalInitialAssignments () |
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virtual void | convertToAmounts () |
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virtual void | computeConservedTotals () |
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virtual void | getRateRuleValues (double *rateRuleValues) |
| get the 'values' i.e. More...
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double | getAmount (const int i) |
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virtual void | initializeRates () |
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virtual std::string | getStateVectorId (int index) |
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virtual void | setRateRuleValues (const double *rateRuleValues) |
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virtual int | getStateVector (double *stateVector) |
| copies the internal model state std::vector into the provided buffer. More...
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virtual int | setStateVector (const double *stateVector) |
| sets the internal model state to the provided packed state std::vector. More...
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virtual void | convertToConcentrations () |
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virtual void | updateDependentSpeciesValues () |
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virtual void | computeAllRatesOfChange () |
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virtual void | getStateVectorRate (double time, const double *y, double *dydt=0) |
| the state std::vector y is the rate rule values and floating species concentrations concatenated. More...
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virtual void | evalEvents (const double time, const double *y) |
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virtual void | resetEvents () |
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virtual void | testConstraints () |
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virtual void | initializeRateRuleSymbols () |
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virtual std::string | getInfo () |
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virtual void | print (std::ostream &stream) |
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virtual void | getIds (int types, std::list< std::string > &ids) |
| populates a given list with all the ids that this class can accept. More...
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virtual int | getSupportedIdTypes () |
| returns a bit field of the ids that this class supports.
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virtual double | getValue (const std::string &id) |
| gets the value for the given id std::string. More...
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virtual void | setValue (const std::string &id, double value) |
| sets the value coresponding to the given selection stringl
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virtual int | getEventDelays (int len, int const *indx, double *values) |
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virtual int | getEventPriorities (int len, int const *indx, double *values) |
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virtual void | eventAssignment (int eventId) |
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virtual double * | evalEventAssignment (int eventId) |
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virtual void | applyEventAssignment (int eventId, double *values) |
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virtual int | getEventTriggers (int len, const int *indx, unsigned char *values) |
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virtual int | getNumConservedMoieties () |
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virtual int | getConservedMoietyIndex (const std::string &name) |
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virtual std::string | getConservedMoietyId (int index) |
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virtual int | getConservedMoietyValues (int len, int const *indx, double *values) |
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virtual int | setConservedMoietyValues (int len, int const *indx, const double *values) |
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virtual int | setCompartmentVolumes (int len, int const *indx, const double *values) |
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virtual int | setFloatingSpeciesInitConcentrations (int len, int const *indx, double const *values) |
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virtual int | getFloatingSpeciesInitConcentrations (int len, int const *indx, double *values) |
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virtual double | getStoichiometry (int speciesIndex, int reactionIndex) |
| Get the current stiochiometry value for the given species / reaction. More...
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virtual int | getStoichiometryMatrix (int *rows, int *cols, double **data) |
| allocate a block of memory and copy the stochiometric values into it, and return it. More...
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double | getFloatingSpeciesConcentration (int index) |
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bool | setupModelData () |
| initialize and allocate space for the ModelData buffers.
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virtual bool | setupDLLFunctions () |
| setup the function pointer variables to point to the C functions in the loaded shared library.
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std::vector< int > | retestEvents (const double &timeEnd, const std::vector< int > &handledEvents, std::vector< int > &removeEvents) |
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std::vector< int > | retestEvents (const double &timeEnd, std::vector< int > &handledEvents, const bool &assignOldState) |
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std::vector< int > | retestEvents (const double &timeEnd, const std::vector< int > &handledEvents, const bool &assignOldState, std::vector< int > &removeEvents) |
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virtual int | applyPendingEvents (double timeEnd) |
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virtual int | applyEvents (double timeEnd, const unsigned char *previousEventStatus, const double *initialState, double *finalState) |
| Itterate through all of the current and pending events and apply them. More...
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virtual void | getEventRoots (double time, const double *y, double *gdot) |
| evaluate the event 'roots' – when events transition form triggered - non-triggered or triggered to non-triggered state. More...
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virtual double | getNextPendingEventTime (bool pop) |
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virtual int | getPendingEventSize () |
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void | removePendingAssignmentForIndex (int eventIndex) |
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void | sortEventsByPriority (std::vector< Event > &firedEvents) |
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void | sortEventsByPriority (std::vector< int > &firedEvents) |
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virtual int | setFloatingSpeciesInitAmounts (int len, int const *indx, double const *values) |
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virtual int | getFloatingSpeciesInitAmounts (int len, int const *indx, double *values) |
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virtual int | setCompartmentInitVolumes (int len, int const *indx, double const *values) |
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virtual int | getCompartmentInitVolumes (int len, int const *indx, double *values) |
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virtual int | getEventIndex (const std::string &) |
| Gets the index for an event id. More...
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virtual std::string | getEventId (int) |
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virtual void | setEventListener (int, rr::EventListenerPtr) |
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virtual rr::EventListenerPtr | getEventListener (int) |
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virtual double | getFloatingSpeciesAmountRate (int index, const double *reactionRates) |
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virtual void | setRandomSeed (int64_t) |
| set the seed used by the random number generator. More...
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virtual int64_t | getRandomSeed () |
| get the seed used by the RNG.
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virtual double | getRandom () |
| Get a uniform random number between 0 and 1 created by the RNG. More...
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virtual uint32_t | getFlags () const |
| Get the current set of flags.
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virtual void | setFlags (uint32_t) |
| Set certain options that determine the state of the ExecutableModel, these are listed in.
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| ExecutableModel () |
| Returns a human-readable description of the code generation backend, e.g. LLVM, legacy C, etc. More...
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virtual std::string | getFloatingSpeciesId (size_t index)=0 |
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virtual int | getFloatingSpeciesAmounts (size_t len, int const *indx, double *values)=0 |
| get the floating species amounts More...
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virtual int | setFloatingSpeciesAmounts (size_t len, int const *indx, const double *values)=0 |
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virtual int | setFloatingSpeciesAmounts (size_t len, int const *indx, const double *values, bool strict)=0 |
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virtual int | getFloatingSpeciesAmountRates (size_t len, int const *indx, double *values)=0 |
| get the floating species amount rates More...
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virtual int | getFloatingSpeciesConcentrationRates (size_t len, int const *indx, double *values)=0 |
| get the floating species concentration rates More...
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virtual int | getFloatingSpeciesConcentrations (size_t len, int const *indx, double *values)=0 |
| get the floating species concentrations More...
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virtual int | setFloatingSpeciesConcentrations (size_t len, int const *indx, double const *values)=0 |
| set the floating species concentrations More...
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virtual int | setFloatingSpeciesInitConcentrations (size_t len, int const *indx, double const *values)=0 |
| Set the initial concentrations of the floating species. More...
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virtual int | getFloatingSpeciesInitConcentrations (size_t len, int const *indx, double *values)=0 |
| Get the initial concentrations of the floating species, uses the same indexing as the other floating species methods.
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virtual int | setFloatingSpeciesInitAmounts (size_t len, int const *indx, double const *values)=0 |
| Set the initial amounts of the floating species. More...
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virtual int | getFloatingSpeciesInitAmounts (size_t len, int const *indx, double *values)=0 |
| Get the initial amounts of the floating species, uses the same indexing as the other floating species methods.
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virtual std::string | getBoundarySpeciesId (size_t index)=0 |
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virtual int | getBoundarySpeciesAmounts (size_t len, int const *indx, double *values)=0 |
| get the boundary species amounts More...
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virtual int | getBoundarySpeciesConcentrations (size_t len, int const *indx, double *values)=0 |
| get the boundary species concentrations More...
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virtual int | setBoundarySpeciesConcentrations (size_t len, int const *indx, double const *values)=0 |
| set the boundary species concentrations More...
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virtual int | setBoundarySpeciesAmounts (size_t len, int const *indx, double const *values)=0 |
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virtual int | setBoundarySpeciesAmounts (size_t len, int const *indx, double const *values, bool strict)=0 |
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virtual int | setBoundarySpeciesInitConcentrations (size_t len, int const *indx, double const *values)=0 |
| Set the initial concentrations of the boundary species. More...
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virtual int | getBoundarySpeciesInitConcentrations (size_t len, int const *indx, double *values)=0 |
| Get the initial concentrations of the boundary species, uses the same indexing as the other boundary species methods.
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virtual int | setBoundarySpeciesInitAmounts (size_t len, int const *indx, double const *values)=0 |
| Set the initial amounts of the boundary species. More...
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virtual int | getBoundarySpeciesInitAmounts (size_t len, int const *indx, double *values)=0 |
| Get the initial amounts of the boundary species, uses the same indexing as the other boundary species methods.
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virtual std::string | getGlobalParameterId (size_t index)=0 |
| id of the indexed global parameter.
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virtual int | getGlobalParameterValues (size_t len, int const *indx, double *values)=0 |
| get the global parameter values More...
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virtual int | setGlobalParameterValues (size_t len, int const *indx, const double *values)=0 |
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virtual int | setGlobalParameterValues (size_t len, int const *indx, const double *values, bool strict)=0 |
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virtual int | setGlobalParameterInitValues (size_t len, int const *indx, double const *values)=0 |
| Set the initial value of the global parameter. More...
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virtual int | getGlobalParameterInitValues (size_t len, int const *indx, double *values)=0 |
| Get the initial amounts of the global parameter, uses the same indexing as the other global parameter methods.
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virtual int | getCompartmentIndexForFloatingSpecies (size_t index)=0 |
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virtual int | getCompartmentIndexForBoundarySpecies (size_t index)=0 |
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virtual std::string | getCompartmentId (size_t index)=0 |
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virtual int | getCompartmentVolumes (size_t len, int const *indx, double *values)=0 |
| get the compartment volumes More...
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virtual int | setCompartmentVolumes (size_t len, int const *indx, const double *values)=0 |
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virtual int | setCompartmentVolumes (size_t len, int const *indx, const double *values, bool strict)=0 |
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virtual int | setCompartmentInitVolumes (size_t len, int const *indx, double const *values)=0 |
| Set the initial volumes of the compartments. More...
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virtual int | getCompartmentInitVolumes (size_t len, int const *indx, double *values)=0 |
| Get the initial volume of the compartments, uses the same indexing as the other compartment methods.
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virtual int | setStoichiometries (size_t len, int const *indx, const double *values)=0 |
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virtual int | setStoichiometries (size_t len, int const *indx, const double *values, bool strict)=0 |
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virtual int | setStoichiometry (int index, double value)=0 |
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virtual int | setStoichiometry (int speciesIndex, int reactionIndex, double value)=0 |
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virtual double | getStoichiometry (int index)=0 |
| Get the current stiochiometry value with the given index. More...
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virtual std::string | getConservedMoietyId (size_t index)=0 |
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virtual int | getConservedMoietyValues (size_t len, int const *indx, double *values)=0 |
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virtual int | setConservedMoietyValues (size_t len, int const *indx, const double *values)=0 |
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virtual std::vector< std::string > | getRateRuleSymbols () const =0 |
| Gets the symbols defined by rate rules, i.e. returns all x such that x' = f(x) is a rule which defines parameter x. More...
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virtual std::string | getReactionId (size_t index)=0 |
| get the name of the specified reaction
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virtual int | getStoichiometryIndex (const std::string &)=0 |
| get the index of a named stoichiometry More...
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virtual int | getStoichiometryIndex (const std::string &, const std::string &)=0 |
| get the index of a named stoichiometry More...
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virtual std::string | getStoichiometryId (size_t index)=0 |
| get the name of the specified stoichiometry
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virtual int | getReactionRates (size_t len, int const *indx, double *values)=0 |
| get the std::vector of reaction rates. More...
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virtual int | getRateRuleRates (size_t len, int const *indx, double *values) |
| get the 'rates' i.e. More...
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virtual std::string | getStateVectorId (size_t index)=0 |
| get the id of an element of the state std::vector.
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virtual int | getEventTriggers (size_t len, const int *indx, unsigned char *values)=0 |
| get the event status, false if the even is not triggered, true if it is. More...
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virtual void | getPiecewiseTriggerRoots (double time, const double *y, double *gdot)=0 |
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virtual int | getNumPiecewiseTriggers ()=0 |
| We do root-finding for 'piecewise triggers': those times in a piecewise function that transition from one condition to the next.
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virtual | ~ExecutableModel () |
| need a virtual destructor as object implementing this interface can be deleted directly, i.e. More...
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virtual std::string | getEventId (size_t index)=0 |
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virtual void | getEventIds (std::list< std::string > &)=0 |
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virtual void | getAssignmentRuleIds (std::list< std::string > &)=0 |
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virtual void | getRateRuleIds (std::list< std::string > &)=0 |
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virtual void | getInitialAssignmentIds (std::list< std::string > &)=0 |
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virtual void | setEventListener (size_t index, EventListenerPtr eventHandler)=0 |
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virtual EventListenerPtr | getEventListener (size_t index)=0 |
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virtual double | getFloatingSpeciesAmountRate (size_t index, const double *reactionRates)=0 |
| Get the amount rate of change for the i'th floating species given a reaction rates std::vector. More...
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void | computeAllRatesOfChange () |
| for source compatability
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virtual void | saveState (std::ostream &out) |
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virtual void | setIntegrationStartTime (double time) |
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