rrc_api.h

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#ifndef rrc_apiH
#define rrc_apiH
#include "rrc_exporter.h"
#include "rrc_types.h"
#include "rrc_utilities.h"
#include "rrc_logging_api.h"
#include "rrc_nom_api.h"
#include "rrc_libstruct_api.h"
 
#if defined(__cplusplus)
namespace rrc { extern "C" {
#endif
 
C_DECL_SPEC RRHandle rrcCallConv createRRInstance(void);
 
C_DECL_SPEC RRHandle rrcCallConv createRRInstanceEx(const char* tempFolder, const char* compiler);
 
C_DECL_SPEC bool rrcCallConv freeRRInstance(RRHandle handle);
 
char* getInstallFolder(void);
 
C_DECL_SPEC bool  rrcCallConv  setInstallFolder(const char* folder);
 
C_DECL_SPEC char* rrcCallConv getAPIVersion(void);
 
C_DECL_SPEC char* rrcCallConv getCPPAPIVersion(RRHandle handle);
 
C_DECL_SPEC int  rrcCallConv getVersion();
 
C_DECL_SPEC char*  rrcCallConv getVersionStr();
 
 
C_DECL_SPEC char*  rrcCallConv getVersionEx();
 
C_DECL_SPEC char*  rrcCallConv getExtendedAPIInfo();
 
C_DECL_SPEC char*  rrcCallConv getBuildDate(void);
 
C_DECL_SPEC char*  rrcCallConv getBuildTime(void);
 
C_DECL_SPEC char*  rrcCallConv getBuildDateTime(void);
 
C_DECL_SPEC char*  rrcCallConv getCopyright(void);
 
C_DECL_SPEC char*  rrcCallConv getInfo(RRHandle handle);
 
C_DECL_SPEC char* rrcCallConv getlibSBMLVersion(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv setTempFolder(RRHandle handle, const char* folder);
 
C_DECL_SPEC char* rrcCallConv getTempFolder(RRHandle handle);
 
C_DECL_SPEC char* rrcCallConv getWorkingDirectory(void);
 
C_DECL_SPEC char* rrcCallConv getRRCAPILocation(void);
 
 
C_DECL_SPEC bool rrcCallConv setCompiler(RRHandle handle, const char* fNameWithPath);
 
C_DECL_SPEC char* rrcCallConv getCompiler(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv setCompilerLocation(RRHandle handle, const char* folder);
 
C_DECL_SPEC char* rrcCallConv getCompilerLocation(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv setSupportCodeFolder(RRHandle handle, const char* folder);
 
C_DECL_SPEC char* rrcCallConv getSupportCodeFolder(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv setCodeGenerationMode(RRHandle handle, int mode);
 
 
C_DECL_SPEC bool rrcCallConv hasError(void);
 
C_DECL_SPEC char* rrcCallConv getLastError(void);
 
// Flags/Options
C_DECL_SPEC bool rrcCallConv setComputeAndAssignConservationLaws(RRHandle handle, const bool On_Or_Off);
 
C_DECL_SPEC int rrcCallConv getComputeAndAssignConservationLaws(RRHandle handle, int* value);
 
// -----------------------------------------------------------------------
// Read and Write models
// -----------------------------------------------------------------------
 
C_DECL_SPEC bool rrcCallConv loadSBML(RRHandle handle, const char* sbml);
 
C_DECL_SPEC bool rrcCallConv loadSBMLEx(RRHandle handle, const char* sbml, bool forceRecompile);
 
C_DECL_SPEC bool rrcCallConv saveState(RRHandle handle, const char* filename);
 
 
C_DECL_SPEC bool rrcCallConv loadState(RRHandle handle, const char* filename);
 
//C_DECL_SPEC bool rrcCallConv loadSBMLFromFile(const char* fileName);
C_DECL_SPEC bool rrcCallConv loadSBMLFromFile(RRHandle handle, const char* fileName);
 
C_DECL_SPEC bool rrcCallConv loadSBMLFromFileE(RRHandle handle, const char* fileName, bool forceRecompile);
 
C_DECL_SPEC bool rrcCallConv clearModel(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv isModelLoaded(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv loadSimulationSettings(RRHandle handle, const char* fileName);
 
C_DECL_SPEC char* rrcCallConv getCurrentSBML(RRHandle handle);
 
C_DECL_SPEC char* rrcCallConv getSBML(RRHandle handle);
 
 
// -------------------------------------------------------------------------------------
// Model editing methods
// -------------------------------------------------------------------------------------
 
 
C_DECL_SPEC bool rrcCallConv addSpecies(RRHandle handle, const char* sid, const char* compartment, double initialAmount, bool hasOnlySubstanceUnits, bool boundaryCondition);
 
C_DECL_SPEC bool rrcCallConv addSpeciesNoRegen(RRHandle handle, const char* sid, const char* compartment, double initialAmount, bool hasOnlySubstanceUnits, bool boundaryCondition);
 
 
C_DECL_SPEC bool rrcCallConv removeSpecies(RRHandle handle, const char* sid);
 
C_DECL_SPEC bool rrcCallConv removeSpeciesNoRegen(RRHandle handle, const char* sid);
 
C_DECL_SPEC bool rrcCallConv setBoundary(RRHandle handle, const char* sid, bool boundaryCondition);
 
C_DECL_SPEC bool rrcCallConv setBoundaryNoRegen(RRHandle handle, const char* sid, bool boundaryCondition);
 
 
C_DECL_SPEC bool rrcCallConv setHasOnlySubstanceUnits(RRHandle handle, const char* sid, bool hasOnlySubstanceUnits);
 
C_DECL_SPEC bool rrcCallConv setHasOnlySubstanceUnitsNoRegen(RRHandle handle, const char* sid, bool hasOnlySubstanceUnits);
 
 
 
C_DECL_SPEC bool rrcCallConv setInitAmount(RRHandle handle, const char* sid, double initAmount);
 
C_DECL_SPEC bool rrcCallConv setInitAmountNoRegen(RRHandle handle, const char* sid, double initAmount);
 
C_DECL_SPEC bool rrcCallConv setInitConcentration(RRHandle handle, const char* sid, double initConcentration);
 
C_DECL_SPEC bool rrcCallConv setInitConcentrationNoRegen(RRHandle handle, const char* sid, double initConcentration);
 
 
C_DECL_SPEC bool rrcCallConv setConstant(RRHandle handle, const char* sid, bool constant);
 
C_DECL_SPEC bool rrcCallConv setConstantNoRegen(RRHandle handle, const char* sid, bool constant);
 
 
C_DECL_SPEC bool rrcCallConv addReactionFromSBML(RRHandle handle, const char* sbmlRep);
 
C_DECL_SPEC bool rrcCallConv addReactionFromSBMLNoRegen(RRHandle handle, const char* sbmlRep);
 
C_DECL_SPEC bool rrcCallConv addReaction(RRHandle handle, const char* rid, const char** reactants, int numReactants,
    const char** products, int numProducts, const char* kineticLaw);
 
C_DECL_SPEC bool rrcCallConv addReactionNoRegen(RRHandle handle, const char* rid, const char** reactants, int numReactants,
    const char** products, int numProducts, const char* kineticLaw);
 
C_DECL_SPEC bool rrcCallConv removeReaction(RRHandle handle, const char* rid);
 
 
C_DECL_SPEC bool rrcCallConv removeReactionNoRegen(RRHandle handle, const char* rid);
 
C_DECL_SPEC bool rrcCallConv setReversible(RRHandle handle, const char* rid, bool reversible);
 
C_DECL_SPEC bool rrcCallConv setReversibleNoRegen(RRHandle handle, const char* rid, bool reversible);
 
 
C_DECL_SPEC bool rrcCallConv setKineticLaw(RRHandle handle, const char* rid, const char* kineticLaw);
 
C_DECL_SPEC bool rrcCallConv setKineticLawNoRegen(RRHandle handle, const char* rid, const char* kineticLaw);
 
 
C_DECL_SPEC char* rrcCallConv getKineticLaw(RRHandle handle, const char* rid);
 
C_DECL_SPEC bool rrcCallConv addParameter(RRHandle handle, const char* pid, double value);
C_DECL_SPEC bool rrcCallConv addParameterNoRegen(RRHandle handle, const char* pid, double value);
 
C_DECL_SPEC bool rrcCallConv removeParameter(RRHandle handle, const char* pid);
 
 
C_DECL_SPEC bool rrcCallConv removeParameterNoRegen(RRHandle handle, const char* pid);
 
 
C_DECL_SPEC bool rrcCallConv addCompartment(RRHandle handle, const char* cid, double initVolume);
C_DECL_SPEC bool rrcCallConv addCompartmentNoRegen(RRHandle handle, const char* cid, double initVolume);
 
 
C_DECL_SPEC bool rrcCallConv removeCompartment(RRHandle handle, const char* cid);
 
 
C_DECL_SPEC bool rrcCallConv removeCompartmentNoRegen(RRHandle handle, const char* cid);
 
 
 
C_DECL_SPEC bool rrcCallConv addAssignmentRule(RRHandle handle, const char* vid, const char* formula);
 
C_DECL_SPEC bool rrcCallConv addAssignmentRuleNoRegen(RRHandle handle, const char* vid, const char* formula);
 
C_DECL_SPEC bool rrcCallConv addRateRule(RRHandle handle, const char* vid, const char* formula);
 
C_DECL_SPEC bool rrcCallConv addRateRuleNoRegen(RRHandle handle, const char* vid, const char* formula);
 
C_DECL_SPEC bool rrcCallConv removeRules(RRHandle handle, const char* vid);
 
 
C_DECL_SPEC bool rrcCallConv removeRulesNoRegen(RRHandle handle, const char* vid);
 
C_DECL_SPEC bool rrcCallConv addEvent(RRHandle handle, const char* eid, bool useValuesFromTriggerTime, const char* trigger);
 
C_DECL_SPEC bool rrcCallConv addEventNoRegen(RRHandle handle, const char* eid, bool useValuesFromTriggerTime, const char* trigger);
 
C_DECL_SPEC bool rrcCallConv addTrigger(RRHandle handle, const char* eid, const char* trigger);
 
C_DECL_SPEC bool rrcCallConv addTriggerNoRegen(RRHandle handle, const char* eid, const char* trigger);
 
C_DECL_SPEC bool rrcCallConv setPersistent(RRHandle handle, const char* eid, bool persistent);
 
C_DECL_SPEC bool rrcCallConv setPersistentNoRegen(RRHandle handle, const char* eid, bool persistent);
 
 
C_DECL_SPEC bool rrcCallConv setTriggerInitialValue(RRHandle handle, const char* eid, bool initValue);
 
C_DECL_SPEC bool rrcCallConv setTriggerInitialValueNoRegen(RRHandle handle, const char* eid, bool initValue);
 
 
C_DECL_SPEC bool rrcCallConv addPriority(RRHandle handle, const char* eid, const char* priority);
 
C_DECL_SPEC bool rrcCallConv addPriorityNoRegen(RRHandle handle, const char* eid, const char* priority);
 
C_DECL_SPEC bool rrcCallConv addDelay(RRHandle handle, const char* eid, const char* delay);
 
C_DECL_SPEC bool rrcCallConv addDelayNoRegen(RRHandle handle, const char* eid, const char* delay);
 
C_DECL_SPEC bool rrcCallConv addEventAssignment(RRHandle handle, const char* eid, const char* vid, const char* formula);
 
C_DECL_SPEC bool rrcCallConv addEventAssignmentNoRegen(RRHandle handle, const char* eid, const char* vid, const char* formula);
 
C_DECL_SPEC bool rrcCallConv removeEventAssignments(RRHandle handle, const char* eid, const char* vid);
 
C_DECL_SPEC bool rrcCallConv removeEventAssignmentsNoRegen(RRHandle handle, const char* eid, const char* vid);
 
C_DECL_SPEC bool rrcCallConv removeEvent(RRHandle handle, const char* eid);
 
C_DECL_SPEC bool rrcCallConv removeEventsNoRegen(RRHandle handle, const char* eid);
 
C_DECL_SPEC bool rrcCallConv validateCurrentSBML(RRHandle handle);
 
 
// -------------------------------------------------------------------------
// SBML utility methods
// -----------------------------------------------------------------------
C_DECL_SPEC char* rrcCallConv getParamPromotedSBML(RRHandle handle, const char* sArg);
 
C_DECL_SPEC bool rrcCallConv setConfigurationXML (RRHandle handle, const char* caps);
 
C_DECL_SPEC char* rrcCallConv getConfigurationXML(RRHandle handle);
 
/* Registered Integrators *****************************************************/
 
C_DECL_SPEC int rrcCallConv getNumRegisteredIntegrators ();
 
C_DECL_SPEC char* rrcCallConv getRegisteredIntegratorName (int n);
 
C_DECL_SPEC char* rrcCallConv getRegisteredIntegratorHint (int n);
 
C_DECL_SPEC char* rrcCallConv getRegisteredIntegratorDescription (int n);
 
/* Instantiated Integrators ***************************************************/
 
C_DECL_SPEC int rrcCallConv getNumInstantiatedIntegrators (RRHandle handle);
 
C_DECL_SPEC int rrcCallConv setCurrentIntegrator (RRHandle handle, char *nameOfIntegrator);
 
C_DECL_SPEC char* rrcCallConv getCurrentIntegratorName (RRHandle handle);
 
C_DECL_SPEC char* rrcCallConv getCurrentIntegratorDescription (RRHandle handle);
 
C_DECL_SPEC char* rrcCallConv getCurrentIntegratorHint (RRHandle handle);
 
C_DECL_SPEC int rrcCallConv getNumberOfCurrentIntegratorParameters (RRHandle handle);
 
C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterName (RRHandle handle, int n);
 
C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterDescription (RRHandle handle, int n);
 
C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterDisplayName (RRHandle handle, int n);
 
C_DECL_SPEC char* rrcCallConv getCurrentIntegratorNthParameterHint (RRHandle handle, int n);
 
C_DECL_SPEC int rrcCallConv getCurrentIntegratorNthParameterType (RRHandle handle, int n);
 
C_DECL_SPEC int rrcCallConv resetCurrentIntegratorParameters (RRHandle handle);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getListOfCurrentIntegratorParameterNames (RRHandle handle);
 
C_DECL_SPEC char* rrcCallConv getCurrentIntegratorParameterDescription (RRHandle handle, char *parameterName);
 
C_DECL_SPEC char* rrcCallConv getCurrentIntegratorParameterHint (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterType (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterInt (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterInt (RRHandle handle, char *parameterName, int value);
 
C_DECL_SPEC unsigned int rrcCallConv getCurrentIntegratorParameterUInt (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterUInt (RRHandle handle, char *parameterName, unsigned int value);
 
C_DECL_SPEC double rrcCallConv getCurrentIntegratorParameterDouble (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterDouble (RRHandle handle, char *parameterName, double value);
 
C_DECL_SPEC char* rrcCallConv getCurrentIntegratorParameterString (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterString (RRHandle handle, char *parameterName, char* value);
 
C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterBoolean (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterBoolean (RRHandle handle, char *parameterName, int value);
 
 
C_DECL_SPEC int rrcCallConv getCurrentIntegratorParameterDoubleArray (RRHandle handle, char *parameterName, double** value, int* len);
 
C_DECL_SPEC int rrcCallConv setCurrentIntegratorParameterDoubleArray(RRHandle handle, char *parameterName, double* value, int len);
 
 
C_DECL_SPEC int rrcCallConv setCurrentIntegratorScalarConcentrationTolerance(RRHandle handle, double value);
 
 
C_DECL_SPEC int rrcCallConv setCurrentIntegratorVectorConcentrationTolerance(RRHandle handle, double* value, int len);
 
 
C_DECL_SPEC int rrcCallConv setCurrentIntegratorIndividualTolerance(RRHandle handle, char* sid, double value);
 
 
/* Steady State Solvers *******************************************************/
 
C_DECL_SPEC int rrcCallConv getNumRegisteredSteadyStateSolvers ();
 
C_DECL_SPEC char* rrcCallConv getRegisteredSteadyStateSolverName (int n);
 
C_DECL_SPEC char* rrcCallConv getRegisteredSteadyStateSolverHint (int n);
 
C_DECL_SPEC char* rrcCallConv getRegisteredSteadyStateSolverDescription (int n);
 
 
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolver (RRHandle handle, char *nameOfSteadyStateSolver);
 
C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverName (RRHandle handle);
 
C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverDescription (RRHandle handle);
 
C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverHint (RRHandle handle);
 
C_DECL_SPEC int rrcCallConv getNumberOfCurrentSteadyStateSolverParameters (RRHandle handle);
 
C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterName (RRHandle handle, int n);
 
C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterDisplayName (RRHandle handle, int n);
 
C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterDescription (RRHandle handle, int n);
 
C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverNthParameterHint (RRHandle handle, int n);
 
C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverNthParameterType (RRHandle handle, int n);
 
C_DECL_SPEC int rrcCallConv resetCurrentSteadyStateSolverParameters (RRHandle handle);
 
C_DECL_SPEC const char* rrcCallConv solverTypeToString (int code);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getListOfCurrentSteadyStateSolverParameterNames (RRHandle handle);
 
C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverParameterDescription (RRHandle handle, char *parameterName);
 
C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverParameterHint (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterType (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterInt (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterInt (RRHandle handle, char *parameterName, int value);
 
C_DECL_SPEC unsigned int rrcCallConv getCurrentSteadyStateSolverParameterUInt (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterUInt (RRHandle handle, char *parameterName, unsigned int value);
 
C_DECL_SPEC double rrcCallConv getCurrentSteadyStateSolverParameterDouble (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterDouble (RRHandle handle, char *parameterName, double value);
 
C_DECL_SPEC char* rrcCallConv getCurrentSteadyStateSolverParameterString (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterString (RRHandle handle, char *parameterName, char* value);
 
C_DECL_SPEC int rrcCallConv getCurrentSteadyStateSolverParameterBoolean (RRHandle handle, char *parameterName);
 
C_DECL_SPEC int rrcCallConv setCurrentSteadyStateSolverParameterBoolean (RRHandle handle, char *parameterName, int value);
 
 
C_DECL_SPEC bool rrcCallConv setTimeStart(RRHandle handle, double timeStart);
 
C_DECL_SPEC bool rrcCallConv setTimeEnd(RRHandle handle, double timeEnd);
 
C_DECL_SPEC bool rrcCallConv setNumPoints(RRHandle handle, int numberOfPoints);
 
 
C_DECL_SPEC bool rrcCallConv setTimeCourseSelectionList(RRHandle handle, const char* list);
//C_DECL_SPEC bool rrcCallConv setTimeCourseSelectionList(const char* list);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getTimeCourseSelectionList(RRHandle handle);
 
C_DECL_SPEC RRCDataPtr rrcCallConv simulate(RRHandle handle);
 
C_DECL_SPEC RRCDataPtr rrcCallConv getSimulationResult(RRHandle handle);
 
 
C_DECL_SPEC RRCDataPtr rrcCallConv simulateEx(RRHandle handle, const double timeStart, const double timeEnd, const int numberOfPoints);
 
C_DECL_SPEC bool rrcCallConv oneStep(RRHandle handle, const double currentTime, const double stepSize, double *value);
 
C_DECL_SPEC bool rrcCallConv getTimeStart(RRHandle handle, double* timeStart);
 
C_DECL_SPEC bool rrcCallConv getTimeEnd(RRHandle handle, double* timeEnd);
 
C_DECL_SPEC bool rrcCallConv getNumPoints (RRHandle handle, int* numPoints);
 
C_DECL_SPEC bool rrcCallConv steadyState(RRHandle handle, double* value);
 
C_DECL_SPEC RRVectorPtr rrcCallConv computeSteadyStateValues(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv setSteadyStateSelectionList(RRHandle handle, const char* list);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getSteadyStateSelectionList(RRHandle handle);
 
 
// --------------------------------------------------------------------------------
// Get and Set Routines
// --------------------------------------------------------------------------------
 
C_DECL_SPEC bool rrcCallConv getValue(RRHandle handle, const char* symbolId, double* value);
 
 
C_DECL_SPEC bool rrcCallConv setValue(RRHandle handle, const char* symbolId, const double value);
 
 
C_DECL_SPEC RRVectorPtr rrcCallConv getFloatingSpeciesConcentrations(RRHandle handle);
 
C_DECL_SPEC RRVectorPtr rrcCallConv getFloatingSpeciesAmounts(RRHandle handle);
 
 
C_DECL_SPEC RRVectorPtr rrcCallConv getBoundarySpeciesConcentrations(RRHandle handle);
 
C_DECL_SPEC RRVectorPtr rrcCallConv getBoundarySpeciesAmounts(RRHandle handle);
 
// --------------------------------------------------------------------------------
// Parameter Group
// --------------------------------------------------------------------------------
 
C_DECL_SPEC RRVectorPtr rrcCallConv getGlobalParameterValues(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv setBoundarySpeciesByIndex(RRHandle handle, const unsigned int index, const double value);
 
C_DECL_SPEC bool rrcCallConv setFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double value);
 
C_DECL_SPEC bool rrcCallConv getFloatingSpeciesInitialConcentrationByIndex(RRHandle handle, int index, double* value);
 
C_DECL_SPEC bool rrcCallConv setFloatingSpeciesByIndex(RRHandle handle, const int index, const double value);
 
C_DECL_SPEC bool rrcCallConv setGlobalParameterByIndex(RRHandle handle, const int index, const double value);
 
C_DECL_SPEC bool rrcCallConv getBoundarySpeciesByIndex(RRHandle handle, const int index, double* value);
 
C_DECL_SPEC bool rrcCallConv getFloatingSpeciesByIndex(RRHandle handle, const int index, double* value);
 
C_DECL_SPEC bool rrcCallConv getGlobalParameterByIndex(RRHandle handle, const int index, double* value);
 
C_DECL_SPEC bool rrcCallConv getCompartmentByIndex (RRHandle handle, const int index, double* value);
 
 
C_DECL_SPEC bool rrcCallConv setCompartmentByIndex (RRHandle handle, const int index, const double value);
 
 
C_DECL_SPEC bool rrcCallConv setFloatingSpeciesConcentrations(RRHandle handle, const RRVectorPtr vec);
 
C_DECL_SPEC bool rrcCallConv setBoundarySpeciesConcentrations(RRHandle handle, const RRVectorPtr vec);
 
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getFullJacobian(RRHandle handle);
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getReducedJacobian(RRHandle handle);
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getEigenvalues(RRHandle handle);
 
 
// --------------------------------------------------------------------------------
// Stoichiometry methods
// --------------------------------------------------------------------------------
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getStoichiometryMatrix(RRHandle handle);
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getLinkMatrix(RRHandle handle);
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getNrMatrix(RRHandle handle);
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getConservationMatrix(RRHandle handle);
 
// --------------------------------------------------------------------------------
// Initial condition Methods
// --------------------------------------------------------------------------------
 
C_DECL_SPEC bool rrcCallConv setFloatingSpeciesInitialConcentrations (RRHandle handle, const RRVectorPtr vec);
 
C_DECL_SPEC RRVectorPtr rrcCallConv getFloatingSpeciesInitialConcentrations (RRHandle handle);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesInitialConditionIds(RRHandle handle);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesInitialConcentrationIds(RRHandle handle);
 
 
// --------------------------------------------------------------------------------
// Reaction rates
// --------------------------------------------------------------------------------
 
C_DECL_SPEC int rrcCallConv getNumberOfReactions(RRHandle handle);
 
 
C_DECL_SPEC bool rrcCallConv getReactionRate(RRHandle handle, const int index, double* rate);
 
 
C_DECL_SPEC RRVectorPtr rrcCallConv getReactionRates(RRHandle handle);
 
 
C_DECL_SPEC RRVectorPtr rrcCallConv getReactionRatesEx (RRHandle handle, const RRVectorPtr vec);
 
 
C_DECL_SPEC RRVectorPtr rrcCallConv getRatesOfChange(RRHandle handle);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getRatesOfChangeIds(RRHandle handle);
 
 
C_DECL_SPEC bool rrcCallConv getRateOfChange(RRHandle handle, const int, double* value);
 
 
C_DECL_SPEC RRVectorPtr rrcCallConv getRatesOfChangeEx (RRHandle handle, const RRVectorPtr vec);
 
C_DECL_SPEC bool rrcCallConv evalModel(RRHandle handle);
 
// Get number family
C_DECL_SPEC int rrcCallConv getNumberOfCompartments (RRHandle handle);
 
 
C_DECL_SPEC int rrcCallConv getNumberOfBoundarySpecies(RRHandle handle);
 
 
C_DECL_SPEC int rrcCallConv getNumberOfFloatingSpecies(RRHandle handle);
 
 
C_DECL_SPEC int rrcCallConv getNumberOfGlobalParameters(RRHandle handle);
 
// --------------------------------------------------------------------------------
// Get number family
// --------------------------------------------------------------------------------
 
C_DECL_SPEC int rrcCallConv getNumberOfDependentSpecies(RRHandle handle);
 
 
C_DECL_SPEC int rrcCallConv getNumberOfIndependentSpecies(RRHandle handle);
 
// --------------------------------------------------------------------------------
// Get Ids family
// --------------------------------------------------------------------------------
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getReactionIds(RRHandle handle);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getBoundarySpeciesIds(RRHandle handle);
 
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getBoundarySpeciesConcentrationIds(RRHandle handle);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesIds(RRHandle handle);
 
 
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getDependentFloatingSpeciesIds(RRHandle handle);
 
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getFloatingSpeciesConcentrationIds(RRHandle handle);
 
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getGlobalParameterIds(RRHandle handle);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getCompartmentIds(RRHandle handle);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getEigenvalueIds(RRHandle handle);
 
C_DECL_SPEC RRListPtr rrcCallConv getAvailableTimeCourseSymbols(RRHandle handle);
 
C_DECL_SPEC RRListPtr rrcCallConv getAvailableSteadyStateSymbols(RRHandle handle);
 
// --------------------------------------------------------------------------------
// MCA methods
// --------------------------------------------------------------------------------
 
C_DECL_SPEC RRListPtr rrcCallConv getElasticityCoefficientIds(RRHandle handle);
 
C_DECL_SPEC RRListPtr rrcCallConv getUnscaledFluxControlCoefficientIds(RRHandle handle);
 
C_DECL_SPEC RRListPtr rrcCallConv getFluxControlCoefficientIds(RRHandle handle);
 
C_DECL_SPEC RRListPtr rrcCallConv getUnscaledConcentrationControlCoefficientIds(RRHandle handle);
 
C_DECL_SPEC RRListPtr rrcCallConv getConcentrationControlCoefficientIds(RRHandle handle);
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getUnscaledElasticityMatrix(RRHandle handle);
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getScaledElasticityMatrix(RRHandle handle);
 
 
C_DECL_SPEC bool rrcCallConv getScaledFloatingSpeciesElasticity(RRHandle handle, const char* reactionId, const char* speciesId, double* value);
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getUnscaledConcentrationControlCoefficientMatrix(RRHandle handle);
 
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getScaledConcentrationControlCoefficientMatrix(RRHandle handle);
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getUnscaledFluxControlCoefficientMatrix(RRHandle handle);
 
C_DECL_SPEC RRDoubleMatrixPtr rrcCallConv getScaledFluxControlCoefficientMatrix(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv getuCC (RRHandle handle, const char* variable, const char* parameter, double* value);
 
C_DECL_SPEC bool  rrcCallConv getCC (RRHandle handle, const char* variable, const char* parameter, double* value);
 
C_DECL_SPEC bool rrcCallConv getEE(RRHandle handle, const char* name, const char* species, double* value);
 
C_DECL_SPEC bool rrcCallConv getuEE(RRHandle handle, const char* name, const char* species, double* value);
 
// --------------------------------------------------------------------------------
// Stochastic methods
// --------------------------------------------------------------------------------
 
C_DECL_SPEC bool rrcCallConv getSeed(RRHandle handle, long* seed);
 
C_DECL_SPEC bool rrcCallConv setSeed(RRHandle handle, long seed);
 
C_DECL_SPEC RRCDataPtr rrcCallConv gillespie(RRHandle handle);
 
C_DECL_SPEC RRCDataPtr rrcCallConv gillespieEx(RRHandle handle, double timeStart, double timeEnd);
 
C_DECL_SPEC RRCDataPtr rrcCallConv gillespieOnGrid(RRHandle handle);
 
C_DECL_SPEC RRCDataPtr rrcCallConv gillespieOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfPoints);
 
C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanOnGrid(RRHandle handle, int numberOfSimulations);
 
C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfPoints, int numberOfSimulations);
 
C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanSDOnGrid(RRHandle handle, int numberOfSimulations);
 
 
C_DECL_SPEC RRCDataPtr rrcCallConv gillespieMeanSDOnGridEx(RRHandle handle, double timeStart, double timeEnd, int numberOfSteps, int numberOfSimulations);
 
// --------------------------------------------------------------------------------
// Reset methods
// --------------------------------------------------------------------------------
 
C_DECL_SPEC bool rrcCallConv reset(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv resetAll(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv resetToOrigin(RRHandle handle);
 
C_DECL_SPEC bool rrcCallConv resetParameter(RRHandle handle);
 
C_DECL_SPEC int rrcCallConv setConfigBool(const char* key, int value);
 
C_DECL_SPEC int rrcCallConv getConfigBool(const char* key);
 
C_DECL_SPEC int rrcCallConv setConfigInt(const char* key, int value);
 
C_DECL_SPEC int rrcCallConv getConfigInt(const char* key);
 
C_DECL_SPEC int rrcCallConv setConfigDouble(const char* key, double value);
 
 
//RRPlugins
C_DECL_SPEC int rrcCallConv _getNumIndFloatingSpecies(RRHandle handle);
 
C_DECL_SPEC int rrcCallConv _getNumRateRules(RRHandle handle);
 
C_DECL_SPEC double rrcCallConv _getTime(RRHandle handle);
 
C_DECL_SPEC int rrcCallConv _getStateVector(RRHandle handle);
 
C_DECL_SPEC void rrcCallConv _getStateVectorRate(RRHandle handle,double time, double *value);
 
 
C_DECL_SPEC double rrcCallConv getConfigDouble(const char* key);
 
C_DECL_SPEC RRStringArrayPtr rrcCallConv getListOfConfigKeys();
 
#if defined( __cplusplus)
}
}//namespace
 
#endif
 
#endif