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);

C_DECL_SPEC char* rrcCallConv  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);

// -----------------------------------------------------------------------
// 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 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 unLoadModel(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);

// -------------------------------------------------------------------------
// 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);


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 RRDataHandle rrcCallConv simulate(RRHandle handle);
C_DECL_SPEC RRCDataPtr rrcCallConv getSimulationResult(RRHandle handle);

C_DECL_SPEC RRDataHandle rrcCallConv getRoadRunnerData(RRHandle handle);

C_DECL_SPEC RRDataHandle 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 getBoundarySpeciesConcentrations(RRHandle handle);

// --------------------------------------------------------------------------------
// Parameter Group
// --------------------------------------------------------------------------------

C_DECL_SPEC RRVectorPtr rrcCallConv getGlobalParameterValues(RRHandle handle);

C_DECL_SPEC bool rrcCallConv setBoundarySpeciesByIndex(RRHandle handle, const 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 reset(RRHandle handle);

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);

// --------------------------------------------------------------------------------
// 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 getFloatingSpeciesIds(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);

// What's this, not sure if we need it?
C_DECL_SPEC bool rrcCallConv getScaledFloatingSpeciesElasticity(RRHandle handle, const char* reactionName, const char* speciesName, double* value);


#if defined( __cplusplus)
}
}//namespace

#endif

#endif