mcell/include/nfsim_c.h

#ifndef NFSIM_CONNECTOR_H 
#define NFSIM_CONNECTOR_H 


//generic map

#ifdef __cplusplus
extern "C" {
#endif

    //helper structures from querying information from the c++ map containing the results
   
    

    //helper structures for the querying methods

    struct resultEntry{
        char* label;
        char* compartment;
        char* originalCompartment;
    };

    struct queryResults{
        int numOfResults;
        //struct resultEntry* results;
        void** results;
    };

    struct reactionResult{
        char** reactionNames;
        double* rates;
    };

    struct observableResults{
        char** observableNames;
        double* observableValues;
        int numResults;
    };


    typedef struct queryResults queryResults;
    typedef struct reactionResult reactionResult;
    typedef struct observableResults observableResults;

    struct observableSetResults{
        observableResults* dataPoints;
        double* timePoints;
        int numTimepoints;
    };


    struct reactantQueryResults{
        int numOfResults;
        char** keys;
        int* numOfAssociatedReactions;
        reactionResult* associatedReactions;
    };

    struct queryOptions{
        const char** initKeys;
        const int* initValues;

        const char** optionKeys;
        char** optionValues;

        int numOfInitElements;
        int numOfOptions;
    };

    struct compartmentStruct{
        char* name;
        int spatialDimensions;
        double size;
        char* outside;
    };

    typedef struct compartmentStruct compartmentStruct;
    typedef struct queryOptions queryOptions;
    typedef struct reactantQueryResults reactantQueryResults;



    //loads up an xml file and keeps it in memory
    int setupNFSim_c(const char*,int);

    //restores the nfsim system before molecule seeding
    int resetSystem_c();

    //calls destructors
    int deleteNFSimSystem_c();

    //seeds the nfsim system with an xml string
    int initSystemXML_c(const char*);
    //seeds the nfsim system with an array of hnauty labels- int pairs
    int initSystemNauty_c(const char**, const int*, int);



    
    //TODO: These functions are specific to the nfsim-mcell implementation. In a future implementation
    // it might be better to implement them directly into the mcell framework.

    //update a seeding table that keeps track of molecules we will use to initialize the system
    int constructNauty_c(const char*, const int);

    //init a system from the incremental list mantained through constructNauty
    int initFromConstruct_c();

    //store the current observable set in a list
    int logNFSimObservables_c(double time);
    int logNFSimReactions_c(const char*);
    //stream observableSet to file
    int outputNFSimObservables_c();
    int outputNFSimObservablesF_c(const char*);
    int outputNFSimReactionsF_c(const char* outputfilename);
    
    //END NFSim-mcell specific functions

    //returns those molecules in the system that are participants in a reaction with <param> reactants that can be fired
    void queryByNumReactant_c(const int, void*);

    //convenience function that calls reset, initNauty and queryByNumReactant
    void  initAndQueryByNumReactant_c(const queryOptions, void*);

    //convenience function that calls reset, init, step and query
    void initAndQuerySystemStatus_c(const queryOptions, void*);

    //given a nauty species string return the compartment information
    const char* extractSpeciesCompartmentFromNauty_c(const char* nauty);

    //returns all possible complexes in the current system
    void querySystemStatus_c(const char* option, void*);

    observableResults queryObservables_c();

    //perform one simulation step
    int stepSimulation_c();
    //performs exactly one simulation step by firying reaction rxn
    int stepSimulationRxn_c(const char* rxn);

    //frees up the reactantQueryResults object
    int delete_reactantQueryResults(reactantQueryResults);
    int delete_compartmentStructs(compartmentStruct);

    //gets information about a bionetgen compartment
    compartmentStruct getCompartmentInformation_c(const char* name);
    void freeCompartmentInformation_c(compartmentStruct*);

#ifdef __cplusplus
}
#endif


#endif