antimony_api.h

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#ifndef ANTIMONY_API_H
#define ANTIMONY_API_H

#ifndef LIBANTIMONY_VERSION_STRING //Should be defined in the makefile (from CMakeLists.txt)
#define LIBANTIMONY_VERSION_STRING "v2.8.0"
#endif

#include "libutil.h"
#include "enums.h"

BEGIN_C_DECLS
LIB_EXTERN long   loadFile(const char* filename);

LIB_EXTERN long   loadString(const char* model);

LIB_EXTERN long   loadAntimonyFile(const char* filename);

LIB_EXTERN long   loadAntimonyString(const char* model);

#ifndef NSBML

LIB_EXTERN long   loadSBMLFile(const char* filename);

LIB_EXTERN long   loadSBMLString(const char* model);

LIB_EXTERN long   loadSBMLStringWithLocation(const char* model, const char* location);
#endif

#ifndef NCELLML

LIB_EXTERN long   loadCellMLFile(const char* filename);

LIB_EXTERN long   loadCellMLString(const char* model);
#endif


LIB_EXTERN unsigned long getNumFiles();

LIB_EXTERN bool   revertTo(long index);

LIB_EXTERN void   clearPreviousLoads();

LIB_EXTERN void   addDirectory(const char* directory);

LIB_EXTERN void   clearDirectories();


LIB_EXTERN int   writeAntimonyFile(const char* filename, const char* moduleName);

LIB_EXTERN char* getAntimonyString(const char* moduleName);

#ifndef NSBML

LIB_EXTERN int   writeSBMLFile(const char* filename, const char* moduleName);
LIB_EXTERN char* getSBMLString(const char* moduleName);

#ifdef USE_COMP

LIB_EXTERN int   writeCompSBMLFile(const char* filename, const char* moduleName);
LIB_EXTERN char* getCompSBMLString(const char* moduleName);
#endif //USE_COMP
#endif //NSBML

#ifndef NCELLML

LIB_EXTERN int   writeCellMLFile(const char* filename, const char* moduleName);
LIB_EXTERN char* getCellMLString(const char* moduleName);
#endif

/*
 * Writes out a jarnac-formatted file containing a 'flattened' version of the current module (one where all the species and reactions are listed in the same model).  This has *not* been very extensively tested, and many aspects of the model may be dropped.  But the basics should be there.  Returns 1 on success, 0 on failure (and sets an error).
 */
//LIB_EXTERN int   writeJarnacFile(const char* filename, const char* moduleName);

/*
 * Returns the same output as writeJarnacFile, but to a char* array instead of to a file.
 */
//LIB_EXTERN char* getJarnacString(const char* moduleName);


LIB_EXTERN void printAllDataFor(const char* moduleName);
LIB_EXTERN bool   checkModule(const char* moduleName);

LIB_EXTERN char*  getLastError();

LIB_EXTERN char*  getWarnings();

#ifndef NSBML

LIB_EXTERN char* getSBMLInfoMessages(const char* moduleName);

LIB_EXTERN char* getSBMLWarnings(const char* moduleName);
#endif

LIB_EXTERN unsigned long getNumModules();

LIB_EXTERN char** getModuleNames();

LIB_EXTERN char*  getNthModuleName(unsigned long n);

LIB_EXTERN char*  getMainModuleName();
LIB_EXTERN unsigned long getNumSymbolsInInterfaceOf(const char* moduleName);

LIB_EXTERN char** getSymbolNamesInInterfaceOf(const char* moduleName);

LIB_EXTERN char* getNthSymbolNameInInterfaceOf(const char* moduleName, unsigned long n);
LIB_EXTERN unsigned long getNumReplacedSymbolNames(const char* moduleName);

LIB_EXTERN char*** getAllReplacementSymbolPairs(const char* moduleName);

LIB_EXTERN char** getNthReplacementSymbolPair(const char* moduleName, unsigned long n);

LIB_EXTERN char* getNthFormerSymbolName(const char* moduleName, unsigned long n);

LIB_EXTERN char* getNthReplacementSymbolName(const char* moduleName, unsigned long n);


LIB_EXTERN unsigned long getNumReplacedSymbolNamesBetween(const char* moduleName, const char* formerSubmodName, const char* replacementSubmodName);

LIB_EXTERN char*** getAllReplacementSymbolPairsBetween(const char* moduleName, const char* formerSubmodName, const char* replacementSubmodName, unsigned long n);

LIB_EXTERN char** getNthReplacementSymbolPairBetween(const char* moduleName, const char* formerSubmodName, const char* replacementSubmodName, unsigned long n);

LIB_EXTERN char* getNthFormerSymbolNameBetween(const char* moduleName, const char* formerSubmodName, const char* replacementSubmodName, unsigned long n);

LIB_EXTERN char* getNthReplacementSymbolNameBetween(const char* moduleName, const char* formerSubmodName, const char* replacementSubmodName, unsigned long n);
LIB_EXTERN unsigned long getNumSymbolsOfType(const char* moduleName, return_type rtype);

LIB_EXTERN char** getSymbolNamesOfType(const char* moduleName, return_type rtype);

LIB_EXTERN char** getSymbolDisplayNamesOfType(const char* moduleName, return_type rtype);

LIB_EXTERN char** getSymbolEquationsOfType(const char* moduleName, return_type rtype);


LIB_EXTERN char** getSymbolInitialAssignmentsOfType(const char* moduleName, return_type rtype);

LIB_EXTERN char** getSymbolAssignmentRulesOfType(const char* moduleName, return_type rtype);

LIB_EXTERN char** getSymbolRateRulesOfType(const char* moduleName, return_type rtype);

LIB_EXTERN char** getSymbolCompartmentsOfType(const char* moduleName, return_type rtype);

LIB_EXTERN char*  getNthSymbolNameOfType(const char* moduleName, return_type rtype, unsigned long n);

LIB_EXTERN char*  getNthSymbolDisplayNameOfType(const char* moduleName, return_type rtype, unsigned long n);

LIB_EXTERN char*  getNthSymbolEquationOfType(const char* moduleName, return_type rtype, unsigned long n);

LIB_EXTERN char*  getNthSymbolInitialAssignmentOfType(const char* moduleName, return_type rtype, unsigned long n);

LIB_EXTERN char*  getNthSymbolAssignmentRuleOfType(const char* moduleName, return_type rtype, unsigned long n);

LIB_EXTERN char*  getNthSymbolRateRuleOfType(const char* moduleName, return_type rtype, unsigned long n);

LIB_EXTERN char*  getNthSymbolCompartmentOfType(const char* moduleName, return_type rtype, unsigned long n);

LIB_EXTERN return_type getTypeOfSymbol(const char* moduleName, const char* symbolName);

LIB_EXTERN formula_type getTypeOfEquationForSymbol(const char* moduleName, const char* symbolName);

LIB_EXTERN char*   getCompartmentForSymbol(const char* moduleName, const char* symbolName);
LIB_EXTERN unsigned long getNumReactions(const char* moduleName);

LIB_EXTERN unsigned long getNumReactants(const char* moduleName, unsigned long rxn);

LIB_EXTERN unsigned long getNumProducts(const char* moduleName, unsigned long rxn);

LIB_EXTERN char*** getReactantNames(const char* moduleName);

LIB_EXTERN char**  getNthReactionReactantNames(const char* modulename, unsigned long rxn);

LIB_EXTERN char*  getNthReactionMthReactantName(const char* modulename, unsigned long rxn, unsigned long reactant);

LIB_EXTERN char*** getProductNames(const char* moduleName);

LIB_EXTERN char**  getNthReactionProductNames(const char* modulename, unsigned long rxn);

LIB_EXTERN char*  getNthReactionMthProductName(const char* modulename, unsigned long rxn, unsigned long product);

LIB_EXTERN double** getReactantStoichiometries(const char* moduleName);

LIB_EXTERN double** getProductStoichiometries(const char* moduleName);

LIB_EXTERN double* getNthReactionReactantStoichiometries(const char* moduleName, unsigned long rxn);

LIB_EXTERN double* getNthReactionProductStoichiometries(const char* moduleName, unsigned long rxn);

LIB_EXTERN double getNthReactionMthReactantStoichiometries(const char* moduleName, unsigned long rxn, unsigned long reactant);

LIB_EXTERN double getNthReactionMthProductStoichiometries(const char* moduleName, unsigned long rxn, unsigned long product);

LIB_EXTERN unsigned long getNumInteractions(const char* moduleName);

LIB_EXTERN unsigned long getNumInteractors(const char* moduleName, unsigned long rxn);

LIB_EXTERN unsigned long getNumInteractees(const char* moduleName, unsigned long rxn);

LIB_EXTERN char*** getInteractorNames(const char* moduleName);

LIB_EXTERN char**  getNthInteractionInteractorNames(const char* modulename, unsigned long rxn);

LIB_EXTERN char*  getNthInteractionMthInteractorName(const char* modulename, unsigned long interaction, unsigned long interactor);

LIB_EXTERN char*** getInteracteeNames(const char* moduleName);

LIB_EXTERN char**  getNthInteractionInteracteeNames(const char* modulename, unsigned long rxn);

LIB_EXTERN char*  getNthInteractionMthInteracteeName(const char* modulename, unsigned long interaction, unsigned long interactee);

LIB_EXTERN rd_type* getInteractionDividers(const char* moduleName);

LIB_EXTERN rd_type  getNthInteractionDivider(const char* moduleName, unsigned long n);

LIB_EXTERN double** getStoichiometryMatrix(const char* moduleName);

LIB_EXTERN char**   getStoichiometryMatrixRowLabels(const char* moduleName);

LIB_EXTERN char**   getStoichiometryMatrixColumnLabels(const char* moduleName);

LIB_EXTERN unsigned long   getStoichiometryMatrixNumRows(const char* moduleName);

LIB_EXTERN unsigned long   getStoichiometryMatrixNumColumns(const char* moduleName);


LIB_EXTERN unsigned long   getNumReactionRates(const char* moduleName);

LIB_EXTERN char**   getReactionRates(const char* moduleName);

LIB_EXTERN char*    getNthReactionRate(const char* moduleName, unsigned long rxn);

LIB_EXTERN unsigned long  getNumEvents(const char* moduleName);

LIB_EXTERN char**  getEventNames(const char* moduleName);

LIB_EXTERN char*   getNthEventName(const char* moduleName, unsigned long event);

LIB_EXTERN unsigned long  getNumAssignmentsForEvent(const char* moduleName, unsigned long event);

LIB_EXTERN char*   getTriggerForEvent(const char* moduleName, unsigned long event);

LIB_EXTERN char*   getDelayForEvent(const char* moduleName, unsigned long event);

LIB_EXTERN bool    getEventHasDelay(const char* moduleName, unsigned long event);

LIB_EXTERN char*   getPriorityForEvent(const char* moduleName, unsigned long event);

LIB_EXTERN bool    getEventHasPriority(const char* moduleName, unsigned long event);

LIB_EXTERN bool   getPersistenceForEvent(const char* moduleName, unsigned long event);

LIB_EXTERN bool   getT0ForEvent(const char* moduleName, unsigned long event);

LIB_EXTERN bool   getFromTriggerForEvent(const char* moduleName, unsigned long event);

LIB_EXTERN char*   getNthAssignmentVariableForEvent(const char* moduleName, unsigned long event, unsigned long n);

LIB_EXTERN char*   getNthAssignmentEquationForEvent(const char* moduleName, unsigned long event, unsigned long n);
LIB_EXTERN unsigned long  getNumDNAStrands(const char* moduleName);

LIB_EXTERN unsigned long* getDNAStrandSizes(const char* moduleName);

LIB_EXTERN unsigned long getSizeOfNthDNAStrand(const char* moduleName, unsigned long n);

LIB_EXTERN char*** getDNAStrands(const char* moduleName);

LIB_EXTERN char**  getNthDNAStrand(const char* moduleName, unsigned long n);

LIB_EXTERN bool    getIsNthDNAStrandOpen(const char* moduleName, unsigned long n, bool upstream);

LIB_EXTERN unsigned long  getNumModularDNAStrands(const char* moduleName);

LIB_EXTERN unsigned long* getModularDNAStrandSizes(const char* moduleName);

LIB_EXTERN char*** getModularDNAStrands(const char* moduleName);

LIB_EXTERN char**  getNthModularDNAStrand(const char* moduleName, unsigned long n);

LIB_EXTERN bool    getIsNthModularDNAStrandOpen(const char* moduleName, unsigned long n, bool upstream);

LIB_EXTERN void freeAll();

LIB_EXTERN bool addDefaultInitialValues(const char* moduleName);

LIB_EXTERN void setBareNumbersAreDimensionless(bool dimensionless);

END_C_DECLS

#endif //ANTIMONY_API_H