libSBML C++ API
libSBML 5.18.0 C++ API
|
Example #1 from the SBML Level 3 Hierarchical Model Composition specification.
#include <iostream>
#include <sstream>
#ifdef WIN32
#include <conio.h>
#endif
using namespace std;
int main(int argc,char** argv)
{
int retval = 0;
model->
setId(
"aggregate");
submod1->
setId(
"submod1");
submod2.
setId(
"submod2");
delete document;
if (document == NULL)
{
cout << "Error reading back in file." << endl;
retval = -1;
}
else
{
{
stringstream errorstream;
cout << "Errors encoutered when round-tripping SBML file: \n"
<< errorstream.str() << endl;
retval = -1;
}
delete document;
}
#ifdef WIN32
if (retval != 0)
{
cout << "(Press any key to exit.)" << endl;
_getch();
}
#endif
return retval;
}
A reference to an SBML species in a reaction.
Definition: SpeciesReference.h:275
The registry class for tracking package extensions.
int setConstant(bool value)
Sets the value of the "constant" attribute of this Compartment object.
Definition: Compartment.cpp:681
An SBML reaction between species in an SBML model.
Definition: Reaction.h:218
virtual int setName(const std::string &name)
Sets the value of the "name" attribute of this Model.
Definition: Model.cpp:744
Include all SBML types in a single header file.
int setReversible(bool value)
Sets the value of the "reversible" attribute of this Reaction.
Definition: Reaction.cpp:607
int addProduct(const SpeciesReference *sr)
Adds a given SpeciesReference object as a product in this Reaction.
Definition: Reaction.cpp:847
A model used in model composition.
Definition: ModelDefinition.h:65
static SBMLExtensionRegister< CompExtension > compExtensionRegistry
Definition: CompExtension.cpp:104
Model * createModel(const std::string sid="")
Creates a new Model inside this SBMLDocument, and returns a pointer to it.
Definition: SBMLDocument.cpp:643
int setFast(bool value)
Sets the value of the "fast" attribute of this Reaction.
Definition: Reaction.cpp:620
Definition of CompModelPlugin, the plugin class of comp package for the Model element.
SBMLErrorLog * getErrorLog()
Returns the list of errors or warnings logged during parsing, consistency checking,...
Definition: SBMLDocument.cpp:1364
virtual int setRequired(bool value)
Sets the bool value of "required" attribute of corresponding package in SBMLDocument element.
Definition: CompSBMLDocumentPlugin.cpp:603
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Compartment object.
Definition: Compartment.cpp:474
int writeSBMLToFile(const SBMLDocument_t *d, const char *filename)
Writes the given SBML document d to the file filename.
int addReactant(const SpeciesReference *sr)
Adds a given SpeciesReference object as a reactant in this Reaction.
Definition: Reaction.cpp:792
int setConstant(bool value)
Sets the "constant" attribute of this Species object.
Definition: Species.cpp:824
An SBML compartment, where species are located.
Definition: Compartment.h:484
Extension of SBMLDocument.
Definition: CompSBMLDocumentPlugin.h:88
Template class for extension package registration
Definition: SBMLExtensionRegister.h:68
int setSpecies(const std::string &sid)
Sets the "species" attribute of this SimpleSpeciesReference.
Definition: SimpleSpeciesReference.cpp:192
An SBML model.
Definition: Model.h:479
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Species.
Definition: Species.cpp:586
int addSubmodel(const Submodel *submodel)
Adds a copy of the given Submodel object to the list of submodels.
Definition: CompModelPlugin.cpp:270
SBMLDocument_t * readSBMLFromFile(const char *filename)
unsigned int checkConsistency()
Performs consistency checking and validation on this SBML document.
Definition: SBMLDocument.cpp:713
Definition of CompSBMLDocumentPlugin, the plugin class of comp package for the Model element.
virtual int setModelRef(const std::string &modelRef)
Sets the value of the "modelRef" attribute of this Submodel.
Definition: Submodel.cpp:249
void printErrors(std::ostream &stream=std::cerr) const
Prints all the errors or warnings encountered trying to parse, check, or translate this SBML document...
Definition: SBMLDocument.cpp:1207
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Submodel.
Definition: Submodel.cpp:173
Definition of CompExtension, the core module of comp package.
ModelDefinition * createModelDefinition()
Creates a ModelDefinition object, adds it to the end of the ModelDefinition objects list and returns ...
Definition: CompSBMLDocumentPlugin.cpp:398
unsigned int getNumFailsWithSeverity(unsigned int severity)
Returns the number of errors that have been logged with the given severity code.
Definition: SBMLErrorLog.cpp:337
Definition of CompSBasePlugin, the plugin class of comp package for the Model element.
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Reaction.
Definition: Reaction.cpp:516
int setStoichiometry(double value)
Sets the value of the "stoichiometry" attribute of this SpeciesReference.
Definition: SpeciesReference.cpp:307
@ LIBSBML_CAT_UNITS_CONSISTENCY
Definition: SBMLError.h:970
Template class for registering extension packages.
int addSpecies(const Species *s)
Adds a copy of the given Species object to this Model.
Definition: Model.cpp:1274
int setConstant(bool flag)
Sets the "constant" attribute of this SpeciesReference to the given boolean flag.
Definition: SpeciesReference.cpp:395
int addReaction(const Reaction *r)
Adds a copy of the given Reaction object to this Model.
Definition: Model.cpp:1394
Set of SBML Level + Version + namespace triples.
Definition: SBMLNamespaces.h:139
Submodel * createSubmodel()
Creates a Submodel object, adds it to the end of the submodel objects list and returns a pointer to t...
Definition: CompModelPlugin.cpp:311
int setCompartment(const std::string &sid)
Sets the "compartment" attribute of this Species object.
Definition: Species.cpp:665
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Model.
Definition: Model.cpp:717
Compartment * createCompartment()
Creates a new Compartment inside this Model and returns it.
Definition: Model.cpp:1563
Extension of Model.
Definition: CompModelPlugin.h:81
void setConsistencyChecks(SBMLErrorCategory_t category, bool apply)
Controls the consistency checks that are performed when SBMLDocument::checkConsistency() is called.
Definition: SBMLDocument.cpp:691
An SBML species – a pool of entities.
Definition: Species.h:423
A model instance inside another model.
Definition: Submodel.h:150
int setSpatialDimensions(unsigned int value)
Sets the "spatialDimensions" attribute of this Compartment object.
Definition: Compartment.cpp:556
#define LIBSBML_CPP_NAMESPACE_USE
Definition: libsbml-namespace.h:67
Overall SBML container object.
Definition: SBMLDocument.h:342
int setSize(double value)
Sets the "size" attribute (or "volume" in SBML Level 1) of this Compartment object.
Definition: Compartment.cpp:605
int setBoundaryCondition(bool value)
Sets the "boundaryCondition" attribute of this Species object.
Definition: Species.cpp:791
SBasePlugin * getPlugin(const std::string &package)
Returns a plug-in object (extension interface) for an SBML Level 3 package extension with the given p...
Definition: SBase.cpp:3460
int setHasOnlySubstanceUnits(bool value)
Sets the "hasOnlySubstanceUnits" attribute of this Species object.
Definition: Species.cpp:771