libSBML C++ API
libSBML 5.17.2 C++ API
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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;
= static_cast<CompSBMLDocumentPlugin*>(document->
getPlugin(
"comp"));
model->
setId(
"aggregate");
submod1->
setId(
"submod1");
submod1->setModelRef("enzyme");
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:271
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:677
An SBML reaction between species in an SBML model.
Definition: Reaction.h:214
virtual int setName(const std::string &name)
Sets the value of the "name" attribute of this Model.
Definition: Model.cpp:736
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:603
int addProduct(const SpeciesReference *sr)
Adds a given SpeciesReference object as a product in this Reaction.
Definition: Reaction.cpp:843
A model used in model composition.
Definition: ModelDefinition.h:61
static SBMLExtensionRegister< CompExtension > compExtensionRegistry
Definition: CompExtension.cpp:100
int setFast(bool value)
Sets the value of the "fast" attribute of this Reaction.
Definition: Reaction.cpp:616
Definition of CompModelPlugin, the plugin class of comp package for the Model element.
virtual int setRequired(bool value)
Sets the bool value of "required" attribute of corresponding package in SBMLDocument element.
Definition: CompSBMLDocumentPlugin.cpp:599
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Compartment object.
Definition: Compartment.cpp:470
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:788
int setConstant(bool value)
Sets the "constant" attribute of this Species object.
Definition: Species.cpp:820
An SBML compartment, where species are located.
Definition: Compartment.h:480
Extension of SBMLDocument.
Definition: CompSBMLDocumentPlugin.h:84
Template class for extension package registration
Definition: SBMLExtensionRegister.h:64
int setSpecies(const std::string &sid)
Sets the "species" attribute of this SimpleSpeciesReference.
Definition: SimpleSpeciesReference.cpp:188
An SBML model.
Definition: Model.h:475
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Species.
Definition: Species.cpp:582
int addSubmodel(const Submodel *submodel)
Adds a copy of the given Submodel object to the list of submodels.
Definition: CompModelPlugin.cpp:266
SBMLDocument_t * readSBMLFromFile(const char *filename)
unsigned int checkConsistency()
Performs consistency checking and validation on this SBML document.
Definition: SBMLDocument.cpp:705
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:245
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:1199
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Submodel.
Definition: Submodel.cpp:169
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:394
unsigned int getNumFailsWithSeverity(unsigned int severity)
Returns the number of errors that have been logged with the given severity code.
Definition: SBMLErrorLog.cpp:333
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:512
int setStoichiometry(double value)
Sets the value of the "stoichiometry" attribute of this SpeciesReference.
Definition: SpeciesReference.cpp:303
Definition: SBMLError.h:964
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:1266
int setConstant(bool flag)
Sets the "constant" attribute of this SpeciesReference to the given boolean flag.
Definition: SpeciesReference.cpp:391
int addReaction(const Reaction *r)
Adds a copy of the given Reaction object to this Model.
Definition: Model.cpp:1386
Set of SBML Level + Version + namespace triples.
Definition: SBMLNamespaces.h:135
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:307
SBMLErrorLog * getErrorLog()
Returns the list of errors or warnings logged during parsing, consistency checking,...
Definition: SBMLDocument.cpp:1356
int setCompartment(const std::string &sid)
Sets the "compartment" attribute of this Species object.
Definition: Species.cpp:661
virtual int setId(const std::string &sid)
Sets the value of the "id" attribute of this Model.
Definition: Model.cpp:709
Compartment * createCompartment()
Creates a new Compartment inside this Model and returns it.
Definition: Model.cpp:1555
Extension of Model.
Definition: CompModelPlugin.h:77
void setConsistencyChecks(SBMLErrorCategory_t category, bool apply)
Controls the consistency checks that are performed when SBMLDocument::checkConsistency() is called.
Definition: SBMLDocument.cpp:683
An SBML species – a pool of entities.
Definition: Species.h:419
A model instance inside another model.
Definition: Submodel.h:146
int setSpatialDimensions(unsigned int value)
Sets the "spatialDimensions" attribute of this Compartment object.
Definition: Compartment.cpp:552
#define LIBSBML_CPP_NAMESPACE_USE
Definition: libsbml-namespace.h:63
Overall SBML container object.
Definition: SBMLDocument.h:338
int setSize(double value)
Sets the "size" attribute (or "volume" in SBML Level 1) of this Compartment object.
Definition: Compartment.cpp:601
int setBoundaryCondition(bool value)
Sets the "boundaryCondition" attribute of this Species object.
Definition: Species.cpp:787
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:3456
int setHasOnlySubstanceUnits(bool value)
Sets the "hasOnlySubstanceUnits" attribute of this Species object.
Definition: Species.cpp:767
Model * createModel(const std::string &sid="")
Creates a new Model inside this SBMLDocument, and returns a pointer to it.
Definition: SBMLDocument.cpp:635