libSBML C++ API  5.18.0
spec_example3.cpp

Example #3 from the SBML Level 3 Hierarchical Model Composition specification.

/**
* @file spec_example3.cpp
* @brief SBML hierarchical composition example
* @author Lucian Smith
*
* <!--------------------------------------------------------------------------
* This sample program is distributed under a different license than the rest
* of libSBML. This program uses the open-source MIT license, as follows:
*
* Copyright (c) 2013-2018 by the California Institute of Technology
* (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
* and the University of Heidelberg (Germany), with support from the National
* Institutes of Health (USA) under grant R01GM070923. All rights reserved.
*
* Permission is hereby granted, free of charge, to any person obtaining a
* copy of this software and associated documentation files (the "Software"),
* to deal in the Software without restriction, including without limitation
* the rights to use, copy, modify, merge, publish, distribute, sublicense,
* and/or sell copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
* THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
* DEALINGS IN THE SOFTWARE.
*
* Neither the name of the California Institute of Technology (Caltech), nor
* of the European Bioinformatics Institute (EMBL-EBI), nor of the University
* of Heidelberg, nor the names of any contributors, may be used to endorse
* or promote products derived from this software without specific prior
* written permission.
* ------------------------------------------------------------------------ -->
*/
#include <iostream>
#include <sstream>
#include <sbml/SBMLTypes.h>
#ifdef WIN32
#include <conio.h>
#endif
using namespace std;
int main(int argc,char** argv)
{
int retval = 0;
SBMLNamespaces sbmlns(3,1,"comp",1);
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
//Define the external model definition
= static_cast<CompSBMLDocumentPlugin*>(document->getPlugin("comp"));
compdoc->setRequired(true);
extmod->setId("ExtMod1");
extmod->setSource("enzyme_model.xml");
extmod->setModelRef("enzyme");
//Define the 'simple' model
mod1->setId("simple");
comp->setSpatialDimensions((unsigned int)3);
comp->setConstant(true);
comp->setId("comp");
comp->setSize(1L);
// We have to construct it this way because we get the comp
// plugin from it later.
Species spec(&sbmlns);
spec.setCompartment("comp");
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
mod1->addSpecies(&spec);
spec.setId("D");
mod1->addSpecies(&spec);
Reaction rxn(&sbmlns);
rxn.setReversible(true);
rxn.setFast(false);
rxn.setId("J0");
SpeciesReference sr(&sbmlns);
sr.setConstant(true);
sr.setSpecies("S");
rxn.addReactant(&sr);
sr.setSpecies("D");
rxn.addProduct(&sr);
mod1->addReaction(&rxn);
CompModelPlugin* mod1plug
= static_cast<CompModelPlugin*>(mod1->getPlugin("comp"));
Port port;
port.setId("S_port");
port.setIdRef("S");
mod1plug->addPort(&port);
Port* port2 = mod1plug->createPort();
port2->setId("D_port");
port2->setIdRef("D");
port.setId("comp_port");
port.setIdRef("comp");
mod1plug->addPort(&port);
port.setId("J0_port");
port.setIdRef("J0");
mod1plug->addPort(&port);
// create the Model
Model* model=document->createModel();
model->setId("complexified");
// Set the submodels
CompModelPlugin* mplugin
= static_cast<CompModelPlugin*>(model->getPlugin("comp"));
Submodel* submod1 = mplugin->createSubmodel();
submod1->setId("A");
submod1->setModelRef("ExtMod1");
Submodel* submod2 = mplugin->createSubmodel();
submod2->setId("B");
submod2->setModelRef("simple");
Deletion* del = submod2->createDeletion();
del->setPortRef("J0_port");
// Synchronize the compartments
Compartment* mcomp=model->createCompartment();
mcomp->setSpatialDimensions((unsigned int)3);
mcomp->setConstant(true);
mcomp->setId("comp");
mcomp->setSize(1L);
CompSBasePlugin* compartplug
= static_cast<CompSBasePlugin*>(mcomp->getPlugin("comp"));
re.setIdRef("comp");
re.setSubmodelRef("A");
compartplug->addReplacedElement(&re);
re.setSubmodelRef("B");
re.unsetIdRef();
re.setPortRef("comp_port");
compartplug->addReplacedElement(&re);
//Synchronize the species
spec.setId("S");
CompSBasePlugin* specplug
= static_cast<CompSBasePlugin*>(spec.getPlugin("comp"));
sre->setSubmodelRef("A");
sre->setIdRef("S");
ReplacedBy* srb = specplug->createReplacedBy();
srb->setSubmodelRef("B");
srb->setPortRef("S_port");
model->addSpecies(&spec);
spec.setId("D");
sre->setIdRef("D");
srb->setPortRef("D_port");
model->addSpecies(&spec);
writeSBMLToFile(document,"eg-ports.xml");
writeSBMLToFile(document,"spec_example3.xml");
delete document;
document = readSBMLFromFile("spec_example3.xml");
if (document == NULL)
{
cout << "Error reading back in file." << endl;
retval = -1;
}
else
{
document->checkConsistency();
if (document->getErrorLog()->getNumFailsWithSeverity(2) > 0
|| document->getErrorLog()->getNumFailsWithSeverity(3) > 0)
{
stringstream errorstream;
document->printErrors(errorstream);
cout << "Errors encoutered when round-tripping SBML file: \n"
<< errorstream.str() << endl;
retval = -1;
}
writeSBMLToFile(document, "spec_example3_rt.xml");
delete document;
}
#ifdef WIN32
if (retval != 0)
{
cout << "(Press any key to exit.)" << endl;
_getch();
}
#endif
return retval;
}