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/**
* @file example2.cpp
* @brief SBML hierarchical composition example
* @author Lucian Smith
*
* This file is part of libSBML. Please visit http://sbml.org for more
* information about SBML, and the latest version of libSBML.
*/
#include <iostream>
#include <sstream>
#include <sbml/SBMLTypes.h>
#include <sbml/extension/SBMLExtensionRegister.h>
#include <sbml/extension/SBMLExtensionRegistry.h>
#include <sbml/packages/comp/extension/CompExtension.h>
#include <sbml/packages/comp/extension/CompSBasePlugin.h>
#include <sbml/packages/comp/extension/CompSBMLDocumentPlugin.h>
#include <sbml/packages/comp/extension/CompModelPlugin.h>
#ifdef WIN32
#include <conio.h>
#endif
LIBSBML_CPP_NAMESPACE_USE
using namespace std;
static SBMLExtensionRegister<CompExtension> compExtensionRegistry;
int main(int argc,char** argv){
int retval = 0;
SBMLNamespaces sbmlns(3,1,"comp",1);
// create the document
SBMLDocument *document = new SBMLDocument(&sbmlns);
CompSBMLDocumentPlugin* compdoc = static_cast<CompSBMLDocumentPlugin*>(document->getPlugin("comp"));
compdoc->setRequired(true);
ExternalModelDefinition* mod1 = compdoc->createExternalModelDefinition();
mod1->setId("teusink_glycolysis");
mod1->setName("Teusink2000_Glycolysis");
mod1->setSource("urn:miriam:biomodels.db:BIOMD0000000064");
// create the Model
Model* model=document->createModel();
model->setId("glycolysis_with_ports");
// Setup the submodel
CompModelPlugin* mplugin = static_cast<CompModelPlugin*>(model->getPlugin("comp"));
Submodel* submod1 = mplugin->createSubmodel();
submod1->setId("glycolysis");
submod1->setModelRef("teusink_glycolysis");
//Now create ports
Port port;
port.setId("cytosol_port");
port.setIdRef("glycolysis");
SBaseRef* sbr = port.createSBaseRef();
sbr->setIdRef("cytosol");
mplugin->addPort(&port);
port.setId("extracellular_port");
sbr->setIdRef("extracellular");
mplugin->addPort(&port);
/*$Glyc in cytosol, $Trh in cytosol, $CO2 in cytosol;
species $SUCC in cytosol, $GLCo in extracellular, $ETOH in cytosol, $GLY in cytosol;
species $ATP in cytosol, $ADP in cytosol, $AMP in cytosol, $SUM_P in cytosol;
species $F26BP in cytosol;
*/
port.setId("Glyc_port");
sbr->setIdRef("Glyc");
mplugin->addPort(&port);
port.setId("Trh_port");
sbr->setIdRef("Trh");
mplugin->addPort(&port);
port.setId("CO2_port");
sbr->setIdRef("CO2");
mplugin->addPort(&port);
port.setId("SUCC_port");
sbr->setIdRef("SUCC");
mplugin->addPort(&port);
port.setId("GLCo_port");
sbr->setIdRef("GLCo");
mplugin->addPort(&port);
port.setId("ETOH_port");
sbr->setIdRef("ETOH");
mplugin->addPort(&port);
port.setId("GLY_port");
sbr->setIdRef("GLY");
mplugin->addPort(&port);
port.setId("ATP_port");
sbr->setIdRef("ATP");
mplugin->addPort(&port);
port.setId("ADP_port");
sbr->setIdRef("ADP");
mplugin->addPort(&port);
port.setId("AMP_port");
sbr->setIdRef("AMP");
mplugin->addPort(&port);
port.setId("SUM_P_port");
sbr->setIdRef("SUM_P");
mplugin->addPort(&port);
port.setId("F26BP_port");
sbr->setIdRef("F26BP");
mplugin->addPort(&port);
writeSBMLToFile(document,"comp_example2.xml");
delete document;
document = readSBMLFromFile("comp_example2.xml");
if (document == NULL) {
cout << "Error reading back in file." << endl;
retval = -1;
}
else {
document->setConsistencyChecks(LIBSBML_CAT_UNITS_CONSISTENCY, false);
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, "comp_example2_rt.xml");
delete document;
}
#ifdef WIN32
if (retval != 0) {
cout << "(Press any key to exit.)" << endl;
_getch();
}
#endif
return retval;
}
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