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/**
* @file example1.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;
int rv;
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);
// create the Model
Model* model=document->createModel();
CompModelPlugin* mplugin = static_cast<CompModelPlugin*>(model->getPlugin("comp"));
// create a parameter to be a conversion factor
Parameter* param3 = model->createParameter();
param3->setId("lcf");
param3->setConstant(true);
// create a replacement parameter
Parameter* parameter = model->createParameter();
parameter->setId("x");
parameter->setConstant(true);
// Convert parameter to the plugin version so we can add the new attributes and replacements to it.
CompSBasePlugin* splugin = static_cast<CompSBasePlugin*>(parameter->getPlugin("comp"));
// Add a replaced element.
ReplacedElement* rep1 = splugin->createReplacedElement();
rv = rep1->setSubmodelRef("submod1");
rv = rep1->setConversionFactor("x_conv");
rv = rep1->setIdRef("param1");
// Add a second replaced element in a different way.
ReplacedElement rep2;
rv = rep2.setSubmodelRef("submod2");
rv = rep2.setDeletion("del1");
rv = splugin->addReplacedElement(&rep2);
//Now create a replaced element that points into a submodel.
rep2.unsetDeletion();
rep2.setIdRef("submod2");
SBaseRef* sbr5 = rep2.createSBaseRef();
sbr5->setIdRef("submodelG");
SBaseRef* sbr6 = sbr5->createSBaseRef();
sbr6->setIdRef("buriedElement");
splugin->addReplacedElement(&rep2);
// create a parameter to be a conversion factor
Parameter* param2 = model->createParameter();
param2->setId("x_conv");
param2->setMetaId("_110013");
param2->setConstant(true);
//Testing getSBMLDocument and getParentSBMLObject.
SBMLDocument* doctest = splugin->getSBMLDocument();
SBase* parenttest = splugin->getParentSBMLObject();
if (doctest == NULL) {
cout << "SBML document not set, for unknown reason.";
}
if (parenttest == NULL) {
cout << "Parent of 'splugin' not found, for unknown reason.";
}
// Create model definitions and external model definitions.
ModelDefinition* moddef1 = compdoc->createModelDefinition();
moddef1->setId("Mod1");
Parameter* m1param1 = moddef1->createParameter();
m1param1->setId("param1");
m1param1->setConstant(true);
Parameter* m1param2 = moddef1->createParameter();
m1param2->setId("param2");
m1param2->setConstant(false);
m1param2->setValue(3.2);
ModelDefinition moddef2;
moddef2.setId("Mod2");
Parameter* subparam2 = moddef2.createParameter();
subparam2->setId("subparam2");
subparam2->setConstant(false);
compdoc->addModelDefinition(&moddef2);
ExternalModelDefinition* extmod1 = compdoc->createExternalModelDefinition();
extmod1->setId("ExtMod1");
extmod1->setSource("urn:miriam:biomodels.db:BIOMD0000000127");
ExternalModelDefinition extmod2;
extmod2.setId("ExtMod2");
extmod2.setSource("otherfile.xml");
extmod2.setModelRef("modelnamethere");
extmod2.setMd5("406022s908ge74sklj");
compdoc->addExternalModelDefinition(&extmod2);
// Create submodels
Submodel* submod1 = mplugin->createSubmodel();
submod1->setId("submod1");
submod1->setModelRef("Mod1");
Deletion* del1 = submod1->createDeletion();
del1->setId("deletionA");
del1->setIdRef("param2");
Submodel submod2;
submod2.setId("submod2");
submod2.setModelRef("ExtMod1");
submod2.setSubstanceConversionFactor("subcf");
submod2.setTimeConversionFactor("tcf");
submod2.setExtentConversionFactor("xtf");
Deletion del2;
del2.setId("deletionB");
del2.setMetaIdRef("_0010110");
rv = submod2.addDeletion(&del2);
del2.setId("deletionC");
del2.unsetMetaIdRef();
del2.setPortRef("port2");
rv = submod2.addDeletion(&del2);
del2.unsetId();
del2.unsetPortRef();
del2.setUnitRef("mph");
rv = submod2.addDeletion(&del2);
del2.unsetUnitRef();
del2.setIdRef("submodG");
SBaseRef* sbr = del2.createSBaseRef();
sbr->setIdRef("element5");
rv = submod2.addDeletion(&del2);
Deletion del3;
del3.setIdRef("submodG");
SBaseRef sbr2;
sbr2.setIdRef("subsubmodQ");
SBaseRef* subsbr = sbr2.createSBaseRef();
subsbr->setPortRef("toBdel");
del3.setSBaseRef(&sbr2);
submod2.addDeletion(&del3);
mplugin->addSubmodel(&submod2);
Port* port1 = mplugin->createPort();
port1->setId("port1");
port1->setMetaIdRef("_110013");
Port port2;
port2.setId("port2");
port2.setIdRef("x");
mplugin->addPort(&port2);
port2.setId("port3");
port2.setIdRef("submod2");
port2.setSBaseRef(&sbr2);
mplugin->addPort(&port2);
Port* testport = mplugin->getPort("port1");
assert(testport != NULL);
writeSBMLToFile(document,"comp_example1.xml");
delete document;
document = readSBMLFromFile("comp_example1.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_example1_rt.xml");
delete document;
}
#ifdef WIN32
if (retval != 0) {
cout << "(Press any key to exit.)" << endl;
_getch();
}
#endif
return retval;
}
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