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/**
* @file example3.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);
// Create units
Unit moles(&sbmlns);
moles.setKind(UNIT_KIND_MOLE);
moles.setExponent(1);
moles.setScale(0);
moles.setMultiplier(1);
Unit millimoles = moles;
millimoles.setScale(-3);
Unit perliter(&sbmlns);
perliter.setKind(UNIT_KIND_LITRE);
perliter.setExponent(-1);
perliter.setScale(0);
perliter.setMultiplier(1);
Unit permole = moles;
permole.setExponent(-1);
UnitDefinition molar(&sbmlns);
molar.setId("M");
molar.addUnit(&moles);
molar.addUnit(&perliter);
UnitDefinition millimolar(&sbmlns);
millimolar.setId("mM");
millimolar.addUnit(&millimoles);
millimolar.addUnit(&perliter);
UnitDefinition mMperM(&sbmlns);
mMperM.setId("mM_per_M");
mMperM.addUnit(&millimoles);
mMperM.addUnit(&permole);
UnitDefinition millimole(&sbmlns);
millimole.setId("millimole");
millimole.addUnit(&millimoles);
// create the Model
Model* model=document->createModel();
model->setId("glycolysis_with_ports");
model->addUnitDefinition(&millimole);
model->addUnitDefinition(&mMperM);
// create a parameter to be a conversion factor
Parameter* cf = model->createParameter();
cf->setId("cf");
cf->setConstant(true);
cf->setValue(1000);
cf->setUnits("mM_per_M");
//Create a compartment
Compartment compartment(&sbmlns);
compartment.setId("cell");
compartment.setSpatialDimensions(3.0);
compartment.setSize(1);
compartment.setConstant(true);
compartment.setUnits("litre");
compartment.setSBOTerm(410);
// Create a species
Species sp(&sbmlns);
sp.setId("A");
sp.setConstant(false);
sp.setUnits("millimole");
sp.setCompartment("cell");
sp.setHasOnlySubstanceUnits(false);
sp.setBoundaryCondition(false);
//Create a reaction
Reaction rxn(&sbmlns);
rxn.setReversible(false);
rxn.setFast(false);
rxn.setId("A_degradation");
SpeciesReference* sr = rxn.createReactant();
sr->setSpecies("A");
sr->setConstant(true);
sr->setStoichiometry(1);
KineticLaw* kl = rxn.createKineticLaw();
ASTNode* astn = SBML_parseFormula("4");
kl->setMath(astn);
//Add just the species to the containing model
model->addCompartment(&compartment);
model->addSpecies(&sp);
// Create two model definitions
ModelDefinition* md1 = compdoc->createModelDefinition();
md1->setId("mod1");
md1->addUnitDefinition(&millimolar);
md1->addCompartment(&compartment);
md1->addSpecies(&sp);
md1->addReaction(&rxn);
ModelDefinition* md2 = compdoc->createModelDefinition();
md2->setId("mod2");
md2->addUnitDefinition(&molar);
md2->addCompartment(&compartment);
sp.setUnits("mole");
md2->addSpecies(&sp);
md2->addReaction(&rxn);
// Create two submodels
CompModelPlugin* mplugin = static_cast<CompModelPlugin*>(model->getPlugin("comp"));
Submodel* submod1 = mplugin->createSubmodel();
submod1->setId("m1");
submod1->setModelRef("mod1");
Submodel* submod2 = mplugin->createSubmodel();
submod2->setId("m2");
submod2->setModelRef("mod2");
//Now synchronize the species:
Species* sp1 = model->getSpecies("A");
CompSBasePlugin* spplug = static_cast<CompSBasePlugin*>(sp1->getPlugin("comp"));
ReplacedElement re;
re.setSubmodelRef("m1");
re.setIdRef("A");
spplug->addReplacedElement(&re);
re.setSubmodelRef("m2");
re.setConversionFactor("cf");
spplug->addReplacedElement(&re);
writeSBMLToFile(document,"comp_example3.xml");
delete document;
document = readSBMLFromFile("comp_example3.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_example3_rt.xml");
delete document;
}
#ifdef WIN32
if (retval != 0) {
cout << "(Press any key to exit.)" << endl;
_getch();
}
#endif
return retval;
}
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