private static int Main(string[] args)
{
var retval = 0;
var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
var document = new SBMLDocument(sbmlns);
var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
var mod1 = compdoc.createModelDefinition();
mod1.setId("enzyme");
mod1.setName("enzyme");
var comp = mod1.createCompartment();
comp.setSpatialDimensions(3);
comp.setConstant(true);
comp.setId("comp");
comp.setSize(1L);
var spec = new Species(sbmlns);
//We have to construct it this way because we get the comp plugin from it later.
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
mod1.addSpecies(spec);
spec.setId("E");
mod1.addSpecies(spec);
spec.setId("D");
mod1.addSpecies(spec);
spec.setId("ES");
mod1.addSpecies(spec);
var rxn = new Reaction(sbmlns);
rxn.setReversible(true);
rxn.setFast(false);
var rxn2 = new Reaction(sbmlns);
rxn2.setReversible(true);
rxn2.setFast(false);
rxn.setId("J0");
rxn2.setId("J1");
var sr = new SpeciesReference(3, 1);
sr.setConstant(true);
sr.setStoichiometry(1);
sr.setSpecies("S");
rxn.addReactant(sr);
sr.setSpecies("E");
rxn.addReactant(sr);
rxn2.addProduct(sr);
sr.setSpecies("ES");
rxn.addProduct(sr);
rxn2.addReactant(sr);
sr.setSpecies("D");
rxn2.addProduct(sr);
mod1.addReaction(rxn);
mod1.addReaction(rxn2);
var mod1plug = (CompModelPlugin)(mod1.getPlugin("comp"));
var m1port = new Port();
m1port.setIdRef("comp");
m1port.setId("comp_port");
mod1plug.addPort(m1port);
m1port.setIdRef("S");
m1port.setId("S_port");
mod1plug.addPort(m1port);
m1port.setIdRef("E");
m1port.setId("E_port");
mod1plug.addPort(m1port);
m1port.setIdRef("D");
m1port.setId("D_port");
mod1plug.addPort(m1port);
m1port.setIdRef("ES");
m1port.setId("ES_port");
mod1plug.addPort(m1port);
m1port.setIdRef("J0");
m1port.setId("J0_port");
mod1plug.addPort(m1port);
m1port.setIdRef("J1");
m1port.setId("J1_port");
mod1plug.addPort(m1port);
//Define the 'simple' model
var mod2 = compdoc.createModelDefinition();
mod2.setId("simple");
var comp2 = mod2.createCompartment();
comp2.setSpatialDimensions(3);
comp2.setConstant(true);
comp2.setId("comp");
comp2.setSize(1L);
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
spec.setInitialConcentration(5);
mod2.addSpecies(spec);
spec.setId("D");
spec.setInitialConcentration(10);
mod2.addSpecies(spec);
var rxn3 = new Reaction(sbmlns);
//We have to construct it this way because we get the comp plugin from it later.
rxn3.setReversible(true);
rxn3.setFast(false);
rxn3.setId("J0");
var sr2 = new SpeciesReference(3, 1); //These will not need plugins.
sr2.setConstant(true);
sr2.setStoichiometry(1);
sr2.setSpecies("S");
rxn3.addReactant(sr2);
sr2.setSpecies("D");
rxn3.addProduct(sr2);
mod2.addReaction(rxn3);
var mod2plug = (CompModelPlugin)(mod2.getPlugin("comp"));
var port = new Port();
port.setId("S_port");
port.setIdRef("S");
mod2plug.addPort(port);
var port2 = mod2plug.createPort();
port2.setId("D_port");
port2.setIdRef("D");
port.setId("comp_port");
port.setIdRef("comp");
mod2plug.addPort(port);
port.setId("J0_port");
port.setIdRef("J0");
mod2plug.addPort(port);
// create the Model
var model = document.createModel();
model.setId("complexified");
// Set the submodels
var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
var submod1 = mplugin.createSubmodel();
submod1.setId("A");
submod1.setModelRef("enzyme");
var submod2 = mplugin.createSubmodel();
submod2.setId("B");
submod2.setModelRef("simple");
var del = submod2.createDeletion();
del.setPortRef("J0_port");
del.setId("oldrxn");
// Synchronize the compartments
var mcomp = model.createCompartment();
mcomp.setSpatialDimensions(3);
mcomp.setConstant(true);
mcomp.setId("comp");
mcomp.setSize(1L);
var compartplug = (CompSBasePlugin)(mcomp.getPlugin("comp"));
var re = new ReplacedElement();
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");
spec.setInitialConcentration(5);
var specplug = (CompSBasePlugin)(spec.getPlugin("comp"));
var sre = specplug.createReplacedElement();
sre.setSubmodelRef("A");
sre.setIdRef("S");
var sre2 = specplug.createReplacedElement();
sre2.setSubmodelRef("B");
sre2.setPortRef("S_port");
model.addSpecies(spec);
spec.setId("D");
spec.setInitialConcentration(10);
sre.setIdRef("D");
sre2.setPortRef("D_port");
model.addSpecies(spec);
spec.setId("E");
spec.unsetInitialConcentration();
sre.unsetIdRef();
sre2.unsetIdRef();
sre.setPortRef("E_port");
sre2.setDeletion("oldrxn");
model.addSpecies(spec);
spec.setId("ES");
spec.unsetInitialConcentration();
sre.setPortRef("ES_port");
sre2.setDeletion("oldrxn");
model.addSpecies(spec);
//Synchronize the reactions
var rxn1plug = (CompSBasePlugin)(rxn.getPlugin("comp"));
var rxn2plug = (CompSBasePlugin)(rxn2.getPlugin("comp"));
var deletion = new ReplacedElement();
deletion.setDeletion("oldrxn");
deletion.setSubmodelRef("B");
rxn1plug.addReplacedElement(deletion);
rxn2plug.addReplacedElement(deletion);
var re2 = new ReplacedElement();
re2.setSubmodelRef("A");
re2.setPortRef("J0_port");
rxn1plug.addReplacedElement(re2);
re2.setPortRef("J1_port");
rxn2plug.addReplacedElement(re2);
model.addReaction(rxn);
model.addReaction(rxn2);
libsbml.writeSBMLToFile(document, "spec_example4.xml");
document = libsbml.readSBMLFromFile("spec_example4.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
var stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "spec_example4_rt.xml");
}
return retval;
}