END_TEST
START_TEST (test_comp_sbmldocument)
{
SBMLNamespaces sbmlns(3,1,"comp",1);
SBMLDocument doc(&sbmlns);
CompSBMLDocumentPlugin* docplugin = static_cast<CompSBMLDocumentPlugin*>(doc.getPlugin("comp"));
doc.setPackageRequired("comp", true);
fail_unless(docplugin->getRequired() == true);
fail_unless(docplugin->getNumModelDefinitions()==0);
ModelDefinition* moddef = docplugin->createModelDefinition();
moddef->setId("moddef1");
fail_unless(docplugin->getNumModelDefinitions()==1);
fail_unless(docplugin->addModelDefinition(NULL)==LIBSBML_INVALID_OBJECT);
ModelDefinition moddef2(3, 1);
moddef2.setId("moddef2");
fail_unless(docplugin->addModelDefinition(&moddef2)==LIBSBML_OPERATION_SUCCESS);
ModelDefinition* moddefref = docplugin->getModelDefinition("moddef2");
fail_unless(moddefref->getId()=="moddef2");
moddefref = docplugin->getModelDefinition(0);
fail_unless(moddefref->getId()=="moddef1");
moddef->setId("ID1");
fail_unless(moddefref->getId()=="ID1");
fail_unless(docplugin->removeModelDefinition(3)==NULL);
fail_unless(docplugin->removeModelDefinition(0)==moddef);
fail_unless(docplugin->getModelDefinition("moddef1")==NULL);
fail_unless(docplugin->getNumExternalModelDefinitions()==0);
ExternalModelDefinition* exmoddef = docplugin->createExternalModelDefinition();
exmoddef->setId("exmoddef1");
fail_unless(docplugin->getNumExternalModelDefinitions()==1);
fail_unless(docplugin->addExternalModelDefinition(NULL)==LIBSBML_INVALID_OBJECT);
ExternalModelDefinition exmoddef2(3, 1);
exmoddef2.setId("exmoddef2");
fail_unless(docplugin->addExternalModelDefinition(&exmoddef2)==LIBSBML_INVALID_OBJECT);
exmoddef2.setSource("where/the/file/is.xml");
fail_unless(docplugin->addExternalModelDefinition(&exmoddef2)==LIBSBML_OPERATION_SUCCESS);
ExternalModelDefinition* exmoddefref = docplugin->getExternalModelDefinition("exmoddef2");
fail_unless(exmoddefref->getId()=="exmoddef2");
exmoddefref = docplugin->getExternalModelDefinition(0);
fail_unless(exmoddefref->getId()=="exmoddef1");
exmoddef->setModelRef("ID1");
fail_unless(exmoddefref->getModelRef()=="ID1");
fail_unless(docplugin->removeExternalModelDefinition(3)==NULL);
fail_unless(docplugin->removeExternalModelDefinition(0)==exmoddef);
fail_unless(docplugin->getExternalModelDefinition("exmoddef1")==NULL);
}
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
CompSBMLDocumentPlugin* compdoc
= static_cast<CompSBMLDocumentPlugin*>(document->getPlugin("comp"));
compdoc->setRequired(true);
ExternalModelDefinition* extmod = compdoc->createExternalModelDefinition();
extmod->setId("ExtMod1");
extmod->setSource("enzyme_model.xml");
extmod->setModelRef("enzyme");
//Define the 'simple' model
ModelDefinition* mod1 = compdoc->createModelDefinition();
mod1->setId("simple");
Compartment* comp=mod1->createCompartment();
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.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
spec.setInitialConcentration(5);
mod1->addSpecies(&spec);
spec.setId("D");
spec.setInitialConcentration(10);
mod1->addSpecies(&spec);
Reaction rxn(&sbmlns);
rxn.setReversible(true);
rxn.setFast(false);
rxn.setId("J0");
SpeciesReference sr(&sbmlns);
sr.setConstant(true);
sr.setStoichiometry(1);
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"));
ReplacedElement re;
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.unsetInitialConcentration();
CompSBasePlugin* specplug
= static_cast<CompSBasePlugin*>(spec.getPlugin("comp"));
ReplacedElement* sre = specplug->createReplacedElement();
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->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, "spec_example3_rt.xml");
delete document;
}
#ifdef WIN32
if (retval != 0)
{
cout << "(Press any key to exit.)" << endl;
_getch();
}
#endif
return retval;
}
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 definitions
CompSBMLDocumentPlugin* compdoc
= static_cast<CompSBMLDocumentPlugin*>(document->getPlugin("comp"));
compdoc->setRequired(true);
ExternalModelDefinition* extmod = compdoc->createExternalModelDefinition();
extmod->setId("ExtMod1");
extmod->setSource("enzyme_model.xml");
extmod->setModelRef("enzyme");
// create the main Model
Model* model=document->createModel();
// 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("ExtMod1");
// create a replacement compartment
Compartment* comp=model->createCompartment();
comp->setSpatialDimensions((unsigned int)3);
comp->setConstant(true);
comp->setId("comp");
comp->setSize(1L);
//Tell the model that this compartment replaces both of the inside ones.
CompSBasePlugin* compartplug = static_cast<CompSBasePlugin*>(comp->getPlugin("comp"));
ReplacedElement re;
re.setIdRef("comp");
re.setSubmodelRef("A");
compartplug->addReplacedElement(&re);
re.setSubmodelRef("B");
compartplug->addReplacedElement(&re);
// create a replacement species
Species* spec = model->createSpecies();
spec->setCompartment("comp");
spec->setHasOnlySubstanceUnits(false);
spec->setConstant(false);
spec->setBoundaryCondition(false);
spec->setId("S");
//Tell the model that this species replaces both of the inside ones.
CompSBasePlugin* spp = static_cast<CompSBasePlugin*>(spec->getPlugin("comp"));
re.setIdRef("S");
re.setSubmodelRef("A");
spp->addReplacedElement(&re);
re.setSubmodelRef("B");
spp->addReplacedElement(&re);
writeSBMLToFile(document,"eg-import-external.xml");
writeSBMLToFile(document,"spec_example2.xml");
delete document;
document = readSBMLFromFile("spec_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, "spec_example2_rt.xml");
delete document;
}
#ifdef WIN32
if (retval != 0)
{
cout << "(Press any key to exit.)" << endl;
_getch();
}
#endif
return retval;
}