void SBMLParser::inputSBMLDocumentFromString(const char *str)
{
SBMLReader *reader;
unsigned long start, stop;
start = getCurrentMillis();
reader = new SBMLReader();
document = reader->readSBMLFromString(str);
stop = getCurrentMillis();
unsigned int errors = document->getNumErrors();
if (verbose)
{
cout << endl;
cout << " filename: <stdin>" << endl;
cout << " file size: "<< strlen(str) << endl;
cout << " read time (ms): " << stop - start << endl;
cout << " validation error(s): " << errors << endl;
cout << endl;
}
document->printErrors(cerr);
delete reader;
}
void SBMLmodel::InitializeFromSBML(std::string &sSBML)
{
SBMLReader oReader;
_Document = oReader.readSBMLFromString(sSBML);
_Model = _Document->getModel();
if (_Model == NULL)
throw new ApplicationException("Invalid SBML Model", "The SBML model was invalid. Please validate it using a SBML validator such as: http://sys-bio.org/validate.");
}
void SBML_sim::loadSBML(std::string sbml_text, bool isFile)
{
SBMLReader * sbmlreader = new SBMLReader;
SBMLDocument * doc;
if (isFile)
doc = sbmlreader->readSBML(sbml_text);
else
doc = sbmlreader->readSBMLFromString(sbml_text);
loadSBML(doc);
delete doc;
delete sbmlreader;
}
// tests whether we are importing global render information
void test000098::test_export_notes()
{
CPPUNIT_ASSERT(pDataModel != NULL);
std::istringstream iss(test000098::CPS_MODEL_1);
CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
std::string s;
try
{
s = pDataModel->exportSBMLToString(NULL, 2, 1);
}
catch (...)
{
CPPUNIT_ASSERT(false);
}
CPPUNIT_ASSERT(!s.empty());
SBMLReader reader;
SBMLDocument* pSBMLDocument = NULL;
try
{
pSBMLDocument = reader.readSBMLFromString(s);
}
catch (...)
{
CPPUNIT_ASSERT(false);
}
CPPUNIT_ASSERT(pSBMLDocument != NULL);
Model* pModel = pSBMLDocument->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->isSetNotes() == true);
std::string notes = pModel->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on model") != std::string::npos);
CPPUNIT_ASSERT(pModel->getNumCompartments() == 1);
CPPUNIT_ASSERT(pModel->getNumSpecies() == 1);
CPPUNIT_ASSERT(pModel->getNumParameters() == 1);
CPPUNIT_ASSERT(pModel->getNumReactions() == 1);
CPPUNIT_ASSERT(pModel->getNumEvents() == 1);
// compartment
SBase* pObject = pModel->getCompartment(0);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isSetNotes() == true);
notes = pObject->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on compartment") != std::string::npos);
// species
pObject = pModel->getSpecies(0);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isSetNotes() == true);
notes = pObject->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on species") != std::string::npos);
// parameter
pObject = pModel->getParameter(0);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isSetNotes() == true);
notes = pObject->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on parameter") != std::string::npos);
// reaction
pObject = pModel->getReaction(0);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isSetNotes() == true);
notes = pObject->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on reaction") != std::string::npos);
// event
pObject = pModel->getEvent(0);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isSetNotes() == true);
notes = pObject->getNotesString();
CPPUNIT_ASSERT(!notes.empty());
CPPUNIT_ASSERT(notes.find("Simple note on event") != std::string::npos);
}