END_TEST
START_TEST (test_GetMultipleObjects_noLocalParameters)
{
SBMLReader reader;
SBMLDocument* d;
std::string filename(TestDataDirectory);
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == NULL)
{
fail("readSBML(\"multiple-ids.xml\") returned a NULL pointer.");
}
SBase* rxn = d->getElementBySId("J0");
fail_unless(rxn != NULL);
SBase* obj = rxn->getElementBySId("x");
fail_unless(obj == NULL);
obj = rxn->getElementByMetaId("meta28");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LOCAL_PARAMETER);
delete d;
}
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::InitializeFromFile(std::string &sFileName)
{
SBMLReader oReader;
_Document = oReader.readSBML(sFileName);
_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.");
}
BEGIN_C_DECLS
int
main (int argc, char* argv[])
{
if (argc != 2)
{
cout << endl << "Usage: getAllElementsWithNotes filename" << endl << endl;
return 1;
}
const char* filename = argv[1];
SBMLDocument* document;
SBMLReader reader;
#ifdef __BORLANDC__
unsigned long start, stop;
#else
unsigned long long start, stop;
#endif
start = getCurrentMillis();
document = reader.readSBML(filename);
stop = getCurrentMillis();
unsigned int errors = document->getNumErrors(LIBSBML_SEV_ERROR);
cout << endl;
cout << " filename: " << filename << endl;
cout << " read time (ms): " << stop - start << endl;
if (errors > 0)
{
cout << " error(s): " << errors << endl;
document->printErrors(cerr);
delete document;
return errors;
}
start = stop;
// create the filter we want to use
NotesFilter filter;
// get a list of all elements with notes
cout << " searching ......:" << endl;
List* allElements = document->getAllElements(&filter);
stop = getCurrentMillis();
cout << " search time (ms): " << stop - start << endl;
cout << " elements with notes: " << allElements->getSize() << endl;
delete document;
return errors;
}
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;
}
/*
* Validates the given SBMLDocument. Failures logged during
* validation may be retrieved via <code>getFailures()</code>.
*
* @return the number of validation errors that occurred.
*/
unsigned int
Validator::validate (const std::string& filename)
{
SBMLReader reader;
SBMLDocument& d = *reader.readSBML(filename);
for (unsigned int n = 0; n < d.getNumErrors(); ++n)
{
logFailure( *d.getError(n) );
}
return validate(d);
}
/*
* Validates the given SBMLDocument. Failures logged during
* validation may be retrieved via <code>getFailures()</code>.
*
* @return the number of validation errors that occurred.
*/
unsigned int
QualValidator::validate (const std::string& filename)
{
SBMLReader reader;
SBMLDocument* d = reader.readSBML(filename);
for (unsigned int n = 0; n < d->getNumErrors(); ++n)
{
logFailure( *(d->getError(n)) );
}
unsigned int ret = validate(*d);
delete d;
return ret;
}
END_TEST
START_TEST (test_GetMultipleObjects_noAssignments)
{
SBMLReader reader;
SBMLDocument* d;
std::string filename(TestDataDirectory);
filename += "assignments-invalid.xml";
d = reader.readSBML(filename);
if (d->getModel() == NULL)
{
fail("readSBML(\"assignments-invalid.xml\") returned an empty model.");
}
SBase* obj = d->getElementBySId("ia");
fail_unless(obj == NULL);
obj = d->getElementByMetaId("ia_meta");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_INITIAL_ASSIGNMENT);
obj = d->getElementBySId("ar");
fail_unless(obj == NULL);
obj = d->getElementByMetaId("ar_meta");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_ASSIGNMENT_RULE);
obj = d->getElementBySId("rr");
fail_unless(obj == NULL);
obj = d->getElementByMetaId("rr_meta");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_RATE_RULE);
obj = d->getElementBySId("ea");
fail_unless(obj == NULL);
obj = d->getElementByMetaId("ea_meta");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_EVENT_ASSIGNMENT);
delete d;
}
END_TEST
START_TEST (test_SBMLTransforms_replaceIA_species)
{
SBMLReader reader;
SBMLDocument* d;
Model* m;
const ASTNode* ast;
FunctionDefinition* fd;
ListOfFunctionDefinitions * lofd;
std::string filename(TestDataDirectory);
filename += "initialAssignments_species.xml";
d = reader.readSBML(filename);
if (d == NULL)
{
fail("readSBML(\"initialAssignments_species.xml\") returned a NULL pointer.");
}
m = d->getModel();
fail_unless( m->getNumInitialAssignments() == 3 );
fail_unless( m->getParameter(1)->getValue() == 0.75);
fail_unless( !(m->getParameter(2)->isSetValue()));
fail_unless( m->getSpecies(2)->isSetInitialAmount());
fail_unless( m->getSpecies(2)->getInitialAmount() == 2);
d->expandInitialAssignments();
m = d->getModel();
fail_unless( m->getNumInitialAssignments() == 0 );
fail_unless( m->getParameter(1)->getValue() == 3);
fail_unless( m->getParameter(2)->isSetValue());
fail_unless( m->getParameter(2)->getValue() == 0.75);
fail_unless( !(m->getSpecies(2)->isSetInitialAmount()));
fail_unless( m->getSpecies(2)->getInitialConcentration() == 2);
}
LIBSBML_CPP_NAMESPACE_USE
BEGIN_C_DECLS
int
main (int argc, char* argv[])
{
if (argc != 2)
{
cout << endl << "Usage: readSBML filename" << endl << endl;
return 1;
}
const char* filename = argv[1];
SBMLDocument* document;
SBMLReader reader;
#ifdef __BORLANDC__
unsigned long start, stop;
#else
unsigned long long start, stop;
#endif
start = getCurrentMillis();
document = reader.readSBML(filename);
stop = getCurrentMillis();
unsigned int errors = document->getNumErrors();
cout << endl;
cout << " filename: " << filename << endl;
cout << " file size: " << getFileSize(filename) << endl;
cout << " read time (ms): " << stop - start << endl;
cout << " validation error(s): " << errors << endl;
cout << endl;
document->printErrors(cerr);
delete document;
return errors;
}
END_TEST
START_TEST (test_GetMultipleObjects_allElements)
{
SBMLReader reader;
SBMLDocument* d;
std::string filename(TestDataDirectory);
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d->getModel() == NULL)
{
fail("readSBML(\"multiple-ids.xml\") returned a NULL pointer.");
}
List* list = d->getAllElements();
fail_unless(list->getSize() == 37);
delete list;
delete d;
}
END_TEST
START_TEST (test_SBMLTransforms_replaceIA)
{
SBMLReader reader;
SBMLDocument* d;
Model* m;
std::string filename(TestDataDirectory);
filename += "initialAssignments.xml";
d = reader.readSBML(filename);
if (d == NULL)
{
fail("readSBML(\"initialAssignments.xml\") returned a NULL pointer.");
}
m = d->getModel();
fail_unless( m->getNumInitialAssignments() == 2 );
fail_unless( !(m->getCompartment(0)->isSetSize()));
fail_unless( m->getParameter(1)->getValue() == 2);
d->expandInitialAssignments();
m = d->getModel();
fail_unless( m->getNumInitialAssignments() == 0 );
fail_unless( m->getCompartment(0)->isSetSize());
fail_unless( m->getCompartment(0)->getSize() == 25.0);
fail_unless( m->getParameter(1)->getValue() == 50);
}
LIBSBML_CPP_NAMESPACE_USE
BEGIN_C_DECLS
int
main (int argc, char* argv[])
{
if (argc != 5)
{
cout << endl << "Usage: renameSId filename oldSId newSId output" << endl << endl;
return 1;
}
const char* filename = argv[1];
const char* oldSId = argv[2];
const char* newSId = argv[3];
const char* output = argv[4];
if (strcmp(oldSId, newSId) == 0)
{
cout << "The Ids are identical, renaming stopped." << endl;
return 1;
}
if (!SyntaxChecker::isValidInternalSId(newSId))
{
cout << "The new SId '" << newSId
<< "' does not represent a valid SId."
<< endl;
return 1;
}
SBMLDocument* document;
SBMLReader reader;
#ifdef __BORLANDC__
unsigned long start, stop;
#else
unsigned long long start, stop;
#endif
start = getCurrentMillis();
document = reader.readSBML(filename);
stop = getCurrentMillis();
unsigned int errors = document->getNumErrors(LIBSBML_SEV_ERROR);
cout << endl;
cout << " filename: " << filename << endl;
cout << " file size: " << getFileSize(filename) << endl;
cout << " read time (ms): " << stop - start << endl;
cout << " error(s): " << errors << endl;
cout << endl;
if (errors > 0)
{
document->printErrors(cerr);
delete document;
return errors;
}
// find elements for old id
SBase* element = document->getElementBySId(oldSId);
if (element == NULL)
{
cout << "Found no element with SId '"
<< oldSId << "'." << endl;
return 1;
}
// found element --> renaming
element->setId(newSId);
// update all references to this element
List *allElements = document->getAllElements();
for (unsigned int i = 0; i < allElements->getSize(); ++i)
static_cast<SBase*>(allElements->get(i))->renameSIdRefs(oldSId, newSId);
// write to file
writeSBMLToFile(document, output);
delete document;
return errors;
}
int
main (int argc, char* argv[])
{
if (argc != 2)
{
cout << endl << "Usage: printNotes filename" << endl << endl;
return 1;
}
unsigned int i,j;
const char* filename = argv[1];
SBMLDocument* document;
SBMLReader reader;
document = reader.readSBML(filename);
unsigned int errors = document->getNumErrors();
cout << endl;
cout << "filename: " << filename << endl;
cout << endl;
if(errors > 0)
{
document->printErrors(cerr);
delete document;
return errors;
}
/* Model */
Model* m = document->getModel();
printNotes(m);
for(i=0; i < m->getNumReactions(); i++)
{
Reaction* re = m->getReaction(i);
printNotes(re);
/* SpeciesReference (Reacatant) */
for(j=0; j < re->getNumReactants(); j++)
{
SpeciesReference* rt = re->getReactant(j);
if (rt->isSetNotes()) cout << " ";
printNotes(rt, (rt->isSetSpecies() ? rt->getSpecies() : std::string("")) );
}
/* SpeciesReference (Product) */
for(j=0; j < re->getNumProducts(); j++)
{
SpeciesReference* rt = re->getProduct(j);
if (rt->isSetNotes()) cout << " ";
printNotes(rt, (rt->isSetSpecies() ? rt->getSpecies() : std::string("")) );
}
/* ModifierSpeciesReference (Modifier) */
for(j=0; j < re->getNumModifiers(); j++)
{
ModifierSpeciesReference* md = re->getModifier(j);
if (md->isSetNotes()) cout << " ";
printNotes(md, (md->isSetSpecies() ? md->getSpecies() : std::string("")) );
}
/* Kineticlaw */
if(re->isSetKineticLaw())
{
KineticLaw* kl = re->getKineticLaw();
if (kl->isSetNotes()) cout << " ";
printNotes(kl);
/* Parameter */
for(j=0; j < kl->getNumParameters(); j++)
{
Parameter* pa = kl->getParameter(j);
if (pa->isSetNotes()) cout << " ";
printNotes(pa);
}
}
}
/* Species */
for(i=0; i < m->getNumSpecies(); i++)
{
Species* sp = m->getSpecies(i);
printNotes(sp);
}
/* Compartment */
for(i=0; i < m->getNumCompartments(); i++)
{
Compartment* sp = m->getCompartment(i);
printNotes(sp);
}
/* FunctionDefinition */
for(i=0; i < m->getNumFunctionDefinitions(); i++)
{
FunctionDefinition* sp = m->getFunctionDefinition(i);
printNotes(sp);
}
/* UnitDefinition */
for(i=0; i < m->getNumUnitDefinitions(); i++)
{
UnitDefinition* sp = m->getUnitDefinition(i);
printNotes(sp);
}
/* Parameter */
for(i=0; i < m->getNumParameters(); i++)
{
Parameter* sp = m->getParameter(i);
printNotes(sp);
}
/* Rule */
for(i=0; i < m->getNumRules(); i++)
{
Rule* sp = m->getRule(i);
printNotes(sp);
}
/* InitialAssignment */
for(i=0; i < m->getNumInitialAssignments(); i++)
{
InitialAssignment* sp = m->getInitialAssignment(i);
printNotes(sp);
}
/* Event */
for(i=0; i < m->getNumEvents(); i++)
{
Event* sp = m->getEvent(i);
printNotes(sp);
/* Trigger */
if(sp->isSetTrigger())
{
const Trigger* tg = sp->getTrigger();
if (tg->isSetNotes()) cout << " ";
printNotes(const_cast<Trigger*>(tg));
}
/* Delay */
if(sp->isSetDelay())
{
const Delay* dl = sp->getDelay();
if (dl->isSetNotes()) cout << " ";
printNotes(const_cast<Delay*>(dl));
}
/* EventAssignment */
for(j=0; j < sp->getNumEventAssignments(); j++)
{
EventAssignment* ea = sp->getEventAssignment(j);
if (ea->isSetNotes()) cout << " ";
printNotes(ea);
}
}
/* SpeciesType */
for(i=0; i < m->getNumSpeciesTypes(); i++)
{
SpeciesType* sp = m->getSpeciesType(i);
printNotes(sp);
}
/* Constraint */
for(i=0; i < m->getNumConstraints(); i++)
{
Constraint* sp = m->getConstraint(i);
printNotes(sp);
}
delete document;
return errors;
}
// 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);
}
BEGIN_C_DECLS
int
main (int argc, char* argv[])
{
if (argc != 3)
{
cout << endl << "Usage: setNamesFromIds filename output" << endl << endl;
return 1;
}
const char* filename = argv[1];
const char* output = argv[2];
SBMLDocument* document;
SBMLReader reader;
#ifdef __BORLANDC__
unsigned long start, stop;
#else
unsigned long long start, stop;
#endif
start = getCurrentMillis();
document = reader.readSBML(filename);
stop = getCurrentMillis();
unsigned int errors = document->getNumErrors(LIBSBML_SEV_ERROR);
cout << endl;
cout << " filename: " << filename << endl;
cout << " read time (ms): " << stop - start << endl;
if (errors > 0)
{
cout << " error(s): " << errors << endl;
document->printErrors(cerr);
delete document;
return errors;
}
start = stop;
// get a list of all elements, as we will need to know all identifiers
List* allElements = document->getAllElements();
// create the transformer
NameIdTransformer trans;
// rename the identifiers (using the elements we already gathered before)
document->getModel()->renameIDs(allElements, &trans);
stop = getCurrentMillis();
cout << " rename time (ms): " << stop - start << endl;
start = stop;
// write to file
writeSBMLToFile(document, output);
stop = getCurrentMillis();
cout << " write time (ms): " << stop - start << endl;
cout << endl;
delete document;
return errors;
}
END_TEST
START_TEST (test_GetMultipleObjects_getMetaId)
{
SBMLReader reader;
SBMLDocument* d;
std::string filename(TestDataDirectory);
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == NULL)
{
fail("readSBML(\"multiple-ids.xml\") returned a NULL pointer.");
}
SBase* obj = d->getElementByMetaId("no_id");
fail_unless(obj == NULL);
obj = d->getElementByMetaId("");
fail_unless(obj == NULL);
obj = d->getElementByMetaId("meta1");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_DOCUMENT);
obj = d->getElementByMetaId("meta2");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_MODEL);
obj = d->getElementByMetaId("meta3");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_COMPARTMENT);
obj = d->getElementByMetaId("meta4");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_COMPARTMENT);
obj = d->getElementByMetaId("meta5");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_SPECIES);
obj = d->getElementByMetaId("meta6");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_SPECIES);
obj = d->getElementByMetaId("meta7");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_REACTION);
obj = d->getElementByMetaId("meta8");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_REACTION);
obj = d->getElementByMetaId("meta9");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_SPECIES_REFERENCE);
obj = d->getElementByMetaId("meta10");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_SPECIES_REFERENCE);
obj = d->getElementByMetaId("meta11");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_KINETIC_LAW);
obj = d->getElementByMetaId("meta12");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_EVENT);
obj = d->getElementByMetaId("meta13");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_EVENT);
obj = d->getElementByMetaId("meta14");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_TRIGGER);
obj = d->getElementByMetaId("meta15");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_EVENT_ASSIGNMENT);
obj = d->getElementByMetaId("meta16");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_EVENT_ASSIGNMENT);
obj = d->getElementByMetaId("meta17");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_DELAY);
obj = d->getElementByMetaId("meta18");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_PARAMETER);
obj = d->getElementByMetaId("meta19");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_PRIORITY);
obj = d->getElementByMetaId("meta20");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_FUNCTION_DEFINITION);
obj = d->getElementByMetaId("meta21");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_FUNCTION_DEFINITION);
obj = d->getElementByMetaId("meta22");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_INITIAL_ASSIGNMENT);
obj = d->getElementByMetaId("meta23");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_INITIAL_ASSIGNMENT);
obj = d->getElementByMetaId("meta24");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_RULE);
obj = d->getElementByMetaId("meta25");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_RATE_RULE);
obj = d->getElementByMetaId("meta26");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_ASSIGNMENT_RULE);
obj = d->getElementByMetaId("meta27");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_LOCAL_PARAMETER);
obj = d->getElementByMetaId("meta28");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LOCAL_PARAMETER);
obj = d->getElementByMetaId("meta29");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_UNIT_DEFINITION);
obj = d->getElementByMetaId("meta30");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_UNIT_DEFINITION);
obj = d->getElementByMetaId("meta31");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_UNIT);
obj = d->getElementByMetaId("meta32");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_UNIT);
obj = d->getElementByMetaId("meta33");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_PARAMETER);
obj = d->getElementByMetaId("meta34");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_LIST_OF);
fail_unless(static_cast<ListOf*>(obj)->getItemTypeCode() == SBML_MODIFIER_SPECIES_REFERENCE);
obj = d->getElementByMetaId("meta35");
fail_unless(obj != NULL);
fail_unless(obj->getTypeCode() == SBML_MODIFIER_SPECIES_REFERENCE);
delete d;
}
END_TEST
START_TEST (test_RemoveFromParent_alreadyRemoved)
{
SBMLReader reader;
SBMLDocument* d;
std::string filename(TestDataDirectory);
filename += "multiple-ids.xml";
d = reader.readSBML(filename);
if (d == NULL)
{
fail("readSBML(\"multiple-ids.xml\") returned a NULL pointer.");
}
SBase* obj;
//List of function definitions
obj = d->getElementByMetaId("meta20");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta20");
fail_unless(obj == NULL);
//Function definition
obj = d->getElementByMetaId("meta21");
fail_unless(obj == NULL);
//Unit Definition
obj = d->getElementByMetaId("meta30");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta30");
fail_unless(obj == NULL);
//Unit
obj = d->getElementByMetaId("meta32");
fail_unless(obj == NULL);
//List of units
obj = d->getElementByMetaId("meta31");
fail_unless(obj == NULL);
//List of compartments
obj = d->getElementByMetaId("meta3");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta3");
fail_unless(obj == NULL);
//Compartment
obj = d->getElementByMetaId("meta4");
fail_unless(obj == NULL);
//List of species
obj = d->getElementByMetaId("meta5");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta5");
fail_unless(obj == NULL);
//Species
obj = d->getElementByMetaId("meta6");
fail_unless(obj == NULL);
//Kinetic law
obj = d->getElementByMetaId("meta11");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta11");
fail_unless(obj == NULL);
//Local parameter
obj = d->getElementByMetaId("meta28");
fail_unless(obj == NULL);
//List of local parameters
obj = d->getElementByMetaId("meta27");
fail_unless(obj == NULL);
//List of modifiers
obj = d->getElementByMetaId("meta34");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta34");
fail_unless(obj == NULL);
//Modifier species reference
obj = d->getElementByMetaId("meta35");
fail_unless(obj == NULL);
//Reaction
obj = d->getElementByMetaId("meta8");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta8");
fail_unless(obj == NULL);
//Species reference
obj = d->getElementByMetaId("meta10");
fail_unless(obj == NULL);
//List of reactants
obj = d->getElementByMetaId("meta9");
fail_unless(obj == NULL);
//List of parameters
obj = d->getElementByMetaId("meta33");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta33");
fail_unless(obj == NULL);
//Parameter
obj = d->getElementByMetaId("meta18");
fail_unless(obj == NULL);
//List of event assignments
obj = d->getElementByMetaId("meta15");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta15");
fail_unless(obj == NULL);
//Event assignment
obj = d->getElementByMetaId("meta16");
fail_unless(obj == NULL);
//Event
obj = d->getElementByMetaId("meta13");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta13");
fail_unless(obj == NULL);
//Trigger
obj = d->getElementByMetaId("meta14");
fail_unless(obj == NULL);
//Delay
obj = d->getElementByMetaId("meta17");
fail_unless(obj == NULL);
//Priority
obj = d->getElementByMetaId("meta19");
fail_unless(obj == NULL);
//List of initial assignments
obj = d->getElementByMetaId("meta22");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta22");
fail_unless(obj == NULL);
//Initial assignment
obj = d->getElementByMetaId("meta23");
fail_unless(obj == NULL);
//List of rules
obj = d->getElementByMetaId("meta24");
fail_unless(obj != NULL);
fail_unless(obj->removeFromParentAndDelete() == LIBSBML_OPERATION_SUCCESS);
obj = d->getElementByMetaId("meta24");
fail_unless(obj == NULL);
//Rate rule
obj = d->getElementByMetaId("meta25");
fail_unless(obj == NULL);
//Assignment rule
obj = d->getElementByMetaId("meta26");
fail_unless(obj == NULL);
delete d;
}
/**
* Load a gene network from an SBML file. Overrides Structure.load(). Format must
* be equal GeneNetwork.SBML. Note, the SBML file must be in the exact same format
* as the SBML files produced by writeSBML(). In particular, we assume that reactions are listed
* *ordered* as we do in writeSBML().
* @param filename URL to the file describing the network to load
* @param format File format (GML, DOT, etc.)
* @throws IOException
*/
void GeneNetwork::load_sbml(const char *filename) {
SBMLDocument* document;
SBMLReader reader;
document = reader.readSBML(filename);
unsigned int errors = document->getNumErrors();
if (errors > 0) {
std::cerr << "Failed to open file " << filename << std::endl;
exit(1);
}
Model *m = document->getModel();
// -----------------------------------------
// Set the network size and create the genes
// do not count the species _void_
int size = m->getNumSpecies() - 1;
ListOfSpecies *species = m->getListOfSpecies();
for (int g=0; g < size; g++) {
if (species->get(g)->getId() != "_void_") {
//HillGene hg = new HillGene(this);
//hg.setLabel(species.get(g).getId());
HillGene *n = new HillGene(species->get(g)->getId());
//n.setLabel(species->get(g)->getId());
nodes_.push_back(*n);
delete n;
}
}
x_ = Vec_DP(nodes_.size());
x_ = 0;
y_ = Vec_DP(nodes_.size());
y_ = 0;
//vector<string> parameterNames; // the names of the parameters
//vector<double> parameterValues; // the values of the parameters
std::map<std::string, double> params;
std::vector<std::string> inputNodes; // the indexes of the inputs
HillGene src, tgt;
Parameter *param;
// 2 loops for one gene: both synthesis and degradation reactions
// (we assume that reactions are listed *ordered* as we do in writeSBML())
//int counter = 0;
for (unsigned int i=0; i < m->getNumReactions(); i++) {
Reaction *re = m->getReaction(i);
std::string id = re->getId();
std::stringstream ss;
ss << i;
//::logging::log::emit<Debug>() << id.c_str() <<
// ::logging::log::endl;
tgt = nodes_.at(getIndexOfNode(getGeneReactantId(id)));
//tgt->setLabel(getGeneReactantId(*re));
//SpeciesReference *rt = re->getReactant(0);
//Node *tgt = new HillGene();
//tgt->setLabel(rt->getSpecies());
//ListOfSpeciesReferences *modifiers = re->getListOfModifiers();
for (unsigned int j=0; j < re->getNumModifiers(); j++) {
ModifierSpeciesReference *md = re->getModifier(j);
src = nodes_.at(getIndexOfNode(md->getSpecies()));
inputNodes.push_back(src.getLabel());
// set output genes
std::vector<std::string> outputs = src.getOutputGenes();
outputs.push_back(tgt.getLabel());
src.setOutputGenes(outputs);
// The edge type is unknown for now, it is initialized later
Edge *e = new Edge(&src, &tgt, "+-");
edges_.push_back(*e);
//delete src;
delete e;
}
KineticLaw *kl = re->getKineticLaw();
for(unsigned int j=0; j < kl->getNumParameters(); j++) {
param = kl->getParameter(j);
params[param->getId()] = param->getValue();
//char buf[256];
//sprintf(buf, "%s\t%f", param->getId().c_str(), param->getValue());
//::logging::log::emit<Info>() << buf << ::logging::log::endl;
}
//::logging::log::emit<Info>() << ::logging::log::dec << params.size() <<
// ::logging::log::endl;
// in the second iteration for this gene
if (i%2 == 1) {
// set parameters in gene
//tgt.initialization(params, inputNodes);
nodes_.at(getIndexOfNode(getGeneReactantId(id))).initialization(params, inputNodes);;
//char buf[256];
//sprintf(buf, "%f", params["k_1"]);
//::logging::log::emit<Info>() << buf << ::logging::log::endl;
inputNodes.clear(); // don't clear because the reference was copied to the gene
//parameterNames.clear(); // reset (they were not copied)
//parameterValues.clear();
params.clear();
}
//counter++;
}
//setEdgeTypesAccordingToDynamicalModel();
//signed_ = true;
//delete document;
//delete n;
//delete e;
}
