/** @cond doxygenLibsbmlInternal */
IdList*
SBMLLevelVersionConverter::collectSpeciesReferenceIds()
{
IdList* srids = new IdList();
for (unsigned int i = 0; i < mDocument->getModel()->getNumReactions(); i++)
{
Reaction *r = mDocument->getModel()->getReaction(i);
for (unsigned int j = 0; j < r->getNumReactants(); j++)
{
if (r->getReactant(j)->isSetId())
{
srids->append(r->getReactant(j)->getId());
}
}
for (unsigned int j = 0; j < r->getNumProducts(); j++)
{
if (r->getProduct(j)->isSetId())
{
srids->append(r->getProduct(j)->getId());
}
}
}
return srids;
}
std::string fixMissingStoich(const std::string sbml) {
SBMLDocument *doc = NULL;
try {
doc = readSBMLFromString (sbml.c_str());
Model *m = doc->getModel();
for (int j = 0; j<m->getNumReactions(); ++j) {
Reaction* r = m->getReaction(j);
if (!r)
throw std::runtime_error("No reaction");
// check stoich defined on reactants / products
for (int k = 0; k<r->getNumReactants(); ++k) {
SpeciesReference* s = r->getReactant(k);
if (!isStoichDefined(s))
if (s->setStoichiometry(1.) != LIBSBML_OPERATION_SUCCESS)
throw std::runtime_error("Unable to set stoichiometry");
}
for (int k = 0; k<r->getNumProducts(); ++k) {
SpeciesReference* s = r->getProduct(k);
if (!isStoichDefined(s))
if (s->setStoichiometry(1.) != LIBSBML_OPERATION_SUCCESS)
throw std::runtime_error("Unable to set stoichiometry");
}
// modifiers have no stoichiometry
}
} catch(...) {
delete doc;
throw;
}
SBMLWriter writer;
char* sbml_cstr = writer.writeSBMLToString(doc);
delete doc;
std::string result(sbml_cstr);
free(sbml_cstr);
return result;
}
void
Model::setSpeciesReferenceConstantValueAndStoichiometry()
{
for (unsigned int i = 0; i < getNumReactions(); i++)
{
Reaction *r = getReaction(i);
unsigned int j;
for (j = 0; j < r->getNumReactants(); j++)
{
if (!(r->getReactant(j)->isSetStoichiometryMath()))
{
r->getReactant(j)->setConstant(true);
if (!(r->getReactant(j)->isSetStoichiometry()))
{
r->getReactant(j)->setStoichiometry(1);
}
}
else
{
r->getReactant(j)->setConstant(false);
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
if (!(r->getProduct(j)->isSetStoichiometryMath()))
{
r->getProduct(j)->setConstant(true);
if (!(r->getProduct(j)->isSetStoichiometry()))
{
r->getProduct(j)->setStoichiometry(1);
}
}
else
{
r->getProduct(j)->setConstant(false);
}
}
}
}
/*
* Checks that all variables referenced in FunctionDefinition bodies are
* bound variables (function arguments).
*/
void
KineticLawVars::check_ (const Model& m, const Reaction& r)
{
unsigned int n;
/* create list of all species in the reaction */
for (n = 0; n < r.getNumReactants(); n++)
{
mSpecies.append(r.getReactant(n)->getSpecies());
}
for (n = 0; n < r.getNumProducts(); n++)
{
mSpecies.append(r.getProduct(n)->getSpecies());
}
for (n = 0; n < r.getNumModifiers(); n++)
{
mSpecies.append(r.getModifier(n)->getSpecies());
}
if ( r.isSetKineticLaw() && r.getKineticLaw()->isSetMath() )
{
const ASTNode* math = r.getKineticLaw()->getMath();
List* names = math->getListOfNodes( ASTNode_isName );
for (n = 0; n < names->getSize(); ++n)
{
ASTNode* node = static_cast<ASTNode*>( names->get(n) );
string name = node->getName() ? node->getName() : "";
if (m.getSpecies(name) != NULL && !mSpecies.contains(name) )
logUndefined(r, name);
}
delete names;
}
mSpecies.clear();
}
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;
}
void
Model::removeDuplicateTopLevelAnnotations()
{
unsigned int i, n;
this->removeDuplicateAnnotations();
if (getNumFunctionDefinitions() > 0)
{
getListOfFunctionDefinitions()->removeDuplicateAnnotations();
for (i = 0; i < getNumFunctionDefinitions(); i++)
{
getFunctionDefinition(i)->removeDuplicateAnnotations();
}
}
if (getNumUnitDefinitions() > 0)
{
getListOfUnitDefinitions()->removeDuplicateAnnotations();
for (i = 0; i < getNumUnitDefinitions(); i++)
{
getUnitDefinition(i)->removeDuplicateAnnotations();
getUnitDefinition(i)->getListOfUnits()->removeDuplicateAnnotations();
for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
{
getUnitDefinition(i)->getUnit(n)->removeDuplicateAnnotations();
}
}
}
if (getNumCompartmentTypes() > 0)
{
getListOfCompartmentTypes()->removeDuplicateAnnotations();
for (i = 0; i < getNumCompartmentTypes(); i++)
{
getCompartmentType(i)->removeDuplicateAnnotations();
}
}
if (getNumSpeciesTypes() > 0)
{
getListOfSpeciesTypes()->removeDuplicateAnnotations();
for (i = 0; i < getNumSpeciesTypes(); i++)
{
getSpeciesType(i)->removeDuplicateAnnotations();
}
}
if (getNumCompartments() > 0)
{
getListOfCompartments()->removeDuplicateAnnotations();
for (i = 0; i < getNumCompartments(); i++)
{
getCompartment(i)->removeDuplicateAnnotations();
}
}
if (getNumSpecies() > 0)
{
getListOfSpecies()->removeDuplicateAnnotations();
for (i = 0; i < getNumSpecies(); i++)
{
getSpecies(i)->removeDuplicateAnnotations();
}
}
if (getNumParameters() > 0)
{
getListOfParameters()->removeDuplicateAnnotations();
for (i = 0; i < getNumParameters(); i++)
{
getParameter(i)->removeDuplicateAnnotations();
}
}
if (getNumInitialAssignments() > 0)
{
getListOfInitialAssignments()->removeDuplicateAnnotations();
for (i = 0; i < getNumInitialAssignments(); i++)
{
getInitialAssignment(i)->removeDuplicateAnnotations();
}
}
if (getNumConstraints() > 0)
{
getListOfConstraints()->removeDuplicateAnnotations();
for (i = 0; i < getNumConstraints(); i++)
{
getConstraint(i)->removeDuplicateAnnotations();
}
}
if (getNumRules() > 0)
{
getListOfRules()->removeDuplicateAnnotations();
for (i = 0; i < getNumRules(); i++)
{
getRule(i)->removeDuplicateAnnotations();
}
}
if (getNumReactions() > 0)
{
getListOfReactions()->removeDuplicateAnnotations();
for (i = 0; i < getNumReactions(); i++)
{
Reaction * r = getReaction(i);
r->removeDuplicateAnnotations();
if (r->getNumReactants() > 0)
{
r->getListOfReactants()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumReactants(); n++)
{
r->getReactant(n)->removeDuplicateAnnotations();
}
}
if (r->getNumProducts() > 0)
{
r->getListOfProducts()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumProducts(); n++)
{
r->getProduct(n)->removeDuplicateAnnotations();
}
}
if (r->getNumModifiers() > 0)
{
r->getListOfModifiers()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumModifiers(); n++)
{
r->getModifier(n)->removeDuplicateAnnotations();
}
}
if (r->isSetKineticLaw())
{
r->getKineticLaw()->removeDuplicateAnnotations();
if (r->getKineticLaw()->getNumParameters() > 0)
{
r->getKineticLaw()->getListOfParameters()
->removeDuplicateAnnotations();
for (n = 0; n < r->getKineticLaw()->getNumParameters(); n++)
{
r->getKineticLaw()->getParameter(n)->removeDuplicateAnnotations();
}
}
}
}
}
if (getNumEvents() > 0)
{
getListOfEvents()->removeDuplicateAnnotations();
for (i = 0; i < getNumEvents(); i++)
{
getEvent(i)->removeDuplicateAnnotations();
if (getEvent(i)->getNumEventAssignments() > 0)
{
getEvent(i)->getListOfEventAssignments()->removeDuplicateAnnotations();
for (n = 0; n < getEvent(i)->getNumEventAssignments(); n++)
{
getEvent(i)->getEventAssignment(n)->removeDuplicateAnnotations();
}
}
}
}
}
void
Model::convertStoichiometryMath()
{
unsigned int n, j;
Reaction * r;
SpeciesReference *sr;
unsigned int idCount = 0;
char newid[15];
std::string id;
for (n = 0; n < getNumReactions(); n++)
{
r = getReaction(n);
for (j = 0; j < r->getNumReactants(); j++)
{
sr = r->getReactant(j);
if (sr->isSetStoichiometryMath())
{
if (!sr->isSetId())
{
sprintf(newid, "generatedId_%u", idCount);
id.assign(newid);
sr->setId(id);
idCount++;
}
else
{
id = sr->getId();
}
sr->setConstant(false);
AssignmentRule * ar = createAssignmentRule();
ar->setVariable(id);
if (sr->getStoichiometryMath()->isSetMath())
{
ar->setMath(sr->getStoichiometryMath()->getMath());
}
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
sr = r->getProduct(j);
if (sr->isSetStoichiometryMath())
{
if (!sr->isSetId())
{
sprintf(newid, "generatedId_%u", idCount);
id.assign(newid);
sr->setId(id);
idCount++;
}
else
{
id = sr->getId();
}
sr->setConstant(false);
AssignmentRule * ar = createAssignmentRule();
ar->setVariable(id);
if (sr->getStoichiometryMath()->isSetMath())
{
ar->setMath(sr->getStoichiometryMath()->getMath());
}
}
}
}
}
void dealWithAssigningL1Stoichiometry(Model & m, bool l2)
{
//char newid[15];
std::string id;
for (unsigned int i = 0; i < m.getNumReactions(); i++)
{
Reaction *r = m.getReaction(i);
unsigned int j;
for (j = 0; j < r->getNumReactants(); j++)
{
SpeciesReference *sr = r->getReactant(j);
// we do not get here unless the stoichiometryMath is an integer
// or a rational
if (l2 == true && sr->isSetStoichiometryMath() == true)
{
const ASTNode* ast = sr->getStoichiometryMath()->getMath();
if (ast->isInteger())
{
int num = ast->getInteger();
sr->setStoichiometry(num);
sr->setDenominator(1);
}
else
{
int num = ast->getNumerator();
int denom = ast->getDenominator();
sr->setStoichiometry(num);
sr->setDenominator(denom);
}
sr->unsetStoichiometryMath();
}
else
{
sr->setStoichiometry(sr->getStoichiometry());
sr->setDenominator(1);
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
SpeciesReference *sr = r->getProduct(j);
// we do not get here unless the stoichiometryMath is an integer
// or a rational
if (l2 == true && sr->isSetStoichiometryMath() == true)
{
const ASTNode* ast = sr->getStoichiometryMath()->getMath();
if (ast->isInteger())
{
int num = ast->getInteger();
sr->setStoichiometry(num);
sr->setDenominator(1);
}
else
{
int num = ast->getNumerator();
int denom = ast->getDenominator();
sr->setStoichiometry(num);
sr->setDenominator(denom);
}
sr->unsetStoichiometryMath();
}
else
{
sr->setStoichiometry(sr->getStoichiometry());
sr->setDenominator(1);
}
}
}
}
void dealWithL1Stoichiometry(Model & m, bool l2)
{
unsigned int idCount = 0;
char newid[15];
std::string id;
for (unsigned int i = 0; i < m.getNumReactions(); i++)
{
Reaction *r = m.getReaction(i);
unsigned int j;
for (j = 0; j < r->getNumReactants(); j++)
{
SpeciesReference *sr = r->getReactant(j);
if (sr->getDenominator() != 1)
{
long stoich = static_cast<long>(sr->getStoichiometry());
int denom = sr->getDenominator();
ASTNode *node = new ASTNode();
node->setValue(stoich, denom);
if (l2 == true)
{
StoichiometryMath * sm = sr->createStoichiometryMath();
sm->setMath(node);
}
else
{
sprintf(newid, "speciesRefId_%u", idCount);
id.assign(newid);
idCount++;
sr->setId(id);
InitialAssignment * ar = m.createInitialAssignment();
ar->setSymbol(id);
ar->setMath(node);
sr->unsetStoichiometry();
}
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
SpeciesReference *sr = r->getProduct(j);
if (sr->getDenominator() != 1)
{
long stoich = static_cast<long>(sr->getStoichiometry());
int denom = sr->getDenominator();
ASTNode *node = new ASTNode();
node->setValue(stoich, denom);
if (l2 == true)
{
StoichiometryMath * sm = sr->createStoichiometryMath();
sm->setMath(node);
}
else
{
sprintf(newid, "speciesRefId_%u", idCount);
id.assign(newid);
idCount++;
sr->setId(id);
InitialAssignment * ar = m.createInitialAssignment();
ar->setSymbol(id);
ar->setMath(node);
sr->unsetStoichiometry();
}
}
}
}
}
void
Model::dealWithStoichiometry()
{
unsigned int idCount = 0;
for (unsigned int i = 0; i < getNumReactions(); i++)
{
Reaction *r = getReaction(i);
unsigned int j;
for (j = 0; j < r->getNumReactants(); j++)
{
SpeciesReference *sr = r->getReactant(j);
if (sr->isSetStoichiometry() == false)
{
if (sr->isSetId() == false)
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
else
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
else
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
}
}
else
{
// stoichiometry is set
if (sr->isSetId())
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
}
// no id set - do not need to do anything
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
SpeciesReference *sr = r->getProduct(j);
if (sr->isSetStoichiometry() == false)
{
if (sr->isSetId() == false)
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
else
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
else
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
}
}
else
{
// stoichiometry is set
if (sr->isSetId())
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
}
// no id set - do not need to do anything
}
}
}
}
void
Model::assignRequiredValues()
{
// when converting to L3 some attributes which have default values in L1/L2
// but are required in L3 are not present or set
unsigned int i, n;
if (getNumUnitDefinitions() > 0)
{
for (i = 0; i < getNumUnitDefinitions(); i++)
{
for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
{
Unit *u = getUnitDefinition(i)->getUnit(n);
if (!u->isSetExponent())
u->setExponent(1.0);
if (!u->isSetScale())
u->setScale(0);
if (!u->isSetMultiplier())
u->setMultiplier(1.0);
}
}
}
if (getNumCompartments() > 0)
{
for (i = 0; i < getNumCompartments(); i++)
{
Compartment *c = getCompartment(i);
c->setConstant(c->getConstant());
}
}
if (getNumSpecies() > 0)
{
for (i = 0; i < getNumSpecies(); i++)
{
Species * s = getSpecies(i);
s->setBoundaryCondition(s->getBoundaryCondition());
s->setHasOnlySubstanceUnits(s->getHasOnlySubstanceUnits());
s->setConstant(s->getConstant());
}
}
if (getNumParameters() > 0)
{
for (i = 0; i < getNumParameters(); i++)
{
Parameter * p = getParameter(i);
p->setConstant(p->getConstant());
}
}
if (getNumReactions() > 0)
{
for (i = 0; i < getNumReactions(); i++)
{
Reaction * r = getReaction(i);
r->setFast(r->getFast());
r->setReversible(r->getReversible());
if (r->getNumReactants() > 0)
{
for (n = 0; n < r->getNumReactants(); n++)
{
SpeciesReference *sr = r->getReactant(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
if (r->getNumProducts() > 0)
{
for (n = 0; n < r->getNumProducts(); n++)
{
SpeciesReference *sr = r->getProduct(n);
if (sr->isSetStoichiometryMath())
{
sr->setConstant(false);
}
else
{
sr->setConstant(true);
}
}
}
}
}
if (getNumEvents() > 0)
{
for (i = 0; i < getNumEvents(); i++)
{
Event * e = getEvent(i);
e->setUseValuesFromTriggerTime(e->getUseValuesFromTriggerTime());
if (e->isSetTrigger())
{
Trigger *t = e->getTrigger();
t->setPersistent(true);
t->setInitialValue(true);
}
}
}
}
void test000009::test_references_to_species()
{
// load the CPS file
// export to SBML
// check the resulting SBML model
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
std::istringstream iss(test000009::MODEL_STRING);
CPPUNIT_ASSERT(load_cps_model_from_stream(iss, *pDataModel) == true);
CPPUNIT_ASSERT(pDataModel->getModel() != NULL);
CPPUNIT_ASSERT(pDataModel->exportSBMLToString(NULL, 2, 3).empty() == false);
SBMLDocument* pDocument = pDataModel->getCurrentSBMLDocument();
CPPUNIT_ASSERT(pDocument != NULL);
Model* pModel = pDocument->getModel();
CPPUNIT_ASSERT(pModel != NULL);
// assert that there is only one compartment and
// assert the compartment is constant
CPPUNIT_ASSERT(pModel->getNumCompartments() == 1);
Compartment* pCompartment = pModel->getCompartment(0);
CPPUNIT_ASSERT(pCompartment->getConstant() == false);
CPPUNIT_ASSERT(pModel->getNumSpecies() == 2);
Species* pSpecies = pModel->getSpecies(1);
CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() == true);
pSpecies = pModel->getSpecies(0);
std::string idSpeciesA = pSpecies->getId();
CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() == true);
CPPUNIT_ASSERT(pModel->getNumRules() == 2);
// there are two rules, one is the rule for the compartment
AssignmentRule* pRule = dynamic_cast<AssignmentRule*>(pModel->getRule(0));
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pModel->getNumParameters() == 1);
Parameter* pParameter = pModel->getParameter(0);
CPPUNIT_ASSERT(pParameter != NULL);
if (pRule->getVariable() != pParameter->getId())
{
pRule = dynamic_cast<AssignmentRule*>(pModel->getRule(1));
}
CPPUNIT_ASSERT(pRule->getVariable() == pParameter->getId());
const ASTNode* pMath = pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// the expression should be the species divided by the volume
CPPUNIT_ASSERT(pMath->getType() == AST_DIVIDE);
CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pSpecies->getId());
CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pCompartment->getId());
CPPUNIT_ASSERT(pModel->getNumReactions() == 2);
Reaction* pReaction = pModel->getReaction(0);
// make sure this is reaction A ->
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
CPPUNIT_ASSERT(pReaction->getNumProducts() == 0);
// check if all references in the kinetic law are unmodified
// math element must be a multiplication of the mass action term by
// the compartment volume
// the mass action term is a multiplication of the parameter node by
// the species node
// the code that multiplies the reaction by the compartments volume
// recognizes the division of the species by the compartment and cancels
// those two
CPPUNIT_ASSERT(pReaction->isSetKineticLaw() == true);
KineticLaw* pLaw = pReaction->getKineticLaw();
CPPUNIT_ASSERT(pLaw != NULL);
CPPUNIT_ASSERT(pLaw->isSetMath() == true);
pMath = pLaw->getMath();
CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(0)->getName() == std::string("k1"));
CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(1)->getName() == idSpeciesA);
pReaction = pModel->getReaction(1);
// make sure this is reaction A -> S
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
CPPUNIT_ASSERT(pReaction->getNumProducts() == 1);
// check if all references in the kinetic law are unmodified
// math element must be a multiplication of the compartments volume with
// a function call with three arguments
// the first argument is the reference to the species
CPPUNIT_ASSERT(pReaction->isSetKineticLaw() == true);
pLaw = pReaction->getKineticLaw();
CPPUNIT_ASSERT(pLaw != NULL);
CPPUNIT_ASSERT(pLaw->isSetMath() == true);
pMath = pLaw->getMath();
CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pCompartment->getId());
pMath = pMath->getChild(1);
CPPUNIT_ASSERT(pMath != NULL);
CPPUNIT_ASSERT(pMath->getType() == AST_FUNCTION);
CPPUNIT_ASSERT(pMath->getNumChildren() == 3);
pMath = pMath->getChild(0);
CPPUNIT_ASSERT(pMath != NULL);
CPPUNIT_ASSERT(pMath->getType() == AST_DIVIDE);
CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(0)->getName() == idSpeciesA);
CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pCompartment->getId());
}
//create REACTION
void SbmlReader::createReaction( map< string,Id > &molMap )
{
map< string,double > rctMap;
map< string,double >::iterator rctMap_iter;
map< string,double >pdtMap;
map< string,double >::iterator pdtMap_iter;
map< string,Eref >::iterator elemt_iter;
map< string,EnzymeInfo >enzInfoMap;
double rctorder,pdtorder;
static const Cinfo* moleculeCinfo = initMoleculeCinfo();
static const Finfo* reacFinfo =moleculeCinfo->findFinfo( "reac" );
static const Cinfo* reactionCinfo = initReactionCinfo();
static const Finfo* subFinfo = reactionCinfo->findFinfo( "sub" );
static const Finfo* prdFinfo = reactionCinfo->findFinfo( "prd" );
static const Finfo* kfFinfo = reactionCinfo->findFinfo( "kf" );
static const Finfo* kbFinfo = reactionCinfo->findFinfo( "kb" );
Reaction* reac;
for ( unsigned int r = 0; r < model_->getNumReactions(); r++ )
{
reac = model_->getReaction( r );
const string id=reac->getId();
//cout<<"reaction is "<<id<<endl;
std::string name;
if ( reac->isSetName() ){
name = reac->getName();
}
string grpname = getAnnotation( reac,enzInfoMap );
if ( (grpname != "") && (enzInfoMap[grpname].stage == 3) )
setupEnzymaticReaction( enzInfoMap[grpname],grpname );
else if ( grpname == "" )
{
if ( reac->getNumModifiers()> 0 )
setupMMEnzymeReaction( reac,id );
else{
bool rev=reac->getReversible();
bool fast=reac->getFast();
if ( fast ){
cout<<"warning: for now fast attribute is not handled"<<endl;
errorFlag_ = true;
}
int numRcts = reac->getNumReactants();
int numPdts = reac->getNumProducts();
if ( numRcts == 0 && numPdts != 0 ){
const SpeciesReference* pdt = reac->getProduct( 0 );
std::string spName = pdt->getSpecies();
Id parent = molMap.find( spName )->second; //gives compartment of spName
string parentCompt = parent()->name();
//cout<<"parent of reactant :"<<parentCompt<<endl;
ostringstream spId;
spId <<id<<"_Src";
molecule_ = Neutral::create( "Molecule",spId.str(),parent,Id::scratchId() );//create Molecule
molMap[spId.str()] = parent;
elmtMap_[spId.str()] = Eref( molecule_ );
::set< double >( molecule_,"conc", 1 );
::set< int >( molecule_,"mode",4 );
reaction_ = Neutral::create( "Reaction",id,parent,Id::scratchId() ); //create Reaction
Eref( reaction_ ).add( subFinfo->msg(),elmtMap_[spId.str()],reacFinfo->msg(),ConnTainer::Default );
}
else{
const SpeciesReference* rect=reac->getReactant(0);
std::string sp=rect->getSpecies();
Id m = molMap.find(sp)->second; //gives compartment of sp
reaction_ = Neutral::create( "Reaction",id,m,Id::scratchId() ); //create Reaction
double rctcount=0.0;
rctMap.clear();
for ( unsigned int rt=0;rt<reac->getNumReactants();rt++ )
{
const SpeciesReference* rct=reac->getReactant(rt);
sp=rct->getSpecies();
rctMap_iter = rctMap.find(sp);
if ( rctMap_iter != rctMap.end() ){
rctcount = rctMap_iter->second;
}
else {
rctcount = 0.0;
}
rctcount += rct->getStoichiometry();
rctMap[sp] = rctcount;
for ( int i=0;(int)i<rct->getStoichiometry();i++ )
{
Eref(reaction_).add( subFinfo->msg(),elmtMap_[sp],reacFinfo->msg(),ConnTainer::Default );
}
}
}
double pdtcount = 0.0;
pdtMap.clear();
for ( unsigned int pt=0;pt<reac->getNumProducts();pt++ )
{
const SpeciesReference* pdt=reac->getProduct(pt);
std::string sp=pdt->getSpecies();
pdtMap_iter = pdtMap.find(sp);
if ( pdtMap_iter != pdtMap.end() ){
pdtcount = pdtMap_iter->second;
}
else {
pdtcount = 0.0;
}
pdtcount += pdt->getStoichiometry();
pdtMap[sp] = pdtcount;
for ( int i=0;i<pdt->getStoichiometry();i++ )
{
Eref(reaction_).add( prdFinfo->msg(),elmtMap_[sp],reacFinfo->msg(),ConnTainer::Default );
}
}
//order of reactants
rctorder = 0.0;
string rsp = "",psp = "";
for ( rctMap_iter=rctMap.begin();rctMap_iter!=rctMap.end();rctMap_iter++ )
{
rctorder += rctMap_iter->second;
rsp=rctMap_iter->first; //species of the reactant
}
//cout<<"rct order = "<<rctorder<<endl;
//order of products
pdtorder = 0.0;
for ( pdtMap_iter=pdtMap.begin();pdtMap_iter!=pdtMap.end();pdtMap_iter++ )
{
pdtorder += pdtMap_iter->second;
psp=pdtMap_iter->first; //species of the product
}
//cout<<"pdt order = "<<pdtorder<<endl;
if ( reac->isSetKineticLaw() )
{ KineticLaw * klaw=reac->getKineticLaw();
//vector< double > rate = getKLaw( klaw,rev );
vector< double > rate;
rate.clear();
getKLaw( klaw,rev,rate );
if ( errorFlag_ )
return;
else if ( !errorFlag_ ){
::set< double >( reaction_, kfFinfo, rate[0] );
::set< double >( reaction_, kbFinfo, rate[1] );
}
}
}//else modifier
}//else
}//reaction
}//create reaction
LIBSBML_CPP_NAMESPACE_USE
int
main (int argc, char *argv[])
{
if (argc != 2)
{
cout << endl << "Usage: printUnits filename" << endl << endl;
return 1;
}
const char* filename = argv[1];
SBMLDocument* document = readSBML(filename);
if (document->getNumErrors() > 0)
{
cerr << "Encountered the following SBML errors:" << endl;
document->printErrors(cerr);
return 1;
}
Model* model = document->getModel();
if (model == 0)
{
cout << "No model present." << endl;
return 1;
}
unsigned int i,j;
for (i = 0; i < model->getNumSpecies(); i++)
{
Species* s = model->getSpecies(i);
cout << "Species " << i << ": "
<< UnitDefinition::printUnits(s->getDerivedUnitDefinition()) << endl;
}
for (i = 0; i < model->getNumCompartments(); i++)
{
Compartment *c = model->getCompartment(i);
cout << "Compartment " << i << ": "
<< UnitDefinition::printUnits(c->getDerivedUnitDefinition())
<< endl;
}
for (i = 0; i < model->getNumParameters(); i++)
{
Parameter *p = model->getParameter(i);
cout << "Parameter " << i << ": "
<< UnitDefinition::printUnits(p->getDerivedUnitDefinition())
<< endl;
}
for (i = 0; i < model->getNumInitialAssignments(); i++)
{
InitialAssignment *ia = model->getInitialAssignment(i);
cout << "InitialAssignment " << i << ": "
<< UnitDefinition::printUnits(ia->getDerivedUnitDefinition()) << endl;
cout << " undeclared units: ";
cout << (ia->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
for (i = 0; i < model->getNumEvents(); i++)
{
Event *e = model->getEvent(i);
cout << "Event " << i << ": " << endl;
if (e->isSetDelay())
{
cout << "Delay: "
<< UnitDefinition::printUnits(e->getDelay()->getDerivedUnitDefinition()) << endl;
cout << " undeclared units: ";
cout << (e->getDelay()->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
for (j = 0; j < e->getNumEventAssignments(); j++)
{
EventAssignment *ea = e->getEventAssignment(j);
cout << "EventAssignment " << j << ": "
<< UnitDefinition::printUnits(ea->getDerivedUnitDefinition()) << endl;
cout << " undeclared units: ";
cout << (ea->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
}
for (i = 0; i < model->getNumReactions(); i++)
{
Reaction *r = model->getReaction(i);
cout << "Reaction " << i << ": " << endl;
if (r->isSetKineticLaw())
{
cout << "Kinetic Law: "
<< UnitDefinition::printUnits(r->getKineticLaw()->getDerivedUnitDefinition()) << endl;
cout << " undeclared units: ";
cout << (r->getKineticLaw()->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
for (j = 0; j < r->getNumReactants(); j++)
{
SpeciesReference *sr = r->getReactant(j);
if (sr->isSetStoichiometryMath())
{
cout << "Reactant stoichiometryMath" << j << ": "
<< UnitDefinition::printUnits(sr->getStoichiometryMath()->getDerivedUnitDefinition()) << endl;
cout << " undeclared units: ";
cout << (sr->getStoichiometryMath()->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
SpeciesReference *sr = r->getProduct(j);
if (sr->isSetStoichiometryMath())
{
cout << "Product stoichiometryMath" << j << ": "
<< UnitDefinition::printUnits(sr->getStoichiometryMath()->getDerivedUnitDefinition()) << endl;
cout << " undeclared units: ";
cout << (sr->getStoichiometryMath()->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
}
}
for (i = 0; i < model->getNumRules(); i++)
{
Rule *r = model->getRule(i);
cout << "Rule " << i << ": "
<< UnitDefinition::printUnits(r->getDerivedUnitDefinition()) << endl;
cout << " undeclared units: ";
cout << (r->containsUndeclaredUnits() ? "yes\n" : "no\n");
}
delete document;
return 0;
}
void SbmlReader::createReaction(const map< string, Id > &molSidcmptMIdMap ) {
Reaction* reac;
map< string,double > rctMap;
map< string,double >::iterator rctMap_iter;
map< string,double >prdMap;
map< string,double >::iterator prdMap_iter;
map< string,EnzymeInfo >enzInfoMap;
for ( unsigned int r = 0; r < model_->getNumReactions(); r++ ) {
Id reaction_;
reac = model_->getReaction( r );
noOfsub_ = 0;
noOfprd_ = 0;
std:: string id; //=reac->getId();
if ( reac->isSetId() )
id = reac->getId();
std::string name;
if ( reac->isSetName() ) {
name = reac->getName();
name = nameString(name);
}
if (name.empty()) {
if (id.empty())
assert("Reaction id and name is empty");
else
name = id;
}
string grpname = getAnnotation( reac,enzInfoMap );
if ( (grpname != "") && (enzInfoMap[grpname].stage == 3) ) {
setupEnzymaticReaction( enzInfoMap[grpname],grpname ,molSidcmptMIdMap,name);
}
//if (grpname != "")
// {
//cout << "\n enz matic reaction " << enzInfoMap[grpname].stage;
//setupEnzymaticReaction( enzInfoMap[grpname],grpname ,molSidcmptMIdMap);
//}
else if ( grpname == "" ) {
if (reac->getNumModifiers() > 0)
setupMMEnzymeReaction( reac,id,name ,molSidcmptMIdMap);
else {
bool rev=reac->getReversible();
bool fast=reac->getFast();
if ( fast ) {
cout<<"warning: for now fast attribute is not handled"<<endl;
errorFlag_ = true;
}
int numRcts = reac->getNumReactants();
int numPdts = reac->getNumProducts();
if ( numRcts == 0 && numPdts != 0 ) {
cout << "Reaction with zero Substrate is not possible but exist in this model";
const SpeciesReference* pdt = reac->getProduct( 0 );
std::string spName = pdt->getSpecies();
Id parent = molSidcmptMIdMap.find( spName )->second; //gives compartment of spName
cout << " \n \t ################################# Sub = 0 and prd != 0 need to the reac ############### ";
const SpeciesReference* rect=reac->getReactant(0);
std::string sp=rect->getSpecies();
Id comptRef = molSidcmptMIdMap.find(sp)->second; //gives compartment of sp
Id meshEntry = Neutral::child( comptRef.eref(), "mesh" );
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
reaction_ = shell->doCreate("Reac", meshEntry, name, 1);
//shell->doAddMsg( "Single", meshEntry, "remeshReacs", reaction_, "remesh");
//Get Substrate
addSubPrd(reac,reaction_,"prd");
} //if numRcts == 0
else {
const SpeciesReference* rect=reac->getReactant(0);
std::string sp=rect->getSpecies();
Id comptRef = molSidcmptMIdMap.find(sp)->second; //gives compartment of sp
Id meshEntry = Neutral::child( comptRef.eref(), "mesh" );
Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
reaction_ = shell->doCreate("Reac", comptRef, name, 1);
//shell->doAddMsg( "Single", meshEntry, "remeshReacs", reaction_, "remesh");
//Get Substrate
addSubPrd(reac,reaction_,"sub");
//Get Product
addSubPrd(reac,reaction_,"prd");
}
if ( reac->isSetKineticLaw() ) {
KineticLaw * klaw=reac->getKineticLaw();
//vector< double > rate = getKLaw( klaw,rev );
vector< double > rate;
rate.clear();
getKLaw( klaw,rev,rate );
if ( errorFlag_ )
return;
else if ( !errorFlag_ ) {
//cout << " Reaction name " << name << " kf " << rate[0] << " kb " << rate[1]<<endl;
Field < double > :: set( reaction_, "Kf", rate[0] );
Field < double > :: set( reaction_, "Kb", rate[1] );
/*if (numRcts > 1)
rate[0] = rate[0]*pow(1e3,1.0);
cout << "Reaction " << id << " " << name << " " << rate[0] << " " << rate[1]<<endl;
Field < double > :: set( reaction_, "Kf", rate[0] );
Field < double > :: set( reaction_, "Kb", rate[1] );
*/
}
} //issetKineticLaw
} //else
} // else grpname == ""
}//for unsigned
} //reaction