void test000047::test_delay()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING));
CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CUnit::mMol);
CPPUNIT_ASSERT(pModel->getVolumeUnitEnum() == CUnit::ml);
CPPUNIT_ASSERT(pModel->getTimeUnitEnum() == CUnit::s);
CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
const CCompartment* pCompartment = pModel->getCompartments()[0];
CPPUNIT_ASSERT(pCompartment != NULL);
CPPUNIT_ASSERT(pCompartment->getStatus() == CModelEntity::FIXED);
CPPUNIT_ASSERT(pModel->getMetabolites().size() == 2);
const CMetab* pB = pModel->getMetabolites()[1];
CPPUNIT_ASSERT(pB != NULL);
CPPUNIT_ASSERT(pB->getStatus() == CModelEntity::FIXED);
CMetab* pA = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pA != NULL);
CPPUNIT_ASSERT(pA->getStatus() == CModelEntity::ASSIGNMENT);
const CExpression* pExpr = pA->getExpressionPtr();
CPPUNIT_ASSERT(pExpr != NULL);
const CEvaluationNode* pNode = pExpr->getRoot();
CPPUNIT_ASSERT(pNode != NULL);
const CEvaluationNodeDelay* pDelayNode = dynamic_cast<const CEvaluationNodeDelay*>(pNode);
CPPUNIT_ASSERT(pDelayNode != NULL);
const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pDelayNode->getChild());
CPPUNIT_ASSERT(pObjectNode != NULL);
CCopasiObjectName objectCN = pObjectNode->getObjectCN();
CPPUNIT_ASSERT(!objectCN.empty());
std::vector<CCopasiContainer*> listOfContainers;
listOfContainers.push_back(pModel);
const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isReference() == true);
CPPUNIT_ASSERT(pObject->getObjectName() == std::string("Concentration"));
CPPUNIT_ASSERT(pObject->getObjectParent() == pB);
const CEvaluationNodeNumber* pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pObjectNode->getSibling());
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(((CEvaluationNodeNumber::SubType)CEvaluationNode::subType(pNumberNode->getType())) == CEvaluationNodeNumber::DOUBLE);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 0.5) / 0.5) < 1e-3);
CPPUNIT_ASSERT(pNumberNode->getSibling() == NULL);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 1);
const CModelValue* pModelValue = pModel->getModelValues()[0];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::FIXED);
CPPUNIT_ASSERT(pModel->getReactions().size() == 0);
//CPPUNIT_ASSERT(CCopasiMessage::size() == 2);
CCopasiMessage message = CCopasiMessage::getLastMessage();
CPPUNIT_ASSERT(message.getType() == CCopasiMessage::WARNING);
std::string s = message.getText();
CPPUNIT_ASSERT(!s.empty());
CPPUNIT_ASSERT(s.find(std::string("COPASI does not support time delays. Calculations on this model will most likely lead to unusable results.")) != std::string::npos);
// right now, we don't care about the last message since it is a units
// warning from libSBML
}
void test000052::test_bug988()
{
CDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING));
CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CUnit::mMol);
CPPUNIT_ASSERT(pModel->getVolumeUnitEnum() == CUnit::ml);
CPPUNIT_ASSERT(pModel->getTimeUnitEnum() == CUnit::s);
CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
const CCompartment* pCompartment = pModel->getCompartments()[0];
CPPUNIT_ASSERT(pCompartment != NULL);
CPPUNIT_ASSERT(pCompartment->getStatus() == CModelEntity::Status::FIXED);
CPPUNIT_ASSERT(pModel->getMetabolites().size() == 1);
CMetab* pA = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pA != NULL);
CPPUNIT_ASSERT(pA->getStatus() == CModelEntity::Status::ASSIGNMENT);
const CExpression* pExpr = pA->getExpressionPtr();
// check the expression
const CEvaluationNode* pNode = pExpr->getRoot();
CPPUNIT_ASSERT(pNode != NULL);
const CEvaluationNodeChoice* pChoiceNode = dynamic_cast<const CEvaluationNodeChoice*>(pNode);
CPPUNIT_ASSERT(pChoiceNode != NULL);
pNode = dynamic_cast<const CEvaluationNode*>(pChoiceNode->getChild());
CPPUNIT_ASSERT(pNode != NULL);
const CEvaluationNodeLogical* pLogicalNode = dynamic_cast<const CEvaluationNodeLogical*>(pNode);
CPPUNIT_ASSERT(pLogicalNode != NULL);
CPPUNIT_ASSERT((pLogicalNode->subType()) == CEvaluationNode::SubType::LT);
const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pLogicalNode->getChild());
CPPUNIT_ASSERT(pObjectNode != NULL);
CCommonName objectCN = pObjectNode->getObjectCN();
CPPUNIT_ASSERT(!objectCN.empty());
CObjectInterface::ContainerList listOfContainers;
listOfContainers.push_back(pModel);
const CDataObject* pObject = CObjectInterface::DataModel(pCOPASIDATAMODEL->getObjectFromCN(listOfContainers, objectCN));
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->hasFlag(CDataObject::Reference) == true);
CPPUNIT_ASSERT(pObject->getObjectName() == std::string("Time"));
CPPUNIT_ASSERT(pObject->getObjectParent() == pModel);
const CEvaluationNodeNumber* pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pObjectNode->getSibling());
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT((pNumberNode->subType()) == CEvaluationNode::SubType::DOUBLE);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 5.0) / 5.0) < 1e-3);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pLogicalNode->getSibling());
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT((pNumberNode->subType()) == CEvaluationNode::SubType::DOUBLE);
CPPUNIT_ASSERT(pNumberNode->getValue() < 1e-3);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pNumberNode->getSibling());
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT((pNumberNode->subType()) == CEvaluationNode::SubType::DOUBLE);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 10.0) / 10.0) < 1e-3);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 0);
CPPUNIT_ASSERT(pModel->getReactions().size() == 0);
}
void CModelExpansion::duplicateMetab(const CMetab* source, const std::string & index, const SetOfModelElements & sourceSet, ElementsMap & emap)
{
//if the source object has already been duplicated: do nothing
if (emap.exists(source))
return;
//is the containing compartment also duplicated?
const CCompartment* sourceParent = source->getCompartment();
const CCompartment * parent = NULL;
bool nameflag;
if (!sourceSet.contains(sourceParent))
{
parent = sourceParent; //use the original parent compartment
nameflag = true; //metab needs renaming
}
else //use a copy of the parent compartment
{
nameflag = false; //no renaming necessary (since the copy is in a different compartment)
//create copy if it does not exist
if (!emap.exists(sourceParent))
{
duplicateCompartment(sourceParent, index, sourceSet, emap);
}
parent = dynamic_cast<CCompartment *>(emap.getDuplicatePtr(sourceParent));
}
//try creating the object until we find a name that is not yet used
CMetab* newObj;
std::ostringstream infix;
do
{
std::ostringstream name;
name << source->getObjectName() << infix.str();
if (nameflag)
name << index;
newObj = mpModel->createMetabolite(name.str(), parent->getObjectName(), source->getInitialConcentration(), source->getStatus());
infix << "_";
}
while (!newObj);
//add duplicated object to the map
emap.add(source, newObj);
//expression (for assignment or ODE)
newObj->setExpression(source->getExpression());
updateExpression(newObj->getExpressionPtr(), index, sourceSet, emap);
//initial expression
newObj->setInitialExpression(source->getInitialExpression());
updateExpression(newObj->getInitialExpressionPtr(), index, sourceSet, emap);
newObj->setNotes(source->getNotes());
newObj->setMiriamAnnotation(source->getMiriamAnnotation(), newObj->getKey(), source->getKey());
}
bool CModelMerging::mergeMetabolites(std::string toKey, std::string key)
{
bool info = false;
//merge in the relevant reactions
size_t i, imax = mpModel->getReactions().size();
size_t j, jmax;
for (i = 0; i < imax; ++i)
{
CReaction * reac = &mpModel->getReactions()[i];
jmax = reac->getChemEq().getSubstrates().size();
for (j = 0; j < jmax; ++j)
{
CChemEqElement * subst = const_cast< CChemEqElement * >(&reac->getChemEq().getSubstrates()[j]);
if (subst->getMetabolite()->getKey() == key)
subst->setMetabolite(toKey);
}
jmax = reac->getChemEq().getProducts().size();
for (j = 0; j < jmax; ++j)
{
CChemEqElement * prod = const_cast< CChemEqElement * >(&reac->getChemEq().getProducts()[j]);
if (prod->getMetabolite()->getKey() == key)
prod->setMetabolite(toKey);
}
jmax = reac->getChemEq().getModifiers().size();
for (j = 0; j < jmax; ++j)
{
CChemEqElement * modif = const_cast< CChemEqElement * >(&reac->getChemEq().getModifiers()[j]);
if (modif->getMetabolite()->getKey() == key)
modif->setMetabolite(toKey);
}
//change parameters of the kinetic function
for (j = 0; j < reac->getFunctionParameters().size(); ++j)
{
switch (reac->getFunctionParameters()[j]->getUsage())
{
case CFunctionParameter::SUBSTRATE:
case CFunctionParameter::PRODUCT:
case CFunctionParameter::MODIFIER:
//translate the metab keys
{
//we assume that only SUBSTRATE, PRODUCT, MODIFIER can be vectors
size_t k, kmax = reac->getParameterMappings()[j].size();
for (k = 0; k < kmax; ++k)
if (reac->getParameterMappings()[j][k] == key)
reac->getParameterMappings()[j][k] = toKey;
}
break;
case CFunctionParameter::TIME:
break;
case CFunctionParameter::VOLUME:
// ??? TODO : have to ask
break;
case CFunctionParameter::PARAMETER:
break;
default:
return info;
break;
}
}
}
imax = mpModel->getEvents().size();
for (i = 0; i < imax; ++i)
{
CEvent * event = &mpModel->getEvents()[i];
if (!event) return info;
/* merge in trigger expressions */
CExpression* pExpression = event->getTriggerExpressionPtr();
if (pExpression == NULL) return info;
if (!mergeInExpression(toKey, key, pExpression)) return info;
pExpression = event->getDelayExpressionPtr();
if (pExpression)
if (!mergeInExpression(toKey, key, pExpression))
return info;
jmax = event->getAssignments().size();
for (j = 0; j < jmax; ++j)
{
CEventAssignment* assignment = &event->getAssignments()[j];
if (!assignment) return info;
std::string assignmentKey = assignment->getTargetKey();
if (assignmentKey == key) assignment->setTargetKey(toKey);
pExpression = assignment->getExpressionPtr();
if (pExpression == NULL) return info;
if (!mergeInExpression(toKey, key, pExpression)) return info;
}
}
imax = mpModel->getMetabolites().size();
for (i = 0; i < imax; ++i)
{
CMetab* metab = &mpModel->getMetabolites()[i];
if (!metab) return info;
switch (metab->getStatus())
{
case CModelEntity::FIXED:
case CModelEntity::REACTIONS:
break;
case CModelEntity::ASSIGNMENT:
if (!mergeInExpression(toKey, key, metab->getExpressionPtr())) return info;
break;
case CModelEntity::ODE:
if (!mergeInExpression(toKey, key, metab->getExpressionPtr())) return info;
if (metab->getInitialExpression() != "")
if (!mergeInExpression(toKey, key, metab->getInitialExpressionPtr())) return info;
break;
default:
return info;
break;
}
}
imax = mpModel->getCompartments().size();
for (i = 0; i < imax; ++i)
{
CCompartment* comp = &mpModel->getCompartments()[i];
if (!comp) return info;
switch (comp ->getStatus())
{
case CModelEntity::FIXED:
break;
case CModelEntity::ASSIGNMENT:
if (!mergeInExpression(toKey, key, comp->getExpressionPtr())) return info;
break;
case CModelEntity::ODE:
if (!mergeInExpression(toKey, key, comp->getExpressionPtr())) return info;
if (comp->getInitialExpression() != "")
if (!mergeInExpression(toKey, key, comp->getInitialExpressionPtr())) return info;
break;
default:
return info;
break;
}
}
imax = mpModel->getModelValues().size();
for (i = 0; i < imax; ++i)
{
CModelValue* modval = &mpModel->getModelValues()[i];
if (!modval) return info;
switch (modval ->getStatus())
{
case CModelEntity::FIXED:
break;
case CModelEntity::ASSIGNMENT:
if (!mergeInExpression(toKey, key, modval->getExpressionPtr())) return info;
break;
case CModelEntity::ODE:
if (!mergeInExpression(toKey, key, modval->getExpressionPtr())) return info;
if (modval->getInitialExpression() != "")
if (!mergeInExpression(toKey, key, modval->getInitialExpressionPtr())) return info;
break;
default:
return info;
break;
}
}
return true;
}