void test000053::test4_bug1000()
{
// load the CPS file
// export to SBML
// check the resulting SBML model
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(test000053::MODEL_STRING_4));
const CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 0);
CPPUNIT_ASSERT(pModel->getReactions().size() == 0);
CPPUNIT_ASSERT(pModel->getMetabolites().size() == 1);
const CMetab* pMetab = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "A");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::ASSIGNMENT);
const CExpression* pExpr = pMetab->getExpressionPtr();
CPPUNIT_ASSERT(pExpr != NULL);
const CEvaluationNode* pRoot = pExpr->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(pRoot->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pRoot->subType()) == CEvaluationNode::S_DOUBLE);
const CEvaluationNodeNumber* pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pRoot);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 1.5) / 1.5) < 1e-6);
}
void test000080::test_mass_action_recognition_bug()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
try
{
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(test000080::MODEL_STRING1));
}
catch (...)
{
// there should not be an exception
CPPUNIT_ASSERT(false);
}
const CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getReactions().size() == 1);
const CReaction* pReaction = pModel->getReactions()[0];
CPPUNIT_ASSERT(pReaction != NULL);
const CFunction* pFun = pReaction->getFunction();
CPPUNIT_ASSERT(pFun != NULL);
CPPUNIT_ASSERT(pFun->getType() == CEvaluationTree::UserDefined);
}
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 test000046::test_stoichiometricExpression()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING));
CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CModel::mMol);
CPPUNIT_ASSERT(pModel->getVolumeUnitEnum() == CModel::ml);
CPPUNIT_ASSERT(pModel->getTimeUnitEnum() == CModel::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);
CMetab* pA = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pA != NULL);
CPPUNIT_ASSERT(pA->getStatus() == CModelEntity::REACTIONS);
const CMetab* pB = pModel->getMetabolites()[1];
CPPUNIT_ASSERT(pB != NULL);
CPPUNIT_ASSERT(pB->getStatus() == CModelEntity::REACTIONS);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 1);
const CModelValue* pModelValue = pModel->getModelValues()[0];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::FIXED);
CPPUNIT_ASSERT(fabs((pModelValue->getInitialValue() - 3.7) / 3.7) < 1e-3);
CPPUNIT_ASSERT(pModel->getReactions().size() == 1);
const CReaction* pReaction1 = pModel->getReactions()[0];
CPPUNIT_ASSERT(pReaction1 != NULL);
CPPUNIT_ASSERT(pReaction1->isReversible() == true);
// check the kinetic law
const CFunction* pKineticFunction = pReaction1->getFunction();
CPPUNIT_ASSERT(pKineticFunction != NULL);
const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
CPPUNIT_ASSERT(pMassAction != NULL);
const CChemEq* pChemEq = &pReaction1->getChemEq();
CPPUNIT_ASSERT(pChemEq != NULL);
CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
CPPUNIT_ASSERT(pElement != NULL);
CPPUNIT_ASSERT(fabs((pElement->getMultiplicity() - 1.85) / 1.85) < 1e-3);
CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
pElement = pChemEq->getProducts()[0];
CPPUNIT_ASSERT(pElement != NULL);
CPPUNIT_ASSERT(fabs((pElement->getMultiplicity() - 3.35) / 3.35) / 3.35 < 1e-3);
CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
//CPPUNIT_ASSERT(CCopasiMessage::size() == 5);
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("One or more stoichiometric expressions were evaluated and converted to constants values.")) != std::string::npos);
// the other four messages are libSBML unit warnings I don't care about right
// now.
}
void test000052::test_bug988()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING));
CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CModel::mMol);
CPPUNIT_ASSERT(pModel->getVolumeUnitEnum() == CModel::ml);
CPPUNIT_ASSERT(pModel->getTimeUnitEnum() == CModel::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() == 1);
CMetab* pA = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pA != NULL);
CPPUNIT_ASSERT(pA->getStatus() == CModelEntity::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(((CEvaluationNodeLogical::SubType)CEvaluationNode::subType(pLogicalNode->getType())) == CEvaluationNodeLogical::LT);
const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pLogicalNode->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("Time"));
CPPUNIT_ASSERT(pObject->getObjectParent() == pModel);
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() - 5.0) / 5.0) < 1e-3);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pLogicalNode->getSibling());
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(((CEvaluationNodeNumber::SubType)CEvaluationNode::subType(pNumberNode->getType())) == CEvaluationNodeNumber::DOUBLE);
CPPUNIT_ASSERT(pNumberNode->getValue() < 1e-3);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pNumberNode->getSibling());
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(((CEvaluationNodeNumber::SubType)CEvaluationNode::subType(pNumberNode->getType())) == CEvaluationNodeNumber::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 test000027::test_hasOnlySubstanceUnits()
{
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);
CMetab* pA = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pA != NULL);
CPPUNIT_ASSERT(pA->getStatus() == CModelEntity::REACTIONS);
const CMetab* pB = pModel->getMetabolites()[1];
CPPUNIT_ASSERT(pB != NULL);
CPPUNIT_ASSERT(pB->getStatus() == CModelEntity::REACTIONS);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 2);
// check the kinetic law
const CModelValue* pFactor = pModel->getModelValues()[1];
CPPUNIT_ASSERT(pFactor != NULL);
CPPUNIT_ASSERT(pFactor->getStatus() == CModelEntity::FIXED);
CPPUNIT_ASSERT(fabs((pFactor->getInitialValue() - pModel->getQuantity2NumberFactor()) / pModel->getQuantity2NumberFactor()) < 1e-3);
const CModelValue* pModelValue = pModel->getModelValues()[0];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::ASSIGNMENT);
const CExpression* pExpr = pModelValue->getExpressionPtr();
// check the expression
const CEvaluationNode* pNode = pExpr->getRoot();
CPPUNIT_ASSERT(pNode != NULL);
const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pNode);
CPPUNIT_ASSERT(pObjectNode != NULL);
CCopasiObjectName objectCN = pObjectNode->getObjectCN();
CPPUNIT_ASSERT(!objectCN.empty());
CObjectInterface::ContainerList listOfContainers;
listOfContainers.push_back(pModel);
const CCopasiObject* pObject = CObjectInterface::DataModel(pCOPASIDATAMODEL->getObjectFromCN(listOfContainers, objectCN));
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isReference() == true);
CPPUNIT_ASSERT(pObject->getObjectName() == std::string("ParticleNumber"));
CPPUNIT_ASSERT(pObject->getObjectParent() == pA);
CPPUNIT_ASSERT(pModel->getReactions().size() == 2);
const CReaction* pReaction1 = pModel->getReactions()[0];
CPPUNIT_ASSERT(pReaction1 != NULL);
CPPUNIT_ASSERT(pReaction1->isReversible() == false);
const CFunction* pKineticFunction = pReaction1->getFunction();
CPPUNIT_ASSERT(pKineticFunction != NULL);
const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
//FTB: this no longer is recognized as mass action reaction because of the
// special case of a species with hOSU
CPPUNIT_ASSERT(pMassAction == NULL);
const CChemEq* pChemEq = &pReaction1->getChemEq();
CPPUNIT_ASSERT(pChemEq != NULL);
CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
CPPUNIT_ASSERT(pElement != NULL);
CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
CPPUNIT_ASSERT(pChemEq->getProducts().size() == 0);
CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
const CReaction* pReaction2 = pModel->getReactions()[1];
CPPUNIT_ASSERT(pReaction2 != NULL);
CPPUNIT_ASSERT(pReaction2->isReversible() == false);
// check the kinetic law
pKineticFunction = pReaction2->getFunction();
CPPUNIT_ASSERT(pKineticFunction != NULL);
CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Henri-Michaelis-Menten (irreversible)"));
// check the function parameters one should be the reference to the substrate
pChemEq = &pReaction2->getChemEq();
CPPUNIT_ASSERT(pChemEq != NULL);
CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
pElement = pChemEq->getSubstrates()[0];
CPPUNIT_ASSERT(pElement != NULL);
CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
pElement = pChemEq->getProducts()[0];
CPPUNIT_ASSERT(pElement != NULL);
CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
CPPUNIT_ASSERT(parameterMappings.size() == 3);
CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
const std::string parameterKey = parameterMappings[0][0];
CPPUNIT_ASSERT(parameterKey == pA->getKey());
}
void test000068::test_bug1068()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING1));
CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CUnit::Mol);
CPPUNIT_ASSERT(pModel->getVolumeUnitEnum() == CUnit::l);
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() == 6);
// check metabolites
const CMetab* pMetab = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "A");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::REACTIONS);
pMetab = pModel->getMetabolites()[1];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "B");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::REACTIONS);
pMetab = pModel->getMetabolites()[2];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "C");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::ASSIGNMENT);
// check assignment
const CEvaluationTree* pTree = pMetab->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
const CEvaluationNode* pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_5");
pMetab = pModel->getMetabolites()[3];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "D");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::ODE);
// check ode
pTree = pMetab->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_2");
pMetab = pModel->getMetabolites()[4];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "E");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::ODE);
// check ode
pTree = pMetab->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_4");
pMetab = pModel->getMetabolites()[5];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "F");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::ODE);
// check ode
pTree = pMetab->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_6");
// check model values
CPPUNIT_ASSERT(pModel->getModelValues().size() == 3);
const CModelValue* pModelValue = pModel->getModelValues()[0];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getObjectName() == "K1");
CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::ASSIGNMENT);
// check assignment
pTree = pModelValue->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_1");
pModelValue = pModel->getModelValues()[1];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getObjectName() == "K2");
CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::FIXED);
pModelValue = pModel->getModelValues()[2];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getObjectName() == "K3");
// check assignment
pTree = pModelValue->getExpressionPtr();
CPPUNIT_ASSERT(pTree != NULL);
pRoot = pTree->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot) != NULL);
CPPUNIT_ASSERT(dynamic_cast<const CEvaluationNodeCall*>(pRoot)->getData() == "function_3");
CPPUNIT_ASSERT(pModel->getReactions().size() == 6);
// check reactions
const CReaction* pReaction = pModel->getReactions()[0];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 1);
const CFunction* pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction1");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
pReaction = pModel->getReactions()[1];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 2);
pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction2");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
pReaction = pModel->getReactions()[2];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 1);
pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction3");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
pReaction = pModel->getReactions()[3];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 0);
pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction4");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
pReaction = pModel->getReactions()[4];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 2);
pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction5");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
pReaction = pModel->getReactions()[5];
CPPUNIT_ASSERT(pReaction != NULL);
CPPUNIT_ASSERT(pReaction->getChemEq().getSubstrates().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getProducts().size() == 1);
CPPUNIT_ASSERT(pReaction->getChemEq().getModifiers().size() == 0);
CPPUNIT_ASSERT(pReaction->isReversible() == true);
// check the kinetic law
CPPUNIT_ASSERT(pReaction->getParameters().size() == 3);
pFunction = pReaction->getFunction();
CPPUNIT_ASSERT(pFunction != NULL);
CPPUNIT_ASSERT(pFunction->getType() == CEvaluationTree::UserDefined);
CPPUNIT_ASSERT(pFunction->getObjectName() == "Function for reaction6");
pRoot = pFunction->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
// export to SBML
std::string s = pDataModel->exportSBMLToString(NULL, 1, 2);
CPPUNIT_ASSERT(s.empty() == false);
// due to the bugfix for Bug 1086 and some issues with libsbml and the current exporter,
// we now no longer have a L1 document in the datamodel if there was an SBMLDocument prior
// to exporting to L1 already.
// To test now, we have to call newModel on the datamodel to delete the old sbml document,
// and reimport the exported model
// This will also lead to a Level 2 Version 1 model since we convert all Level 1 model to
// Level 2 Version 1 on import, but we can at least test if the export worked.
pCOPASIDATAMODEL->newModel(NULL, true);
CPPUNIT_ASSERT(pCOPASIDATAMODEL->importSBMLFromString(s));
// check the sbml model
const SBMLDocument* pDocument = pCOPASIDATAMODEL->getCurrentSBMLDocument();
CPPUNIT_ASSERT(pDocument != NULL);
CPPUNIT_ASSERT(pDocument->getLevel() == 2);
CPPUNIT_ASSERT(pDocument->getVersion() == 1);
const Model* pSBMLModel = pDocument->getModel();
CPPUNIT_ASSERT(pSBMLModel != NULL);
CPPUNIT_ASSERT(pSBMLModel->getListOfFunctionDefinitions()->size() == 0);
CPPUNIT_ASSERT(pSBMLModel->getListOfCompartments()->size() == 1);
CPPUNIT_ASSERT(pSBMLModel->getListOfSpecies()->size() == 6);
CPPUNIT_ASSERT(pSBMLModel->getListOfParameters()->size() == 3);
CPPUNIT_ASSERT(pSBMLModel->getListOfRules()->size() == 6);
CPPUNIT_ASSERT(pSBMLModel->getListOfReactions()->size() == 6);
std::map<std::string, const Rule*> ruleMap;
unsigned int i, iMax = pSBMLModel->getListOfRules()->size();
const Rule* pRule = NULL;
for (i = 0; i < iMax; ++i)
{
pRule = pSBMLModel->getRule(i);
ruleMap.insert(std::pair<std::string, const Rule*>(pRule->getVariable(), pRule));
}
// check the rules
std::map<std::string, const Rule*>::const_iterator pos = ruleMap.find("parameter_1");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "parameter_1");
const ASTNode* pMath = pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
std::string formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "3 * 4.5");
pos = ruleMap.find("parameter_3");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "parameter_3");
pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "parameter_1 - 2 * 1.3");
pos = ruleMap.find("species_3");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "species_3");
pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "parameter_1 - 3.5 * 1.3 + (3 * 2.4 - 5.23)");
pos = ruleMap.find("species_4");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "species_4");
pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "3.4 + parameter_1");
pos = ruleMap.find("species_5");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "species_5");
pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "(parameter_2 + 1.4) / 2");
pos = ruleMap.find("species_6");
CPPUNIT_ASSERT(pos != ruleMap.end());
pRule = pos->second;
CPPUNIT_ASSERT(pRule != NULL);
CPPUNIT_ASSERT(pRule->getVariable() == "species_6");
pRule->getMath();
CPPUNIT_ASSERT(pMath != NULL);
// only check the infix
formula = pRule->getFormula();
CPPUNIT_ASSERT(formula == "parameter_3 - 3.4 * 1.3 + (3 * parameter_1 - 5.23)");
// check the reactions
const Reaction* pSBMLReaction = pSBMLModel->getReaction(0);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * 3 * parameter_1");
pSBMLReaction = pSBMLModel->getReaction(1);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * (parameter_2 + parameter_1)");
pSBMLReaction = pSBMLModel->getReaction(2);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * (species_2 - parameter_1 * 1.3)");
pSBMLReaction = pSBMLModel->getReaction(3);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * ((species_2 + species_1) / 2)");
pSBMLReaction = pSBMLModel->getReaction(4);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * (parameter_1 - species_2 * 1.3 + (3 * parameter_3 - 5.23))");
pSBMLReaction = pSBMLModel->getReaction(5);
CPPUNIT_ASSERT(pSBMLReaction != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getListOfReactants()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfProducts()->size() == 1);
CPPUNIT_ASSERT(pSBMLReaction->getListOfModifiers()->size() == 0);
CPPUNIT_ASSERT(pSBMLReaction->getReversible() == true);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw() != NULL);
CPPUNIT_ASSERT(pSBMLReaction->getKineticLaw()->getListOfParameters()->size() == 0);
pMath = pSBMLReaction->getKineticLaw()->getMath();
CPPUNIT_ASSERT(pMath != NULL);
formula = pSBMLReaction->getKineticLaw()->getFormula();
CPPUNIT_ASSERT(formula == "compartment_1 * (parameter_1 - parameter_3 * 1.3 + (3 * parameter_2 - 5.23))");
}
void test000043::test_hasOnlySubstanceUnits()
{
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING));
CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CUnit::number);
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);
CMetab* pA = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pA != NULL);
CPPUNIT_ASSERT(pA->getStatus() == CModelEntity::REACTIONS);
const CMetab* pB = pModel->getMetabolites()[1];
CPPUNIT_ASSERT(pB != NULL);
CPPUNIT_ASSERT(pB->getStatus() == CModelEntity::REACTIONS);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 1);
const CModelValue* pModelValue = pModel->getModelValues()[0];
CPPUNIT_ASSERT(pModelValue != NULL);
CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::FIXED);
CPPUNIT_ASSERT(pModelValue->getInitialExpression() != "");
const CExpression* pExpr = pModelValue->getInitialExpressionPtr();
CPPUNIT_ASSERT(pExpr != NULL);
// check the expression
const CEvaluationNode* pNode = pExpr->getRoot();
CPPUNIT_ASSERT(pNode != NULL);
const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pNode);
CPPUNIT_ASSERT(pObjectNode != NULL);
CCopasiObjectName objectCN = pObjectNode->getObjectCN();
CPPUNIT_ASSERT(!objectCN.empty());
CObjectInterface::ContainerList listOfContainers;
listOfContainers.push_back(pModel);
const CCopasiObject* pObject = CObjectInterface::DataModel(pCOPASIDATAMODEL->getObjectFromCN(listOfContainers, objectCN));
CPPUNIT_ASSERT(pObject != NULL);
CPPUNIT_ASSERT(pObject->isReference() == true);
CPPUNIT_ASSERT(pObject->getObjectName() == std::string("InitialParticleNumber"));
CPPUNIT_ASSERT(pObject->getObjectParent() == pA);
// check the reactions
CPPUNIT_ASSERT(pModel->getReactions().size() == 2);
const CReaction* pReaction1 = pModel->getReactions()[0];
CPPUNIT_ASSERT(pReaction1 != NULL);
CPPUNIT_ASSERT(pReaction1->isReversible() == false);
// check the kinetic law
const CFunction* pKineticFunction = pReaction1->getFunction();
CPPUNIT_ASSERT(pKineticFunction != NULL);
const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
//FTB: this no longer is recognized as mass action reaction because of the
// special case of a species with hOSU
CPPUNIT_ASSERT(pMassAction == NULL);
const CChemEq* pChemEq = &pReaction1->getChemEq();
CPPUNIT_ASSERT(pChemEq != NULL);
CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
CPPUNIT_ASSERT(pElement != NULL);
CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
CPPUNIT_ASSERT(pChemEq->getProducts().size() == 0);
CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
const CReaction* pReaction2 = pModel->getReactions()[1];
CPPUNIT_ASSERT(pReaction2 != NULL);
CPPUNIT_ASSERT(pReaction2->isReversible() == false);
// check the kinetic law
pKineticFunction = pReaction2->getFunction();
CPPUNIT_ASSERT(pKineticFunction != NULL);
CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Function for reaction_1"));
const CFunctionParameters* pFunctionParameters = &pKineticFunction->getVariables();
CPPUNIT_ASSERT(pFunctionParameters->size() == 4);
const CFunctionParameter* pFunctionParameter = (*pFunctionParameters)[0];
CPPUNIT_ASSERT(pFunctionParameter != NULL);
CPPUNIT_ASSERT(pFunctionParameter->getType() == CFunctionParameter::FLOAT64);
CPPUNIT_ASSERT(pFunctionParameter->getUsage() == CFunctionParameter::PARAMETER);
pFunctionParameter = (*pFunctionParameters)[1];
CPPUNIT_ASSERT(pFunctionParameter != NULL);
CPPUNIT_ASSERT(pFunctionParameter->getType() == CFunctionParameter::FLOAT64);
CPPUNIT_ASSERT(pFunctionParameter->getUsage() == CFunctionParameter::PARAMETER);
pFunctionParameter = (*pFunctionParameters)[2];
CPPUNIT_ASSERT(pFunctionParameter != NULL);
CPPUNIT_ASSERT(pFunctionParameter->getType() == CFunctionParameter::FLOAT64);
CPPUNIT_ASSERT(pFunctionParameter->getUsage() == CFunctionParameter::VOLUME);
pFunctionParameter = (*pFunctionParameters)[3];
CPPUNIT_ASSERT(pFunctionParameter != NULL);
CPPUNIT_ASSERT(pFunctionParameter->getType() == CFunctionParameter::FLOAT64);
CPPUNIT_ASSERT(pFunctionParameter->getUsage() == CFunctionParameter::SUBSTRATE);
pNode = pKineticFunction->getRoot();
const CEvaluationNodeCall* pCallNode = dynamic_cast<const CEvaluationNodeCall*>(pNode);
CPPUNIT_ASSERT(pCallNode != NULL);
CPPUNIT_ASSERT((pCallNode->subType()) == CEvaluationNode::S_FUNCTION);
CPPUNIT_ASSERT(pCallNode->getData() == std::string("Henri-Michaelis-Menten (irreversible)_2"));
const CEvaluationNodeOperator* pOperatorNode = dynamic_cast<const CEvaluationNodeOperator*>(pCallNode->getChild());
CPPUNIT_ASSERT(pOperatorNode != NULL);
CPPUNIT_ASSERT((pOperatorNode->subType()) == CEvaluationNode::S_MULTIPLY);
const CEvaluationNodeVariable* pVariableNode = dynamic_cast<const CEvaluationNodeVariable*>(pOperatorNode->getChild());
CPPUNIT_ASSERT(pVariableNode != NULL);
CPPUNIT_ASSERT(pVariableNode->getIndex() == 3);
pVariableNode = dynamic_cast<const CEvaluationNodeVariable*>(pOperatorNode->getChild()->getSibling());
CPPUNIT_ASSERT(pVariableNode != NULL);
CPPUNIT_ASSERT(pVariableNode->getIndex() == 2);
pVariableNode = dynamic_cast<const CEvaluationNodeVariable*>(pCallNode->getChild()->getSibling());
CPPUNIT_ASSERT(pVariableNode != NULL);
CPPUNIT_ASSERT(pVariableNode->getIndex() == 0);
pVariableNode = dynamic_cast<const CEvaluationNodeVariable*>(pCallNode->getChild()->getSibling()->getSibling());
CPPUNIT_ASSERT(pVariableNode != NULL);
CPPUNIT_ASSERT(pVariableNode->getIndex() == 1);
pKineticFunction = dynamic_cast<const CFunction*>(pCallNode->getCalledTree());
CPPUNIT_ASSERT(pKineticFunction != NULL);
CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Henri-Michaelis-Menten (irreversible)_2"));
pNode = pKineticFunction->getRoot();
CPPUNIT_ASSERT(pNode != NULL);
pOperatorNode = dynamic_cast<const CEvaluationNodeOperator*>(pNode);
CPPUNIT_ASSERT(pOperatorNode != NULL);
CPPUNIT_ASSERT((pOperatorNode->subType()) == CEvaluationNode::S_DIVIDE);
const CEvaluationNodeOperator* pOperatorNode2 = dynamic_cast<const CEvaluationNodeOperator*>(pOperatorNode->getChild());
CPPUNIT_ASSERT(pOperatorNode2 != NULL);
CPPUNIT_ASSERT((pOperatorNode2->subType()) == CEvaluationNode::S_MULTIPLY);
pVariableNode = dynamic_cast<const CEvaluationNodeVariable*>(pOperatorNode2->getChild());
CPPUNIT_ASSERT(pVariableNode != NULL);
CPPUNIT_ASSERT(pVariableNode->getIndex() == 2);
pVariableNode = dynamic_cast<const CEvaluationNodeVariable*>(pOperatorNode2->getChild()->getSibling());
CPPUNIT_ASSERT(pVariableNode != NULL);
CPPUNIT_ASSERT(pVariableNode->getIndex() == 0);
pOperatorNode2 = dynamic_cast<const CEvaluationNodeOperator*>(pOperatorNode->getChild()->getSibling());
CPPUNIT_ASSERT(pOperatorNode2 != NULL);
CPPUNIT_ASSERT((pOperatorNode2->subType()) == CEvaluationNode::S_PLUS);
pVariableNode = dynamic_cast<const CEvaluationNodeVariable*>(pOperatorNode2->getChild());
CPPUNIT_ASSERT(pVariableNode != NULL);
CPPUNIT_ASSERT(pVariableNode->getIndex() == 1);
pVariableNode = dynamic_cast<const CEvaluationNodeVariable*>(pOperatorNode2->getChild()->getSibling());
CPPUNIT_ASSERT(pVariableNode != NULL);
CPPUNIT_ASSERT(pVariableNode->getIndex() == 0);
// check the function parameters one should be the reference to the substrate
pChemEq = &pReaction2->getChemEq();
CPPUNIT_ASSERT(pChemEq != NULL);
CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
pElement = pChemEq->getSubstrates()[0];
CPPUNIT_ASSERT(pElement != NULL);
CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
pElement = pChemEq->getProducts()[0];
CPPUNIT_ASSERT(pElement != NULL);
CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
CPPUNIT_ASSERT(parameterMappings.size() == 4);
CPPUNIT_ASSERT(parameterMappings[2].size() == 1);
std::string parameterKey = parameterMappings[2][0];
CPPUNIT_ASSERT(parameterKey == pCompartment->getKey());
CPPUNIT_ASSERT(parameterMappings[3].size() == 1);
parameterKey = parameterMappings[3][0];
CPPUNIT_ASSERT(parameterKey == pA->getKey());
}
void test000053::test5_bug1000()
{
// load the CPS file
// export to SBML
// check the resulting SBML model
CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
CPPUNIT_ASSERT(pDataModel->importSBMLFromString(test000053::MODEL_STRING_5));
const CModel* pModel = pDataModel->getModel();
CPPUNIT_ASSERT(pModel != NULL);
CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
CPPUNIT_ASSERT(pModel->getModelValues().size() == 0);
CPPUNIT_ASSERT(pModel->getReactions().size() == 0);
CPPUNIT_ASSERT(pModel->getMetabolites().size() == 1);
const CMetab* pMetab = pModel->getMetabolites()[0];
CPPUNIT_ASSERT(pMetab != NULL);
CPPUNIT_ASSERT(pMetab->getObjectName() == "A");
CPPUNIT_ASSERT(pMetab->getStatus() == CModelEntity::ASSIGNMENT);
const CExpression* pExpr = pMetab->getExpressionPtr();
CPPUNIT_ASSERT(pExpr != NULL);
const CEvaluationNode* pRoot = pExpr->getRoot();
CPPUNIT_ASSERT(pRoot != NULL);
CPPUNIT_ASSERT(pRoot->mainType() == CEvaluationNode::T_CHOICE);
const CEvaluationNodeChoice* pChoiceNode = dynamic_cast<const CEvaluationNodeChoice*>(pRoot);
CPPUNIT_ASSERT(pChoiceNode != NULL);
const CEvaluationNode* pChild1 = dynamic_cast<const CEvaluationNode*>(pChoiceNode->getChild());
CPPUNIT_ASSERT(pChild1 != NULL);
const CEvaluationNode* pChild2 = dynamic_cast<const CEvaluationNode*>(pChild1->getSibling());
CPPUNIT_ASSERT(pChild2 != NULL);
CPPUNIT_ASSERT(pChild2->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild2->subType()) == CEvaluationNode::S_DOUBLE);
const CEvaluationNodeNumber* pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild2);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 0.1) / 0.1) < 1e-6);
const CEvaluationNode* pChild3 = dynamic_cast<const CEvaluationNode*>(pChild2->getSibling());
CPPUNIT_ASSERT(pChild3 != NULL);
CPPUNIT_ASSERT(pChild3->mainType() == CEvaluationNode::T_CHOICE);
pChoiceNode = dynamic_cast<const CEvaluationNodeChoice*>(pChild3);
CPPUNIT_ASSERT(pChoiceNode);
CPPUNIT_ASSERT(pChild1->mainType() == CEvaluationNode::T_LOGICAL);
CPPUNIT_ASSERT((pChild1->subType()) == CEvaluationNode::S_LT);
pChild1 = dynamic_cast<const CEvaluationNode*>(pChild1->getChild());
CPPUNIT_ASSERT(pChild1 != NULL);
CPPUNIT_ASSERT(pChild1->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild1->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild1);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 3.0) / 3.0) < 1e-6);
pChild2 = dynamic_cast<const CEvaluationNode*>(pChild1->getSibling());
CPPUNIT_ASSERT(pChild2 != NULL);
CPPUNIT_ASSERT(pChild2->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild2->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild2);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 4.0) / 4.0) < 1e-6);
// second choice level (child3 of first choice level)
pChild1 = dynamic_cast<const CEvaluationNode*>(pChoiceNode->getChild());
CPPUNIT_ASSERT(pChild1 != NULL);
pChild2 = dynamic_cast<const CEvaluationNode*>(pChild1->getSibling());
CPPUNIT_ASSERT(pChild2 != NULL);
CPPUNIT_ASSERT(pChild2->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild2->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild2);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 0.2) / 0.2) < 1e-6);
pChild3 = dynamic_cast<const CEvaluationNode*>(pChild2->getSibling());
CPPUNIT_ASSERT(pChild3 != NULL);
CPPUNIT_ASSERT(pChild3->mainType() == CEvaluationNode::T_CHOICE);
pChoiceNode = dynamic_cast<const CEvaluationNodeChoice*>(pChild3);
CPPUNIT_ASSERT(pChoiceNode);
CPPUNIT_ASSERT(pChild1->mainType() == CEvaluationNode::T_LOGICAL);
CPPUNIT_ASSERT((pChild1->subType()) == CEvaluationNode::S_GT);
pChild1 = dynamic_cast<const CEvaluationNode*>(pChild1->getChild());
CPPUNIT_ASSERT(pChild1 != NULL);
CPPUNIT_ASSERT(pChild1->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild1->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild1);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 3.0) / 3.0) < 1e-6);
pChild2 = dynamic_cast<const CEvaluationNode*>(pChild1->getSibling());
CPPUNIT_ASSERT(pChild2 != NULL);
CPPUNIT_ASSERT(pChild2->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild2->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild2);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 4.0) / 4.0) < 1e-6);
// third choice level (child3 of second choice level)
pChild1 = dynamic_cast<const CEvaluationNode*>(pChoiceNode->getChild());
CPPUNIT_ASSERT(pChild1 != NULL);
pChild2 = dynamic_cast<const CEvaluationNode*>(pChild1->getSibling());
CPPUNIT_ASSERT(pChild2 != NULL);
CPPUNIT_ASSERT(pChild2->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild2->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild2);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 0.3) / 0.3) < 1e-6);
pChild3 = dynamic_cast<const CEvaluationNode*>(pChild2->getSibling());
CPPUNIT_ASSERT(pChild3 != NULL);
CPPUNIT_ASSERT(pChild3->mainType() == CEvaluationNode::T_CHOICE);
pChoiceNode = dynamic_cast<const CEvaluationNodeChoice*>(pChild3);
CPPUNIT_ASSERT(pChoiceNode);
CPPUNIT_ASSERT(pChild1->mainType() == CEvaluationNode::T_LOGICAL);
CPPUNIT_ASSERT((pChild1->subType()) == CEvaluationNode::S_LE);
pChild1 = dynamic_cast<const CEvaluationNode*>(pChild1->getChild());
CPPUNIT_ASSERT(pChild1 != NULL);
CPPUNIT_ASSERT(pChild1->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild1->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild1);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 3.0) / 3.0) < 1e-6);
pChild2 = dynamic_cast<const CEvaluationNode*>(pChild1->getSibling());
CPPUNIT_ASSERT(pChild2 != NULL);
CPPUNIT_ASSERT(pChild2->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild2->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild2);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 4.0) / 4.0) < 1e-6);
// fourth choice level (child3 of third choice level)
pChild1 = dynamic_cast<const CEvaluationNode*>(pChoiceNode->getChild());
CPPUNIT_ASSERT(pChild1 != NULL);
pChild2 = dynamic_cast<const CEvaluationNode*>(pChild1->getSibling());
CPPUNIT_ASSERT(pChild2 != NULL);
CPPUNIT_ASSERT(pChild2->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild2->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild2);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 0.4) / 0.4) < 1e-6);
pChild3 = dynamic_cast<const CEvaluationNode*>(pChild2->getSibling());
CPPUNIT_ASSERT(pChild3 != NULL);
// the third child of the fourth choice level must be the otherwise element
CPPUNIT_ASSERT(pChild3->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild3->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild3);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 1.5) / 1.5) < 1e-6);
CPPUNIT_ASSERT(pChild3->getSibling() == NULL);
CPPUNIT_ASSERT(pChild1->mainType() == CEvaluationNode::T_LOGICAL);
CPPUNIT_ASSERT((pChild1->subType()) == CEvaluationNode::S_EQ);
pChild1 = dynamic_cast<const CEvaluationNode*>(pChild1->getChild());
CPPUNIT_ASSERT(pChild1 != NULL);
CPPUNIT_ASSERT(pChild1->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild1->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild1);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 3.0) / 3.0) < 1e-6);
pChild2 = dynamic_cast<const CEvaluationNode*>(pChild1->getSibling());
CPPUNIT_ASSERT(pChild2 != NULL);
CPPUNIT_ASSERT(pChild2->mainType() == CEvaluationNode::T_NUMBER);
CPPUNIT_ASSERT((pChild2->subType()) == CEvaluationNode::S_DOUBLE);
pNumberNode = dynamic_cast<const CEvaluationNodeNumber*>(pChild2);
CPPUNIT_ASSERT(pNumberNode != NULL);
CPPUNIT_ASSERT(fabs((pNumberNode->getValue() - 4.0) / 4.0) < 1e-6);
}
