COPASI API  4.16.103
Public Member Functions | Static Protected Attributes | Private Member Functions | List of all members
test000041 Class Reference

#include <test000041.h>

Inheritance diagram for test000041:
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Collaboration diagram for test000041:
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Public Member Functions

void setUp ()
 
void tearDown ()
 
void test_hasOnlySubstanceUnits ()
 

Static Protected Attributes

static const char * MODEL_STRING
 
static CCopasiDataModelpCOPASIDATAMODEL = NULL
 

Private Member Functions

 CPPUNIT_TEST (test_hasOnlySubstanceUnits)
 
 CPPUNIT_TEST_SUITE (test000041)
 
 CPPUNIT_TEST_SUITE_END ()
 

Detailed Description

Definition at line 24 of file test000041.h.

Member Function Documentation

test000041::CPPUNIT_TEST ( test_hasOnlySubstanceUnits  )
private
test000041::CPPUNIT_TEST_SUITE ( test000041  )
private
test000041::CPPUNIT_TEST_SUITE_END ( )
private
void test000041::setUp ( )

Definition at line 36 of file test000041.cpp.

References CCopasiRootContainer::addDatamodel(), CCopasiRootContainer::init(), and pCOPASIDATAMODEL.

37 {
38  // Create the root container.
39  CCopasiRootContainer::init(0, NULL, false);
40  // Create the global data model.
42 }
static CCopasiDataModel * pCOPASIDATAMODEL
Definition: test000041.h:32
static CCopasiDataModel * addDatamodel()
static void init(int argc, char *argv[], const bool &withGui=false)
void test000041::tearDown ( )

Definition at line 44 of file test000041.cpp.

References CCopasiRootContainer::destroy().

void test000041::test_hasOnlySubstanceUnits ( )

Definition at line 49 of file test000041.cpp.

References CModelEntity::FIXED, CChemEq::getCompartmentNumber(), CModelEntity::getInitialExpression(), CModelEntity::getInitialExpressionPtr(), CCopasiDataModel::getModel(), CChemEq::getModifiers(), CEvaluationNodeObject::getObjectCN(), CCopasiObject::getObjectName(), CCopasiObject::getObjectParent(), CChemEq::getProducts(), CModelEntity::getStatus(), CChemEq::getSubstrates(), CCopasiDataModel::importSBMLFromString(), CCopasiObject::isReference(), CModel::ml, CModel::mMol, MODEL_STRING, CCopasiDataModel::ObjectFromName(), pCOPASIDATAMODEL, CModelEntity::REACTIONS, CModel::s, and CCopasiVector< T >::size().

50 {
51  CCopasiDataModel* pDataModel = pCOPASIDATAMODEL;
52  CPPUNIT_ASSERT(pDataModel->importSBMLFromString(MODEL_STRING));
53  CModel* pModel = pDataModel->getModel();
54  CPPUNIT_ASSERT(pModel != NULL);
55  CPPUNIT_ASSERT(pModel->getQuantityUnitEnum() == CModel::mMol);
56  CPPUNIT_ASSERT(pModel->getVolumeUnitEnum() == CModel::ml);
57  CPPUNIT_ASSERT(pModel->getTimeUnitEnum() == CModel::s);
58  CPPUNIT_ASSERT(pModel->getCompartments().size() == 1);
59  const CCompartment* pCompartment = pModel->getCompartments()[0];
60  CPPUNIT_ASSERT(pCompartment != NULL);
61  CPPUNIT_ASSERT(pCompartment->getStatus() == CModelEntity::FIXED);
62  CPPUNIT_ASSERT(pModel->getMetabolites().size() == 2);
63  CMetab* pA = pModel->getMetabolites()[0];
64  CPPUNIT_ASSERT(pA != NULL);
65  CPPUNIT_ASSERT(pA->getStatus() == CModelEntity::REACTIONS);
66  const CMetab* pB = pModel->getMetabolites()[1];
67  CPPUNIT_ASSERT(pB != NULL);
68  CPPUNIT_ASSERT(pB->getStatus() == CModelEntity::REACTIONS);
69  CPPUNIT_ASSERT(pModel->getModelValues().size() == 2);
70  // check the factor
71  const CModelValue* pFactor = pModel->getModelValues()[1];
72  CPPUNIT_ASSERT(pFactor != NULL);
73  CPPUNIT_ASSERT(pFactor->getStatus() == CModelEntity::FIXED);
74  CPPUNIT_ASSERT(fabs((pFactor->getInitialValue() - pModel->getQuantity2NumberFactor()) / pModel->getQuantity2NumberFactor()) < 1e-3);
75  // check the first parameter and its initial assignment
76  const CModelValue* pModelValue = pModel->getModelValues()[0];
77  CPPUNIT_ASSERT(pModelValue != NULL);
78  CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::FIXED);
79  CPPUNIT_ASSERT(pModelValue->getInitialExpression() != "");
80  const CExpression* pExpr = pModelValue->getInitialExpressionPtr();
81  // check the expression
82  const CEvaluationNode* pNode = pExpr->getRoot();
83  CPPUNIT_ASSERT(pNode != NULL);
84  const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pNode);
85  CPPUNIT_ASSERT(pObjectNode != NULL);
86  CCopasiObjectName objectCN = pObjectNode->getObjectCN();
87  CPPUNIT_ASSERT(!objectCN.empty());
88  std::vector<CCopasiContainer*> listOfContainers;
89  listOfContainers.push_back(pModel);
90  const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
91  CPPUNIT_ASSERT(pObject != NULL);
92  CPPUNIT_ASSERT(pObject->isReference() == true);
93  CPPUNIT_ASSERT(pObject->getObjectName() == std::string("InitialParticleNumber"));
94  CPPUNIT_ASSERT(pObject->getObjectParent() == pA);
95 
96  CPPUNIT_ASSERT(pModel->getReactions().size() == 2);
97  const CReaction* pReaction1 = pModel->getReactions()[0];
98  CPPUNIT_ASSERT(pReaction1 != NULL);
99  CPPUNIT_ASSERT(pReaction1->isReversible() == false);
100  // check the kinetic law
101  const CFunction* pKineticFunction = pReaction1->getFunction();
102  CPPUNIT_ASSERT(pKineticFunction != NULL);
103  const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
104  //FTB: this no longer is recognized as mass action reaction because of the
105  // special case of a species with hOSU
106  CPPUNIT_ASSERT(pMassAction == NULL);
107  const CChemEq* pChemEq = &pReaction1->getChemEq();
108  CPPUNIT_ASSERT(pChemEq != NULL);
109  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
110  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
111  const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
112  CPPUNIT_ASSERT(pElement != NULL);
113  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
114  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
115  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 0);
116  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
117 
118  const CReaction* pReaction2 = pModel->getReactions()[1];
119  CPPUNIT_ASSERT(pReaction2 != NULL);
120  CPPUNIT_ASSERT(pReaction2->isReversible() == false);
121  // check the kinetic law
122  pKineticFunction = pReaction2->getFunction();
123  CPPUNIT_ASSERT(pKineticFunction != NULL);
124  CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Henri-Michaelis-Menten (irreversible)"));
125  // check the function parameters one should be the reference to the substrate
126  pChemEq = &pReaction2->getChemEq();
127  CPPUNIT_ASSERT(pChemEq != NULL);
128  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
129  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
130  pElement = pChemEq->getSubstrates()[0];
131  CPPUNIT_ASSERT(pElement != NULL);
132  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
133  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
134  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
135  pElement = pChemEq->getProducts()[0];
136  CPPUNIT_ASSERT(pElement != NULL);
137  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
138  CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
139  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
140  const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
141  CPPUNIT_ASSERT(parameterMappings.size() == 3);
142  CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
143  const std::string parameterKey = parameterMappings[0][0];
144  CPPUNIT_ASSERT(parameterKey == pA->getKey());
145 }
size_t getCompartmentNumber() const
Definition: CChemEq.cpp:110
static CCopasiDataModel * pCOPASIDATAMODEL
Definition: test000041.h:32
const std::string & getObjectName() const
virtual size_t size() const
const CRegisteredObjectName & getObjectCN() const
Definition: CMetab.h:178
const CCopasiVector< CChemEqElement > & getProducts() const
Definition: CChemEq.cpp:63
bool isReference() const
std::string getInitialExpression() const
const CCopasiVector< CChemEqElement > & getSubstrates() const
Definition: CChemEq.cpp:60
const CCopasiVector< CChemEqElement > & getModifiers() const
Definition: CChemEq.cpp:66
bool importSBMLFromString(const std::string &sbmlDocumentText, CProcessReport *pImportHandler=NULL, const bool &deleteOldData=true)
static const char * MODEL_STRING
Definition: test000041.h:31
The class for handling a chemical kinetic function.
Definition: CFunction.h:29
Definition: CModel.h:50
const CModelEntity::Status & getStatus() const
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const
CCopasiContainer * getObjectParent() const
const CExpression * getInitialExpressionPtr() const

Member Data Documentation

const char * test000041::MODEL_STRING
staticprotected

Definition at line 31 of file test000041.h.

Referenced by test_hasOnlySubstanceUnits().

CCopasiDataModel * test000041::pCOPASIDATAMODEL = NULL
staticprotected

Definition at line 32 of file test000041.h.

Referenced by setUp(), and test_hasOnlySubstanceUnits().


The documentation for this class was generated from the following files: