COPASI API  4.16.103
Public Member Functions | Static Protected Attributes | Private Member Functions | List of all members
test000039 Class Reference

#include <test000039.h>

Inheritance diagram for test000039:
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Collaboration diagram for test000039:
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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 (test000039)
 
 CPPUNIT_TEST_SUITE_END ()
 

Detailed Description

Definition at line 24 of file test000039.h.

Member Function Documentation

test000039::CPPUNIT_TEST ( test_hasOnlySubstanceUnits  )
private
test000039::CPPUNIT_TEST_SUITE ( test000039  )
private
test000039::CPPUNIT_TEST_SUITE_END ( )
private
void test000039::setUp ( )

Definition at line 36 of file test000039.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: test000039.h:32
static CCopasiDataModel * addDatamodel()
static void init(int argc, char *argv[], const bool &withGui=false)
void test000039::tearDown ( )

Definition at line 44 of file test000039.cpp.

References CCopasiRootContainer::destroy().

void test000039::test_hasOnlySubstanceUnits ( )

Definition at line 49 of file test000039.cpp.

References CModelEntity::FIXED, CChemEq::getCompartmentNumber(), CCopasiDataModel::getModel(), CChemEq::getModifiers(), CEvaluationNodeObject::getObjectCN(), CCopasiObject::getObjectName(), CCopasiObject::getObjectParent(), CChemEq::getProducts(), CChemEq::getSubstrates(), CCopasiDataModel::importSBMLFromString(), CCopasiObject::isReference(), CModel::microMol, CModel::ml, 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::microMol);
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() == 1);
70  const CModelValue* pModelValue = pModel->getModelValues()[0];
71  CPPUNIT_ASSERT(pModelValue != NULL);
72  CPPUNIT_ASSERT(pModelValue->getStatus() == CModelEntity::FIXED);
73  CPPUNIT_ASSERT(pModelValue->getInitialExpression() != "");
74  const CExpression* pExpr = pModelValue->getInitialExpressionPtr();
75  // check the expression
76  const CEvaluationNode* pNode = pExpr->getRoot();
77  CPPUNIT_ASSERT(pNode != NULL);
78  const CEvaluationNodeObject* pObjectNode = dynamic_cast<const CEvaluationNodeObject*>(pNode);
79  CPPUNIT_ASSERT(pObjectNode != NULL);
80  CCopasiObjectName objectCN = pObjectNode->getObjectCN();
81  CPPUNIT_ASSERT(!objectCN.empty());
82  std::vector<CCopasiContainer*> listOfContainers;
83  listOfContainers.push_back(pModel);
84  const CCopasiObject* pObject = pCOPASIDATAMODEL->ObjectFromName(listOfContainers, objectCN);
85  CPPUNIT_ASSERT(pObject != NULL);
86  CPPUNIT_ASSERT(pObject->isReference() == true);
87  CPPUNIT_ASSERT(pObject->getObjectName() == std::string("InitialParticleNumber"));
88  CPPUNIT_ASSERT(pObject->getObjectParent() == pA);
89  // check reactions
90  CPPUNIT_ASSERT(pModel->getReactions().size() == 2);
91  const CReaction* pReaction1 = pModel->getReactions()[0];
92  CPPUNIT_ASSERT(pReaction1 != NULL);
93  CPPUNIT_ASSERT(pReaction1->isReversible() == false);
94  // check the kinetic law
95  const CFunction* pKineticFunction = pReaction1->getFunction();
96  CPPUNIT_ASSERT(pKineticFunction != NULL);
97  const CMassAction* pMassAction = dynamic_cast<const CMassAction*>(pKineticFunction);
98  //FTB: this no longer is recognized as mass action reaction because of the
99  // special case of a species with hOSU
100  CPPUNIT_ASSERT(pMassAction == NULL);
101  const CChemEq* pChemEq = &pReaction1->getChemEq();
102  CPPUNIT_ASSERT(pChemEq != NULL);
103  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
104  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
105  const CChemEqElement* pElement = pChemEq->getSubstrates()[0];
106  CPPUNIT_ASSERT(pElement != NULL);
107  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
108  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
109  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 0);
110  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
111 
112  const CReaction* pReaction2 = pModel->getReactions()[1];
113  CPPUNIT_ASSERT(pReaction2 != NULL);
114  CPPUNIT_ASSERT(pReaction2->isReversible() == false);
115  // check the kinetic law
116  pKineticFunction = pReaction2->getFunction();
117  CPPUNIT_ASSERT(pKineticFunction != NULL);
118  CPPUNIT_ASSERT(pKineticFunction->getObjectName() == std::string("Henri-Michaelis-Menten (irreversible)"));
119  // check the function parameters one should be the reference to the substrate
120  pChemEq = &pReaction2->getChemEq();
121  CPPUNIT_ASSERT(pChemEq != NULL);
122  CPPUNIT_ASSERT(pChemEq->getCompartmentNumber() == 1);
123  CPPUNIT_ASSERT(pChemEq->getSubstrates().size() == 1);
124  pElement = pChemEq->getSubstrates()[0];
125  CPPUNIT_ASSERT(pElement != NULL);
126  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
127  CPPUNIT_ASSERT(pElement->getMetabolite() == pA);
128  CPPUNIT_ASSERT(pChemEq->getProducts().size() == 1);
129  pElement = pChemEq->getProducts()[0];
130  CPPUNIT_ASSERT(pElement != NULL);
131  CPPUNIT_ASSERT(fabs(pElement->getMultiplicity() - 1.0) < 1e-3);
132  CPPUNIT_ASSERT(pElement->getMetabolite() == pB);
133  CPPUNIT_ASSERT(pChemEq->getModifiers().size() == 0);
134  const std::vector<std::vector<std::string> > parameterMappings = pReaction2->getParameterMappings();
135  CPPUNIT_ASSERT(parameterMappings.size() == 3);
136  CPPUNIT_ASSERT(parameterMappings[0].size() == 1);
137  const std::string parameterKey = parameterMappings[0][0];
138  CPPUNIT_ASSERT(parameterKey == pA->getKey());
139 }
static const char * MODEL_STRING
Definition: test000039.h:31
size_t getCompartmentNumber() const
Definition: CChemEq.cpp:110
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
const CCopasiVector< CChemEqElement > & getSubstrates() const
Definition: CChemEq.cpp:60
static CCopasiDataModel * pCOPASIDATAMODEL
Definition: test000039.h:32
const CCopasiVector< CChemEqElement > & getModifiers() const
Definition: CChemEq.cpp:66
bool importSBMLFromString(const std::string &sbmlDocumentText, CProcessReport *pImportHandler=NULL, const bool &deleteOldData=true)
The class for handling a chemical kinetic function.
Definition: CFunction.h:29
Definition: CModel.h:50
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const
CCopasiContainer * getObjectParent() const

Member Data Documentation

const char * test000039::MODEL_STRING
staticprotected

Definition at line 31 of file test000039.h.

Referenced by test_hasOnlySubstanceUnits().

CCopasiDataModel * test000039::pCOPASIDATAMODEL = NULL
staticprotected

Definition at line 32 of file test000039.h.

Referenced by setUp(), and test_hasOnlySubstanceUnits().


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