| __SIZE enum value | CDataObject | |
| add(CDataObject *pObject, const bool &adopt=true) | CDataContainer | virtual |
| addAnalysisEvent(const CEvent *pDataEvent) | CMathContainer | |
| addAnalysisObject(const CMath::Entity< CDataObject > &dataObjects, const CMath::SimulationType &simulationType, const std::string &infix) | CMathContainer | |
| addIssue(const CIssue &issue) | CDataObject | |
| addMatrixReference(const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) | CDataContainer | protected |
| addNoiseInputObject(const CMathObject *pObject) | CMathContainer | |
| addObjectReference(const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) | CDataContainer | protected |
| addReference(const CDataContainer *pReference) | CDataObject | |
| addVectorReference(const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None) | CDataContainer | protected |
| allocate() | CMathContainer | private |
| analyzeRoots() | CMathContainer | private |
| appendDeletedDependentData(CUndoData &undoData) const | CDataContainer | virtual |
| applyData(const CData &data, CUndoData::CChangeSet &changes) override | CDataContainer | virtual |
| applyInitialValues() | CMathContainer | |
| applyUpdateSequence(const CCore::CUpdateSequence &updateSequence) | CMathContainer | |
| areObjectsConstant(const CObjectInterface::ObjectSet &objects) const | CMathContainer | |
| Array enum value | CDataObject | |
| calculateElasticityDependencies(CMatrix< C_INT32 > &elasticityDependencies, const bool &reduced) | CMathContainer | |
| calculateJacobian(CMatrix< C_FLOAT64 > &jacobian, const C_FLOAT64 &derivationFactor, const bool &reduced, const bool &includeTime=false) | CMathContainer | |
| calculateJacobianDependencies(CMatrix< C_INT32 > &jacobianDependencies, const bool &reduced) | CMathContainer | |
| calculateRootDerivatives(CVector< C_FLOAT64 > &rootDerivatives) | CMathContainer | |
| calculateRootJacobian(CMatrix< C_FLOAT64 > &jacobian) | CMathContainer | private |
| calculateRootJacobian(CMatrix< C_FLOAT64 > &jacobian, const CVector< C_FLOAT64 > &rates) | CMathContainer | private |
| calculateValue() override | CDataObject | virtual |
| CDataContainer() | CDataContainer | private |
| CDataContainer(const CDataContainer &src) | CDataContainer | protected |
| CDataContainer(const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None) | CDataContainer | |
| CDataContainer(const CDataContainer &src, const CDataContainer *pParent) | CDataContainer | |
| CDataObject() | CDataObject | protected |
| CDataObject(const std::string &name, const CDataContainer *pParent=static_cast< CDataContainer * >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None) | CDataObject | protected |
| CDataObject(const CDataObject &src, const CDataContainer *pParent=NULL) | CDataObject | |
| CMathContainer() | CMathContainer | private |
| CMathContainer(CModel &model) | CMathContainer | |
| CMathContainer(const CMathContainer &src) | CMathContainer | |
| CObjectInterface() | CObjectInterface | |
| CObjectInterface(const CObjectInterface &src) | CObjectInterface | |
| compile() | CMathContainer | |
| compileDiscreteChanges() | CMathContainer | private |
| compileEvents() | CMathContainer | private |
| compileObjects() | CMathContainer | private |
| Container enum value | CDataObject | |
| ContainerList typedef | CObjectInterface | |
| copy() const | CMathContainer | |
| copyBranch(const CEvaluationNode *pSrc, const bool &replaceDiscontinuousNodes) | CMathContainer | |
| copyBranch(const CEvaluationNode *pSrc, const CMath::Variables< CEvaluationNode * > &variables, const bool &replaceDiscontinuousNodes) | CMathContainer | |
| createApplyInitialValuesSequence() | CMathContainer | private |
| createDelays() | CMathContainer | private |
| createDependencyGraphs() | CMathContainer | private |
| createDiscontinuityDataEvent(const CEvaluationNode *pNode) | CMathContainer | private |
| createDiscontinuityEvents() | CMathContainer | private |
| createDiscontinuityEvents(const CEvaluationTree *pTree, const std::vector< CEvaluationNode * > &variables) | CMathContainer | private |
| createDiscontinuityTriggerInfix(const CEvaluationNode *pNode) | CMathContainer | private |
| createNodeFromObject(const CObjectInterface *pMathObject) | CMathContainer | private |
| createNodeFromValue(const C_FLOAT64 *pDataValue) | CMathContainer | private |
| createRelocation(const size_t &oldSize, const size_t &newSize, CMath::sRelocate &relocate, std::vector< CMath::sRelocate > &relocations, const bool &modifiedAtEnd=true) | CMathContainer | privatestatic |
| createRelocations(const sSize &size, std::vector< CMath::sRelocate > &Relocations) | CMathContainer | private |
| createSynchronizeInitialValuesSequence() | CMathContainer | private |
| createUndoData(CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const override | CDataContainer | virtual |
| createUpdateAllTransientDataValuesSequence() | CMathContainer | private |
| createUpdateSequences() | CMathContainer | private |
| createUpdateSimulationValuesSequence() | CMathContainer | private |
| createValueChangeProhibited() | CMathContainer | private |
| CUndoObjectInterface() | CUndoObjectInterface | |
| CUndoObjectInterface(const CUndoObjectInterface &src) | CUndoObjectInterface | |
| DataModel enum value | CDataObject | |
| DataObject(const CObjectInterface *pInterface) | CObjectInterface | static |
| DataObjectSet typedef | CDataObject | |
| deregisterUpdateSequence(CMathUpdateSequence *pUpdateSequence) | CMathContainer | |
| destruct() override | CDataObject | virtual |
| DisplayName enum value | CDataObject | |
| EmptyList | CDataContainer | static |
| fetchInitialState() | CMathContainer | |
| fetchState() | CMathContainer | |
| finishResize() | CMathContainer | private |
| Flag enum name | CDataObject | |
| fromData(const CData &data, CUndoObjectInterface *pParent) | CDataContainer | static |
| generateUuid() | CUndoObjectInterface | |
| getApplyInitialValuesSequence() const | CMathContainer | |
| getChildObjectUnits(const CDataObject *pObject) const | CDataContainer | virtual |
| getCN() const | CMathContainer | virtual |
| getCompartment(const CMathObject *pObject) const | CMathContainer | |
| getCompleteInitialState() const | CMathContainer | |
| getCountAssignments() const | CMathContainer | |
| getCountDependentSpecies() const | CMathContainer | |
| getCountFixed() const | CMathContainer | |
| getCountFixedEventTargets() const | CMathContainer | |
| getCountIndependentSpecies() const | CMathContainer | |
| getCountNoise() const | CMathContainer | |
| getCountODEs() const | CMathContainer | |
| getDataObject(const C_FLOAT64 *pDataValue) const | CMathContainer | |
| CDataContainer::getDataObject() const override | CDataObject | virtual |
| getDelayLags() const | CMathContainer | |
| getDescendants(CDataObject::DataObjectSet &descendants, const bool &recursive=false) const | CDataContainer | |
| getEntityType(const CModelEntity *pEntity) | CMathContainer | privatestatic |
| getEvents() const | CMathContainer | |
| getFluxes() const | CMathContainer | |
| getHistory(const bool &reduced) const | CMathContainer | |
| getIndex(const CDataObject *pObject) const | CDataContainer | virtual |
| getInitialDependencies() const | CMathContainer | |
| getInitialState() const | CMathContainer | |
| getInitialState() | CMathContainer | |
| getInitialStateObjects() const | CMathContainer | |
| getInitialValueObject(const CMathObject *pObject) const | CMathContainer | |
| getInitialValuePointer(const C_FLOAT64 *pValue) const | CMathContainer | |
| getKey() const | CDataObject | virtual |
| getLargestReactionCompartment(const CMathReaction *pReaction) const | CMathContainer | |
| getMathObject(const CObjectInterface *pObject) const | CMathContainer | |
| getMathObject(const C_FLOAT64 *pDataValue) const | CMathContainer | |
| getMathObject(const CCommonName &cn) const | CMathContainer | |
| getMathReaction(const CReaction *pReaction) const | CMathContainer | |
| getModel() const | CMathContainer | |
| getNoise(const bool &reduced) const | CMathContainer | |
| getNoiseInputObjects() const | CMathContainer | |
| getNoiseSequence(const bool &useMoieties) const | CMathContainer | |
| getObject(const CCommonName &cn) const | CMathContainer | virtual |
| getObjectAncestor(const std::string &type) const | CDataObject | |
| getObjectDataModel() const | CDataObject | |
| getObjectDisplayName() const override | CDataObject | virtual |
| GetObjectFromCN(const ContainerList &listOfContainer, const CCommonName &objName) | CObjectInterface | static |
| getObjectFromCN(const CCommonName &cn) const | CMathContainer | virtual |
| getObjectName() const | CDataObject | |
| getObjectParent() const | CDataObject | |
| getObjects() const | CDataContainer | virtual |
| getObjects() | CDataContainer | virtual |
| getObjectType() const | CDataObject | |
| getParticleFluxes() const | CMathContainer | |
| getPrerequisites() const override | CDataObject | virtual |
| getProcessQueue() | CMathContainer | |
| getProcessQueueExecutionTime() const | CMathContainer | |
| getPropensities() const | CMathContainer | |
| getQuantity2NumberFactor() const | CMathContainer | |
| getQuantity2NumberFactorObject() const | CMathContainer | |
| getRandomGenerator() const | CMathContainer | |
| getRandomObject() const | CMathContainer | |
| getRate(const bool &reduced) const | CMathContainer | |
| getReactions() | CMathContainer | |
| getReactions() const | CMathContainer | |
| getRootIsDiscrete() const | CMathContainer | |
| getRootIsTimeDependent() const | CMathContainer | |
| getRootProcessors() | CMathContainer | |
| getRoots() const | CMathContainer | |
| getSimulationUpToDateObjects() const | CMathContainer | |
| getSimulationValuesSequence(const bool &useMoieties) const | CMathContainer | |
| getState(const bool &reduced) const | CMathContainer | |
| getStateObjects(const bool &reduced=false) const | CMathContainer | |
| getStoichiometry(const bool &reduced=false) const | CMathContainer | |
| getSynchronizeInitialValuesSequence(const CCore::Framework &framework) const | CMathContainer | |
| getTotalMasses() const | CMathContainer | |
| getTransientDataValueSequence() const | CMathContainer | |
| getTransientDependencies() const | CMathContainer | |
| getUnits() const override | CDataContainer | virtual |
| getUuid() const | CUndoObjectInterface | |
| getValidity() const override | CDataObject | virtual |
| getValueChangeProhibited() const | CMathContainer | |
| getValueObject(const CMathObject *pInitialObject) const | CMathContainer | |
| CDataContainer::getValueObject() const override | CDataContainer | virtual |
| getValuePointer(const C_FLOAT64 *pInitialValue) const | CMathContainer | |
| CDataContainer::getValuePointer() const override | CDataObject | virtual |
| getValues() const | CMathContainer | |
| getValues() | CMathContainer | |
| Gui enum value | CDataObject | |
| hasFlag(const Flag &flag) const | CDataObject | |
| ignoreDiscontinuityEvent(CMathEvent *pEvent) | CMathContainer | private |
| initializeAtolVector(const C_FLOAT64 &baseTolerance, const bool &reduced) const | CMathContainer | |
| initializeDiscontinuousCreationPointer() | CMathContainer | private |
| initializeEvents(CMath::sPointers &pointers) | CMathContainer | private |
| initializeMathObjects(const std::vector< const CModelEntity * > &entities, const CMath::SimulationType &simulationType, CMath::sPointers &pointers) | CMathContainer | private |
| initializeMathObjects(const std::vector< const CDataObject * > ¶meters, CMath::sPointers &p) | CMathContainer | private |
| initializeMathObjects(const CDataVector< CReaction > &reactions, CMath::sPointers &p) | CMathContainer | private |
| initializeMathObjects(const CDataVector< CMoiety > &moieties, CMath::sPointers &p) | CMathContainer | private |
| initializeObjects(CMath::sPointers &pointers) | CMathContainer | private |
| initializePointers(CMath::sPointers &pointers) | CMathContainer | private |
| initObjects() | CDataContainer | protected |
| insert(const CData &data) override | CDataContainer | virtual |
| isAutonomous() const | CMathContainer | |
| isPrerequisiteForContext(const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override | CDataObject | virtual |
| isStateValid() const | CMathContainer | |
| mAggregateValidity | CDataObject | private |
| map() | CMathContainer | private |
| mApplyInitialValuesSequence | CMathContainer | private |
| Matrix enum value | CDataObject | |
| mCompileTime | CMathContainer | private |
| mCompleteInitialState | CMathContainer | private |
| mCreateDiscontinuousPointer | CMathContainer | private |
| mDataObject2MathObject | CMathContainer | private |
| mDataValue2DataObject | CMathContainer | private |
| mDataValue2MathObject | CMathContainer | private |
| mDelayLags | CMathContainer | private |
| mDelays | CMathContainer | private |
| mDelayValues | CMathContainer | private |
| mDependentMasses | CMathContainer | private |
| mDiscontinuityEvents | CMathContainer | private |
| mDiscontinuityInfix2Object | CMathContainer | private |
| mDiscontinuous | CMathContainer | private |
| mEventAssignments | CMathContainer | private |
| mEventDelays | CMathContainer | private |
| mEventPriorities | CMathContainer | private |
| mEventRoots | CMathContainer | private |
| mEventRootStates | CMathContainer | private |
| mEvents | CMathContainer | private |
| mEventTriggers | CMathContainer | private |
| mExtensiveNoise | CMathContainer | private |
| mExtensiveRates | CMathContainer | private |
| mExtensiveValues | CMathContainer | private |
| mFluxes | CMathContainer | private |
| mHistory | CMathContainer | private |
| mHistoryReduced | CMathContainer | private |
| mInitialDependencies | CMathContainer | private |
| mInitialEventTriggers | CMathContainer | private |
| mInitialExtensiveRates | CMathContainer | private |
| mInitialExtensiveValues | CMathContainer | private |
| mInitialFluxes | CMathContainer | private |
| mInitialIntensiveRates | CMathContainer | private |
| mInitialIntensiveValues | CMathContainer | private |
| mInitialParticleFluxes | CMathContainer | private |
| mInitialState | CMathContainer | private |
| mInitialStateValueAll | CMathContainer | private |
| mInitialStateValueExtensive | CMathContainer | private |
| mInitialStateValueIntensive | CMathContainer | private |
| mInitialTotalMasses | CMathContainer | private |
| mIntensiveNoise | CMathContainer | private |
| mIntensiveRates | CMathContainer | private |
| mIntensiveValues | CMathContainer | private |
| mIsAutonomous | CMathContainer | private |
| mNoiseInputObjects | CMathContainer | private |
| mNoiseReduced | CMathContainer | private |
| mNoiseSequence | CMathContainer | private |
| mNoiseSequenceReduced | CMathContainer | private |
| mNumTotalRootsIgnored | CMathContainer | private |
| mObjectDisplayName | CDataObject | mutableprivate |
| mObjectFlag | CDataObject | private |
| mObjectName | CDataObject | private |
| mObjects | CMathContainer | private |
| mObjectType | CDataObject | private |
| ModelEntity enum value | CDataObject | |
| mOldObjects | CMathContainer | private |
| mOldValues | CMathContainer | private |
| move(sSize &size) | CMathContainer | private |
| mParticleFluxes | CMathContainer | private |
| mpAvogadro | CMathContainer | private |
| mpModel | CMathContainer | private |
| mpObjectDisplayName | CDataObject | mutableprivate |
| mpObjectName | CDataObject | mutableprivate |
| mpObjectParent | CDataObject | private |
| mpObjectsBuffer | CMathContainer | private |
| mpProcessQueue | CMathContainer | private |
| mpQuantity2NumberFactor | CMathContainer | private |
| mpRandomGenerator | CMathContainer | private |
| mPrerequisits | CDataObject | protected |
| mPrioritySequence | CMathContainer | private |
| mPropensities | CMathContainer | private |
| mpUuid | CUndoObjectInterface | private |
| mpValuesBuffer | CMathContainer | private |
| mRandom | CMathContainer | private |
| mRate | CMathContainer | private |
| mRateReduced | CMathContainer | private |
| mReactionNoise | CMathContainer | private |
| mReactionParticleNoise | CMathContainer | private |
| mReactions | CMathContainer | private |
| mReducedStateValues | CMathContainer | private |
| mReferencedValidities | CDataObject | private |
| mReferences | CDataObject | protected |
| mRootCount2Events | CMathContainer | private |
| mRootDerivatives | CMathContainer | private |
| mRootDerivativesState | CMathContainer | private |
| mRootIsDiscrete | CMathContainer | private |
| mRootIsTimeDependent | CMathContainer | private |
| mRootProcessors | CMathContainer | private |
| mRootSequence | CMathContainer | private |
| mRootSequenceReduced | CMathContainer | private |
| mSimulationRequiredValues | CMathContainer | private |
| mSimulationValuesSequence | CMathContainer | private |
| mSimulationValuesSequenceReduced | CMathContainer | private |
| mSize | CMathContainer | private |
| mState | CMathContainer | private |
| mStateReduced | CMathContainer | private |
| mStateValues | CMathContainer | private |
| mSynchronizeInitialValuesSequenceExtensive | CMathContainer | private |
| mSynchronizeInitialValuesSequenceIntensive | CMathContainer | private |
| mTotalMasses | CMathContainer | private |
| mTransientDataObjectSequence | CMathContainer | private |
| mTransientDependencies | CMathContainer | private |
| mTransitionTimes | CMathContainer | private |
| mTriggerInfix2Event | CMathContainer | private |
| mUpdateSequences | CMathContainer | private |
| mUuidLocked | CUndoObjectInterface | private |
| mValidity | CObjectInterface | mutableprotected |
| mValueChangeProhibited | CMathContainer | private |
| mValues | CMathContainer | private |
| NameVector enum value | CDataObject | |
| NonUniqueName enum value | CDataObject | |
| objectMap typedef | CDataContainer | |
| objectRenamed(CDataObject *pObject, const std::string &oldName) | CDataContainer | |
| ObjectSet typedef | CObjectInterface | |
| operator==(const CMathContainer &rhs) | CMathContainer | |
| prerequisitsContains(const DataObjectSet &objects) const | CDataObject | |
| print(std::ostream *ostream) const override | CDataObject | virtual |
| processQueue(const bool &equality) | CMathContainer | |
| processRoots(const bool &equality, const CVector< C_INT > &rootsFound) | CMathContainer | |
| processRoots(const CVector< C_INT > &rootsFound) | CMathContainer | |
| pushAllTransientValues() | CMathContainer | |
| pushInitialState() | CMathContainer | |
| pushState() | CMathContainer | |
| Reference enum value | CDataObject | |
| refreshAggregateValidity() | CDataObject | private |
| registerUpdateSequence(CMathUpdateSequence *pUpdateSequence) | CMathContainer | |
| relocate(const sSize &size, const std::vector< CMath::sRelocate > &Relocations) | CMathContainer | private |
| relocateObject(CObjectInterface *&pObject, const std::vector< CMath::sRelocate > &relocations) const | CMathContainer | |
| relocateObject(const CObjectInterface *&pObject, const std::vector< CMath::sRelocate > &relocations) const | CMathContainer | |
| relocateObject(CMathObject *&pObject, const std::vector< CMath::sRelocate > &relocations) const | CMathContainer | |
| relocateObject(const CMathObject *&pObject, const std::vector< CMath::sRelocate > &relocations) const | CMathContainer | |
| relocateObjectSet(CObjectInterface::ObjectSet &objectSet, const std::vector< CMath::sRelocate > &relocations) const | CMathContainer | |
| relocateUpdateSequence(CCore::CUpdateSequence &sequence, const std::vector< CMath::sRelocate > &relocations) const | CMathContainer | |
| relocateValue(C_FLOAT64 *&pValue, const std::vector< CMath::sRelocate > &relocations) const | CMathContainer | |
| relocateValue(const C_FLOAT64 *&pValue, const std::vector< CMath::sRelocate > &relocations) const | CMathContainer | |
| relocateVector(CVectorCore< CType > &vector, size_t size, const std::vector< CMath::sRelocate > &relocations) | CMathContainer | inlineprivate |
| remove(CDataObject *pObject) | CDataContainer | virtual |
| removeAnalysisEvent(CMathEvent *&pMathEvent) | CMathContainer | |
| removeAnalysisObject(CMath::Entity< CMathObject > &mathObjects) | CMathContainer | |
| removeDataObject(const CDataObject *pObject) | CMathContainer | |
| removeIssue(const CIssue &issue) | CDataObject | |
| removeReference(const CDataContainer *pReference) | CDataObject | |
| replaceDiscontinuousNode(const CEvaluationNode *pSrc, const std::vector< CEvaluationNode * > &children) | CMathContainer | |
| resetNoise() | CMathContainer | |
| resize(sSize &size) | CMathContainer | private |
| Root enum value | CDataObject | |
| sanitizeDataValue2DataObject() | CMathContainer | private |
| sanitizeObjectName(std::string &name) | CDataObject | static |
| Separator enum value | CDataObject | |
| setCompleteInitialState(const CVectorCore< C_FLOAT64 > &initialState) | CMathContainer | |
| setHistory(const CMathHistoryCore &history) | CMathContainer | |
| setInitialState(const CVectorCore< C_FLOAT64 > &initialState) | CMathContainer | |
| setObjectName(const std::string &name) | CDataObject | |
| setObjectParent(const CDataContainer *pParent) | CDataObject | virtual |
| setState(const CVectorCore< C_FLOAT64 > &state) | CMathContainer | |
| setUuid(const xg::Guid &uuid) | CUndoObjectInterface | |
| setUuid(const std::string &uuid) | CUndoObjectInterface | |
| setValues(const CVectorCore< C_FLOAT64 > &values) | CMathContainer | |
| StaticString enum value | CDataObject | |
| toData() const override | CDataContainer | virtual |
| updateHistoryValues(const bool &useMoieties) | CMathContainer | |
| updateIndex(const size_t &index, const CUndoObjectInterface *pUndoObject) | CUndoObjectInterface | virtual |
| updateInitialValues(const CCore::Framework &framework) | CMathContainer | |
| updateNoiseValues(const bool &useMoieties) | CMathContainer | |
| updatePriorityValues() | CMathContainer | |
| updateRootValues(const bool &useMoieties) | CMathContainer | |
| updateSimulatedValues(const bool &useMoieties) | CMathContainer | |
| updateTransientDataValues() | CMathContainer | |
| validityChanged(const CValidity &changedValidity) override | CDataObject | virtual |
| validityRemoved(const CValidity &changedValidity) | CDataObject | |
| ValueBool enum value | CDataObject | |
| ValueDbl enum value | CDataObject | |
| ValueInt enum value | CDataObject | |
| ValueInt64 enum value | CDataObject | |
| ValueString enum value | CDataObject | |
| Vector enum value | CDataObject | |
| ~CDataContainer() | CDataContainer | virtual |
| ~CDataObject() | CDataObject | virtual |
| ~CMathContainer() | CMathContainer | virtual |
| ~CObjectInterface() | CObjectInterface | virtual |
| ~CUndoObjectInterface() | CUndoObjectInterface | virtual |
1.9.1