add(CCopasiObject *pObject, const bool &adopt=true) | CCopasiContainer | virtual |
addDirectDependency(const CCopasiObject *pObject) | CCopasiObject | |
addMatrixReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) | CCopasiContainer | inlineprotected |
addObjectReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) | CCopasiContainer | inlineprotected |
addVectorReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) | CCopasiContainer | inlineprotected |
allocate() | CMathContainer | private |
applyInitialValues() | CMathContainer | |
applyUpdateSequence(const CObjectInterface::UpdateSequence &updateSequence) | CMathContainer | |
Array enum value | CCopasiObject | protected |
buildUpdateSequence(const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) | CCopasiObject | static |
CCopasiContainer(const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container) | CCopasiContainer | |
CCopasiContainer(const CCopasiContainer &src, const CCopasiContainer *pParent=NULL) | CCopasiContainer | |
CCopasiObject() | CCopasiObject | protected |
CCopasiObject(const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | CCopasiObject | protected |
CCopasiObject(const CCopasiObject &src, const CCopasiContainer *pParent=NULL) | CCopasiObject | |
clearDirectDependencies() | CCopasiObject | |
clearRefresh() | CCopasiObject | |
CMathContainer() | CMathContainer | private |
CMathContainer(CModel &model) | CMathContainer | |
CMathContainer(const CMathContainer &src) | CMathContainer | |
CObjectInterface() | CObjectInterface | inline |
compileDiscreteChanges() | CMathContainer | private |
compileEvents() | CMathContainer | private |
compileObjects() | CMathContainer | private |
Container enum value | CCopasiObject | protected |
copyBranch(const CEvaluationNode *pSrc, const bool &replaceDiscontinuousNodes) | CMathContainer | |
copyBranch(const CEvaluationNode *pSrc, const CMath::Variables< CEvaluationNode * > &variables, const bool &replaceDiscontinuousNodes) | CMathContainer | |
createApplyInitialValuesSequence() | CMathContainer | private |
createDependencyGraphs() | CMathContainer | private |
createDiscontinuityDataEvent(const CEvaluationNode *pNode) | CMathContainer | private |
createDiscontinuityEvents() | CMathContainer | private |
createDiscontinuityEvents(const CEvaluationTree *pTree) | CMathContainer | private |
createDiscontinuityTriggerInfix(const CEvaluationNode *pNode) | CMathContainer | private |
createNodeFromObject(const CObjectInterface *pMathObject) | CMathContainer | private |
createNodeFromValue(const C_FLOAT64 *pDataValue) | CMathContainer | private |
createSynchronizeInitialValuesSequence() | CMathContainer | private |
createUpdateSimulationValuesSequence() | CMathContainer | private |
DataModel enum value | CCopasiObject | protected |
DataObjectSet typedef | CCopasiObject | |
DataUpdateSequence typedef | CCopasiObject | |
dependsOn(DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const | CCopasiObject | |
EmptyList | CCopasiContainer | static |
fetchInitialState() | CMathContainer | |
fetchState() | CMathContainer | |
Flag enum name | CCopasiObject | protected |
getAllDependencies(DataObjectSet &dependencies, const DataObjectSet &context) const | CCopasiObject | |
getChildObjectUnits(const CCopasiObject *pObject) const | CCopasiContainer | virtual |
getCN() const | CMathContainer | virtual |
getDirectDependencies(const DataObjectSet &context=DataObjectSet()) const | CCopasiObject | virtual |
getEntityType(const CModelEntity *pEntity) | CMathContainer | privatestatic |
getInitialState() const | CMathContainer | |
getInitialState() | CMathContainer | |
getInitialValuePointer(const C_FLOAT64 *pValue) const | CMathContainer | |
getKey() const | CCopasiObject | virtual |
getMathObject(const CObjectInterface *pObject) const | CMathContainer | |
getMathObject(const C_FLOAT64 *pDataValue) const | CMathContainer | |
getMathObject(const CCopasiObjectName &cn) const | CMathContainer | |
getModel() const | CMathContainer | |
getObject(const CCopasiObjectName &cn) const | CMathContainer | virtual |
getObjectAncestor(const std::string &type) const | CCopasiObject | |
getObjectDataModel() | CCopasiObject | |
getObjectDataModel() const | CCopasiObject | |
getObjectDisplayName(bool regular=true, bool richtext=false) const | CCopasiObject | virtual |
getObjectName() const | CCopasiObject | |
getObjectParent() const | CCopasiObject | |
getObjects() const | CCopasiContainer | virtual |
getObjectType() const | CCopasiObject | |
getPrerequisites() const | CCopasiObject | virtual |
getRefresh() const | CCopasiObject | virtual |
getState() const | CMathContainer | |
getState() | CMathContainer | |
getStateReduced() const | CMathContainer | |
getStateReduced() | CMathContainer | |
getUnits() const | CCopasiContainer | virtual |
getUpdateMethod() const | CCopasiObject | |
getValueObject() const | CCopasiContainer | virtual |
getValuePointer() const | CCopasiObject | virtual |
getValues() const | CMathContainer | |
getValues() | CMathContainer | |
Gui enum value | CCopasiObject | protected |
hasCircularDependencies(DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const | CCopasiObject | |
hasDependencies(const CCopasiObject *pObject) | CMathContainer | privatestatic |
hasUpdateMethod() const | CCopasiObject | |
init() | CMathContainer | private |
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 CCopasiObject * > ¶meters, CMath::sPointers &p) | CMathContainer | private |
initializeMathObjects(const CCopasiVector< CReaction > &reactions, CMath::sPointers &p) | CMathContainer | private |
initializeMathObjects(const CCopasiVector< CMoiety > &moieties, CMath::sPointers &p) | CMathContainer | private |
initializeObjects(CMath::sPointers &pointers) | CMathContainer | private |
initializePointers(CMath::sPointers &pointers) | CMathContainer | private |
initObjects() | CCopasiContainer | protected |
isArray() const | CCopasiObject | |
isContainer() const | CCopasiObject | |
isDataModel() const | CCopasiObject | |
isMatrix() const | CCopasiObject | |
isNameVector() const | CCopasiObject | |
isNonUniqueName() const | CCopasiObject | |
isPrerequisiteForContext(const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const | CCopasiObject | virtual |
isReference() const | CCopasiObject | |
isRoot() const | CCopasiObject | |
isSeparator() const | CCopasiObject | |
isStaticString() const | CCopasiObject | |
isValueBool() const | CCopasiObject | |
isValueDbl() const | CCopasiObject | |
isValueInt() const | CCopasiObject | |
isValueInt64() const | CCopasiObject | |
isValueString() const | CCopasiObject | |
isVector() const | CCopasiObject | |
map(CCopasiObject *pDataObject, CMathObject *pMathObject) | CMathContainer | private |
mApplyInitialValuesSequence | CMathContainer | private |
mAssignmentCount | CMathContainer | private |
Matrix enum value | CCopasiObject | protected |
mCreateDiscontinuousPointer | CMathContainer | private |
mDataObject2MathObject | CMathContainer | private |
mDataValue2MathObject | CMathContainer | private |
mDependentCount | 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 |
mEventTargetCount | CMathContainer | private |
mEventTriggers | CMathContainer | private |
mExtensiveRates | CMathContainer | private |
mExtensiveValues | CMathContainer | private |
mFixedCount | CMathContainer | private |
mFluxes | CMathContainer | private |
mIndependentCount | 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 |
mInitialStateValueExtensive | CMathContainer | private |
mInitialStateValueIntensive | CMathContainer | private |
mInitialTotalMasses | CMathContainer | private |
mIntensiveRates | CMathContainer | private |
mIntensiveValues | CMathContainer | private |
mObjects | CMathContainer | private |
mODECount | CMathContainer | private |
ModelEntity enum value | CCopasiObject | protected |
mParticleFluxes | CMathContainer | private |
mpAvogadro | CMathContainer | private |
mpModel | CMathContainer | private |
mpQuantity2NumberFactor | CMathContainer | private |
mPropensities | CMathContainer | private |
mReactions | CMathContainer | private |
mReducedStateValues | CMathContainer | private |
mSimulationRequiredValues | CMathContainer | private |
mSimulationValuesSequence | CMathContainer | private |
mSimulationValuesSequenceReduced | CMathContainer | private |
mState | CMathContainer | private |
mStateReduced | CMathContainer | private |
mStateValues | CMathContainer | private |
mSynchronizeInitialValuesSequenceExtensive | CMathContainer | private |
mSynchronizeInitialValuesSequenceIntensive | CMathContainer | private |
mTotalMasses | CMathContainer | private |
mTransientDependencies | CMathContainer | private |
mTriggerInfix2Event | CMathContainer | private |
mustBeDeleted(const DataObjectSet &deletedObjects) const | CCopasiObject | virtual |
mValues | CMathContainer | private |
NameVector enum value | CCopasiObject | protected |
NonUniqueName enum value | CCopasiObject | protected |
objectMap typedef | CCopasiContainer | |
ObjectSet typedef | CObjectInterface | |
print(std::ostream *ostream) const | CCopasiObject | virtual |
pushInitialState() | CMathContainer | |
pushState() | CMathContainer | |
Reference enum value | CCopasiObject | protected |
remove(CCopasiObject *pObject) | CCopasiContainer | virtual |
removeDirectDependency(const CCopasiObject *pObject) | CCopasiObject | |
replaceDiscontinuousNode(const CEvaluationNode *pSrc, const std::vector< CEvaluationNode * > &children) | CMathContainer | |
Root enum value | CCopasiObject | protected |
Separator enum value | CCopasiObject | protected |
setDirectDependencies(const DataObjectSet &directDependencies) | CCopasiObject | |
setInitialState(const CVectorCore< C_FLOAT64 > &initialState) | CMathContainer | |
setObjectName(const std::string &name) | CCopasiObject | |
setObjectParent(const CCopasiContainer *pParent) | CCopasiObject | virtual |
setObjectValue(const C_FLOAT64 &value) | CCopasiObject | |
setObjectValue(const C_INT32 &value) | CCopasiObject | |
setObjectValue(const bool &value) | CCopasiObject | |
setRefresh(CType *pType, void(CType::*method)(void)) | CCopasiObject | inline |
setRenameHandler(CRenameHandler *rh) | CCopasiObject | inlinestatic |
setState(const CVectorCore< C_FLOAT64 > &state) | CMathContainer | |
setStateReduced(const CVectorCore< C_FLOAT64 > &stateReduced) | CMathContainer | |
setUpdateMethod(CType *pType, void(CType::*method)(const C_FLOAT64 &)) | CCopasiObject | inline |
setUpdateMethod(CType *pType, void(CType::*method)(const C_INT32 &)) | CCopasiObject | inline |
setUpdateMethod(CType *pType, void(CType::*method)(const bool &)) | CCopasiObject | inline |
setValues(const CVectorCore< C_FLOAT64 > &values) | CMathContainer | |
smpRenameHandler | CCopasiObject | protectedstatic |
StaticString enum value | CCopasiObject | protected |
updateInitialValues(const CModelParameter::Framework &framework) | CMathContainer | |
UpdateSequence typedef | CObjectInterface | |
updateSimulatedValues(const bool &useMoieties) | CMathContainer | |
ValueBool enum value | CCopasiObject | protected |
ValueDbl enum value | CCopasiObject | protected |
ValueInt enum value | CCopasiObject | protected |
ValueInt64 enum value | CCopasiObject | protected |
ValueString enum value | CCopasiObject | protected |
Vector enum value | CCopasiObject | protected |
~CCopasiContainer() | CCopasiContainer | virtual |
~CCopasiObject() | CCopasiObject | virtual |
~CMathContainer() | CMathContainer | virtual |
~CObjectInterface() | CObjectInterface | inlinevirtual |