COPASI API  4.40.278
CMathContainer Member List

This is the complete list of members for CMathContainer, including all inherited members.

__SIZE enum valueCDataObject
add(CDataObject *pObject, const bool &adopt=true)CDataContainervirtual
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)CDataContainerprotected
addNoiseInputObject(const CMathObject *pObject)CMathContainer
addObjectReference(const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)CDataContainerprotected
addReference(const CDataContainer *pReference)CDataObject
addVectorReference(const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)CDataContainerprotected
allocate()CMathContainerprivate
analyzeRoots()CMathContainerprivate
appendDeletedDependentData(CUndoData &undoData) constCDataContainervirtual
applyData(const CData &data, CUndoData::CChangeSet &changes) overrideCDataContainervirtual
applyInitialValues()CMathContainer
applyUpdateSequence(const CCore::CUpdateSequence &updateSequence)CMathContainer
areObjectsConstant(const CObjectInterface::ObjectSet &objects) constCMathContainer
Array enum valueCDataObject
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)CMathContainerprivate
calculateRootJacobian(CMatrix< C_FLOAT64 > &jacobian, const CVector< C_FLOAT64 > &rates)CMathContainerprivate
calculateValue() overrideCDataObjectvirtual
CDataContainer()CDataContainerprivate
CDataContainer(const CDataContainer &src)CDataContainerprotected
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()CDataObjectprotected
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)CDataObjectprotected
CDataObject(const CDataObject &src, const CDataContainer *pParent=NULL)CDataObject
CMathContainer()CMathContainerprivate
CMathContainer(CModel &model)CMathContainer
CMathContainer(const CMathContainer &src)CMathContainer
CObjectInterface()CObjectInterface
CObjectInterface(const CObjectInterface &src)CObjectInterface
compile()CMathContainer
compileDiscreteChanges()CMathContainerprivate
compileEvents()CMathContainerprivate
compileObjects()CMathContainerprivate
Container enum valueCDataObject
ContainerList typedefCObjectInterface
copy() constCMathContainer
copyBranch(const CEvaluationNode *pSrc, const bool &replaceDiscontinuousNodes)CMathContainer
copyBranch(const CEvaluationNode *pSrc, const CMath::Variables< CEvaluationNode * > &variables, const bool &replaceDiscontinuousNodes)CMathContainer
createApplyInitialValuesSequence()CMathContainerprivate
createDelays()CMathContainerprivate
createDependencyGraphs()CMathContainerprivate
createDiscontinuityDataEvent(const CEvaluationNode *pNode)CMathContainerprivate
createDiscontinuityEvents()CMathContainerprivate
createDiscontinuityEvents(const CEvaluationTree *pTree, const std::vector< CEvaluationNode * > &variables)CMathContainerprivate
createDiscontinuityTriggerInfix(const CEvaluationNode *pNode)CMathContainerprivate
createNodeFromObject(const CObjectInterface *pMathObject)CMathContainerprivate
createNodeFromValue(const C_FLOAT64 *pDataValue)CMathContainerprivate
createRelocation(const size_t &oldSize, const size_t &newSize, CMath::sRelocate &relocate, std::vector< CMath::sRelocate > &relocations, const bool &modifiedAtEnd=true)CMathContainerprivatestatic
createRelocations(const sSize &size, std::vector< CMath::sRelocate > &Relocations)CMathContainerprivate
createSynchronizeInitialValuesSequence()CMathContainerprivate
createUndoData(CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const overrideCDataContainervirtual
createUpdateAllTransientDataValuesSequence()CMathContainerprivate
createUpdateSequences()CMathContainerprivate
createUpdateSimulationValuesSequence()CMathContainerprivate
createValueChangeProhibited()CMathContainerprivate
CUndoObjectInterface()CUndoObjectInterface
CUndoObjectInterface(const CUndoObjectInterface &src)CUndoObjectInterface
DataModel enum valueCDataObject
DataObject(const CObjectInterface *pInterface)CObjectInterfacestatic
DataObjectSet typedefCDataObject
deregisterUpdateSequence(CMathUpdateSequence *pUpdateSequence)CMathContainer
destruct() overrideCDataObjectvirtual
DisplayName enum valueCDataObject
EmptyListCDataContainerstatic
fetchInitialState()CMathContainer
fetchState()CMathContainer
finishResize()CMathContainerprivate
Flag enum nameCDataObject
fromData(const CData &data, CUndoObjectInterface *pParent)CDataContainerstatic
generateUuid()CUndoObjectInterface
getApplyInitialValuesSequence() constCMathContainer
getChildObjectUnits(const CDataObject *pObject) constCDataContainervirtual
getCN() constCMathContainervirtual
getCompartment(const CMathObject *pObject) constCMathContainer
getCompleteInitialState() constCMathContainer
getCountAssignments() constCMathContainer
getCountDependentSpecies() constCMathContainer
getCountFixed() constCMathContainer
getCountFixedEventTargets() constCMathContainer
getCountIndependentSpecies() constCMathContainer
getCountNoise() constCMathContainer
getCountODEs() constCMathContainer
getDataObject(const C_FLOAT64 *pDataValue) constCMathContainer
CDataContainer::getDataObject() const overrideCDataObjectvirtual
getDelayLags() constCMathContainer
getDescendants(CDataObject::DataObjectSet &descendants, const bool &recursive=false) constCDataContainer
getEntityType(const CModelEntity *pEntity)CMathContainerprivatestatic
getEvents() constCMathContainer
getFluxes() constCMathContainer
getHistory(const bool &reduced) constCMathContainer
getIndex(const CDataObject *pObject) constCDataContainervirtual
getInitialDependencies() constCMathContainer
getInitialState() constCMathContainer
getInitialState()CMathContainer
getInitialStateObjects() constCMathContainer
getInitialValueObject(const CMathObject *pObject) constCMathContainer
getInitialValuePointer(const C_FLOAT64 *pValue) constCMathContainer
getKey() constCDataObjectvirtual
getLargestReactionCompartment(const CMathReaction *pReaction) constCMathContainer
getMathObject(const CObjectInterface *pObject) constCMathContainer
getMathObject(const C_FLOAT64 *pDataValue) constCMathContainer
getMathObject(const CCommonName &cn) constCMathContainer
getMathReaction(const CReaction *pReaction) constCMathContainer
getModel() constCMathContainer
getNoise(const bool &reduced) constCMathContainer
getNoiseInputObjects() constCMathContainer
getNoiseSequence(const bool &useMoieties) constCMathContainer
getObject(const CCommonName &cn) constCMathContainervirtual
getObjectAncestor(const std::string &type) constCDataObject
getObjectDataModel() constCDataObject
getObjectDisplayName() const overrideCDataObjectvirtual
GetObjectFromCN(const ContainerList &listOfContainer, const CCommonName &objName)CObjectInterfacestatic
getObjectFromCN(const CCommonName &cn) constCMathContainervirtual
getObjectName() constCDataObject
getObjectParent() constCDataObject
getObjects() constCDataContainervirtual
getObjects()CDataContainervirtual
getObjectType() constCDataObject
getParticleFluxes() constCMathContainer
getPrerequisites() const overrideCDataObjectvirtual
getProcessQueue()CMathContainer
getProcessQueueExecutionTime() constCMathContainer
getPropensities() constCMathContainer
getQuantity2NumberFactor() constCMathContainer
getQuantity2NumberFactorObject() constCMathContainer
getRandomGenerator() constCMathContainer
getRandomObject() constCMathContainer
getRate(const bool &reduced) constCMathContainer
getReactions()CMathContainer
getReactions() constCMathContainer
getRootIsDiscrete() constCMathContainer
getRootIsTimeDependent() constCMathContainer
getRootProcessors()CMathContainer
getRoots() constCMathContainer
getSimulationUpToDateObjects() constCMathContainer
getSimulationValuesSequence(const bool &useMoieties) constCMathContainer
getState(const bool &reduced) constCMathContainer
getStateObjects(const bool &reduced=false) constCMathContainer
getStoichiometry(const bool &reduced=false) constCMathContainer
getSynchronizeInitialValuesSequence(const CCore::Framework &framework) constCMathContainer
getTotalMasses() constCMathContainer
getTransientDataValueSequence() constCMathContainer
getTransientDependencies() constCMathContainer
getUnits() const overrideCDataContainervirtual
getUuid() constCUndoObjectInterface
getValidity() const overrideCDataObjectvirtual
getValueChangeProhibited() constCMathContainer
getValueObject(const CMathObject *pInitialObject) constCMathContainer
CDataContainer::getValueObject() const overrideCDataContainervirtual
getValuePointer(const C_FLOAT64 *pInitialValue) constCMathContainer
CDataContainer::getValuePointer() const overrideCDataObjectvirtual
getValues() constCMathContainer
getValues()CMathContainer
Gui enum valueCDataObject
hasFlag(const Flag &flag) constCDataObject
ignoreDiscontinuityEvent(CMathEvent *pEvent)CMathContainerprivate
initializeAtolVector(const C_FLOAT64 &baseTolerance, const bool &reduced) constCMathContainer
initializeDiscontinuousCreationPointer()CMathContainerprivate
initializeEvents(CMath::sPointers &pointers)CMathContainerprivate
initializeMathObjects(const std::vector< const CModelEntity * > &entities, const CMath::SimulationType &simulationType, CMath::sPointers &pointers)CMathContainerprivate
initializeMathObjects(const std::vector< const CDataObject * > &parameters, CMath::sPointers &p)CMathContainerprivate
initializeMathObjects(const CDataVector< CReaction > &reactions, CMath::sPointers &p)CMathContainerprivate
initializeMathObjects(const CDataVector< CMoiety > &moieties, CMath::sPointers &p)CMathContainerprivate
initializeObjects(CMath::sPointers &pointers)CMathContainerprivate
initializePointers(CMath::sPointers &pointers)CMathContainerprivate
initObjects()CDataContainerprotected
insert(const CData &data) overrideCDataContainervirtual
isAutonomous() constCMathContainer
isPrerequisiteForContext(const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const overrideCDataObjectvirtual
isStateValid() constCMathContainer
mAggregateValidityCDataObjectprivate
map()CMathContainerprivate
mApplyInitialValuesSequenceCMathContainerprivate
Matrix enum valueCDataObject
mCompileTimeCMathContainerprivate
mCompleteInitialStateCMathContainerprivate
mCreateDiscontinuousPointerCMathContainerprivate
mDataObject2MathObjectCMathContainerprivate
mDataValue2DataObjectCMathContainerprivate
mDataValue2MathObjectCMathContainerprivate
mDelayLagsCMathContainerprivate
mDelaysCMathContainerprivate
mDelayValuesCMathContainerprivate
mDependentMassesCMathContainerprivate
mDiscontinuityEventsCMathContainerprivate
mDiscontinuityInfix2ObjectCMathContainerprivate
mDiscontinuousCMathContainerprivate
mEventAssignmentsCMathContainerprivate
mEventDelaysCMathContainerprivate
mEventPrioritiesCMathContainerprivate
mEventRootsCMathContainerprivate
mEventRootStatesCMathContainerprivate
mEventsCMathContainerprivate
mEventTriggersCMathContainerprivate
mExtensiveNoiseCMathContainerprivate
mExtensiveRatesCMathContainerprivate
mExtensiveValuesCMathContainerprivate
mFluxesCMathContainerprivate
mHistoryCMathContainerprivate
mHistoryReducedCMathContainerprivate
mInitialDependenciesCMathContainerprivate
mInitialEventTriggersCMathContainerprivate
mInitialExtensiveRatesCMathContainerprivate
mInitialExtensiveValuesCMathContainerprivate
mInitialFluxesCMathContainerprivate
mInitialIntensiveRatesCMathContainerprivate
mInitialIntensiveValuesCMathContainerprivate
mInitialParticleFluxesCMathContainerprivate
mInitialStateCMathContainerprivate
mInitialStateValueAllCMathContainerprivate
mInitialStateValueExtensiveCMathContainerprivate
mInitialStateValueIntensiveCMathContainerprivate
mInitialTotalMassesCMathContainerprivate
mIntensiveNoiseCMathContainerprivate
mIntensiveRatesCMathContainerprivate
mIntensiveValuesCMathContainerprivate
mIsAutonomousCMathContainerprivate
mNoiseInputObjectsCMathContainerprivate
mNoiseReducedCMathContainerprivate
mNoiseSequenceCMathContainerprivate
mNoiseSequenceReducedCMathContainerprivate
mNumTotalRootsIgnoredCMathContainerprivate
mObjectDisplayNameCDataObjectmutableprivate
mObjectFlagCDataObjectprivate
mObjectNameCDataObjectprivate
mObjectsCMathContainerprivate
mObjectTypeCDataObjectprivate
ModelEntity enum valueCDataObject
mOldObjectsCMathContainerprivate
mOldValuesCMathContainerprivate
move(sSize &size)CMathContainerprivate
mParticleFluxesCMathContainerprivate
mpAvogadroCMathContainerprivate
mpModelCMathContainerprivate
mpObjectDisplayNameCDataObjectmutableprivate
mpObjectNameCDataObjectmutableprivate
mpObjectParentCDataObjectprivate
mpObjectsBufferCMathContainerprivate
mpProcessQueueCMathContainerprivate
mpQuantity2NumberFactorCMathContainerprivate
mpRandomGeneratorCMathContainerprivate
mPrerequisitsCDataObjectprotected
mPrioritySequenceCMathContainerprivate
mPropensitiesCMathContainerprivate
mpUuidCUndoObjectInterfaceprivate
mpValuesBufferCMathContainerprivate
mRandomCMathContainerprivate
mRateCMathContainerprivate
mRateReducedCMathContainerprivate
mReactionNoiseCMathContainerprivate
mReactionParticleNoiseCMathContainerprivate
mReactionsCMathContainerprivate
mReducedStateValuesCMathContainerprivate
mReferencedValiditiesCDataObjectprivate
mReferencesCDataObjectprotected
mRootCount2EventsCMathContainerprivate
mRootDerivativesCMathContainerprivate
mRootDerivativesStateCMathContainerprivate
mRootIsDiscreteCMathContainerprivate
mRootIsTimeDependentCMathContainerprivate
mRootProcessorsCMathContainerprivate
mRootSequenceCMathContainerprivate
mRootSequenceReducedCMathContainerprivate
mSimulationRequiredValuesCMathContainerprivate
mSimulationValuesSequenceCMathContainerprivate
mSimulationValuesSequenceReducedCMathContainerprivate
mSizeCMathContainerprivate
mStateCMathContainerprivate
mStateReducedCMathContainerprivate
mStateValuesCMathContainerprivate
mSynchronizeInitialValuesSequenceExtensiveCMathContainerprivate
mSynchronizeInitialValuesSequenceIntensiveCMathContainerprivate
mTotalMassesCMathContainerprivate
mTransientDataObjectSequenceCMathContainerprivate
mTransientDependenciesCMathContainerprivate
mTransitionTimesCMathContainerprivate
mTriggerInfix2EventCMathContainerprivate
mUpdateSequencesCMathContainerprivate
mUuidLockedCUndoObjectInterfaceprivate
mValidityCObjectInterfacemutableprotected
mValueChangeProhibitedCMathContainerprivate
mValuesCMathContainerprivate
NameVector enum valueCDataObject
NonUniqueName enum valueCDataObject
objectMap typedefCDataContainer
objectRenamed(CDataObject *pObject, const std::string &oldName)CDataContainer
ObjectSet typedefCObjectInterface
operator==(const CMathContainer &rhs)CMathContainer
prerequisitsContains(const DataObjectSet &objects) constCDataObject
print(std::ostream *ostream) const overrideCDataObjectvirtual
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 valueCDataObject
refreshAggregateValidity()CDataObjectprivate
registerUpdateSequence(CMathUpdateSequence *pUpdateSequence)CMathContainer
relocate(const sSize &size, const std::vector< CMath::sRelocate > &Relocations)CMathContainerprivate
relocateObject(CObjectInterface *&pObject, const std::vector< CMath::sRelocate > &relocations) constCMathContainer
relocateObject(const CObjectInterface *&pObject, const std::vector< CMath::sRelocate > &relocations) constCMathContainer
relocateObject(CMathObject *&pObject, const std::vector< CMath::sRelocate > &relocations) constCMathContainer
relocateObject(const CMathObject *&pObject, const std::vector< CMath::sRelocate > &relocations) constCMathContainer
relocateObjectSet(CObjectInterface::ObjectSet &objectSet, const std::vector< CMath::sRelocate > &relocations) constCMathContainer
relocateUpdateSequence(CCore::CUpdateSequence &sequence, const std::vector< CMath::sRelocate > &relocations) constCMathContainer
relocateValue(C_FLOAT64 *&pValue, const std::vector< CMath::sRelocate > &relocations) constCMathContainer
relocateValue(const C_FLOAT64 *&pValue, const std::vector< CMath::sRelocate > &relocations) constCMathContainer
relocateVector(CVectorCore< CType > &vector, size_t size, const std::vector< CMath::sRelocate > &relocations)CMathContainerinlineprivate
remove(CDataObject *pObject)CDataContainervirtual
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)CMathContainerprivate
Root enum valueCDataObject
sanitizeDataValue2DataObject()CMathContainerprivate
sanitizeObjectName(std::string &name)CDataObjectstatic
Separator enum valueCDataObject
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)CDataObjectvirtual
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 valueCDataObject
toData() const overrideCDataContainervirtual
updateHistoryValues(const bool &useMoieties)CMathContainer
updateIndex(const size_t &index, const CUndoObjectInterface *pUndoObject)CUndoObjectInterfacevirtual
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) overrideCDataObjectvirtual
validityRemoved(const CValidity &changedValidity)CDataObject
ValueBool enum valueCDataObject
ValueDbl enum valueCDataObject
ValueInt enum valueCDataObject
ValueInt64 enum valueCDataObject
ValueString enum valueCDataObject
Vector enum valueCDataObject
~CDataContainer()CDataContainervirtual
~CDataObject()CDataObjectvirtual
~CMathContainer()CMathContainervirtual
~CObjectInterface()CObjectInterfacevirtual
~CUndoObjectInterface()CUndoObjectInterfacevirtual