CModel Member List

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

__SIZE enum value	CDataObject
add(CDataObject *pObject, const bool &adopt=true)	CDataContainer	virtual
addIssue(const CIssue &issue)	CDataObject
addMatrixReference(const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)	CDataContainer	protected
addModelEntity(const CModelEntity *pModelEntity)	CModel
addObjectReference(const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)	CDataContainer	protected
addReference(const CDataContainer *pReference)	CDataObject
addUnsupportedAnnotation(const std::string &name, const std::string &xml)	CAnnotation
addVectorReference(const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)	CDataContainer	protected
allocateMiriamInfo(CDataContainer *pParent)	CAnnotation	static
appendAllDependents(const CDataContainer &container, DataObjectSet &dependentReactions, DataObjectSet &dependentMetabolites, DataObjectSet &dependentCompartments, DataObjectSet &dependentModelValues, DataObjectSet &dependentEvents, DataObjectSet &dependentEventAssignments, const bool &onlyStructural=false) const	CModel
appendAllDependents(const ObjectSet &objects, DataObjectSet &dependentReactions, DataObjectSet &dependentMetabolites, DataObjectSet &dependentCompartments, DataObjectSet &dependentModelValues, DataObjectSet &dependentEvents, DataObjectSet &dependentEventAssignments, const bool &onlyStructural=false) const	CModel
appendDeletedDependentData(CUndoData &undoData) const	CDataContainer	virtual
appendDirectDependents(const CDataContainer &container, DataObjectSet &dependentReactions, DataObjectSet &dependentMetabolites, DataObjectSet &dependentCompartments, DataObjectSet &dependentModelValues, DataObjectSet &dependentEvents, DataObjectSet &dependentEventAssignments, const bool &onlyStructural=false) const	CModel
appendDirectDependents(const ObjectSet &objects, DataObjectSet &dependentReactions, DataObjectSet &dependentMetabolites, DataObjectSet &dependentCompartments, DataObjectSet &dependentModelValues, DataObjectSet &dependentEvents, DataObjectSet &dependentEventAssignments, const bool &onlyStructural=false) const	CModel
applyActiveParameterSet()	CModel
applyData(const CData &data, CUndoData::CChangeSet &changes)	CModel	virtual
applyInitialValues()	CModel
area enum value	CModel
Array enum value	CDataObject
buildDependencyGraphs()	CModel
buildInitialRefreshSequence(std::set< const CDataObject * > &changedObjects)	CModel
buildLinkZero()	CModel
buildMoieties()	CModel
buildRedStoi()	CModel
buildStateTemplate()	CModel	private
buildStoi()	CModel
buildUserOrder()	CModel	private
calculate()	CModelEntity	virtual
calculateValue() override	CDataObject	virtual
CAnnotation()	CAnnotation
CAnnotation(const CAnnotation &src)	CAnnotation
castObject(CDataObject *pObject)	CAnnotation	static
castObject(const CDataObject *pObject)	CAnnotation	static
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
CFunctionDB class	CModel	friend
changeUnitExpressionSymbols(std::string oldSymbol, std::string newSymbol)	CModel
clearMoieties()	CModel	private
clearSbmlIds()	CModel
CModel(const CModel &src)	CModel	private
CModel(CDataContainer *pParent)	CModel
CModelEntity(const CModelEntity &src)	CModelEntity	protected
CModelEntity(const std::string &name="NoName", const CDataContainer *pParent=NO_PARENT, const std::string &type="ModelEntity", const CFlags< Flag > &flag=CFlags< Flag >::None)	CModelEntity
CModelEntity(const CModelEntity &src, const CDataContainer *pParent)	CModelEntity
CObjectInterface()	CObjectInterface
CObjectInterface(const CObjectInterface &src)	CObjectInterface
compile()	CModel	privatevirtual
compileEvents()	CModel	private
compileIfNecessary(CProcessReport *pProcessReport)	CModel
Container enum value	CDataObject
Container2Info	CAnnotation	privatestatic
ContainerList typedef	CObjectInterface
convert2NonReversible()	CModel
createCompartment(const std::string &name, const C_FLOAT64 &volume=1.0)	CModel
createEvent(const std::string &name)	CModel
createEventsForTimeseries(CExperiment *experiment=NULL)	CModel
createMetabolite(const std::string &name, const std::string &compartment, const C_FLOAT64 &iconc=1.0, const CModelEntity::Status &status=CModelEntity::Status::REACTIONS)	CModel
createModelValue(const std::string &name, const C_FLOAT64 &value=0.0)	CModel
createReaction(const std::string &name)	CModel
createUndoData(CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const	CModel	virtual
CUndoObjectInterface()	CUndoObjectInterface
CUndoObjectInterface(const CUndoObjectInterface &src)	CUndoObjectInterface
DataModel enum value	CDataObject
DataObject(const CObjectInterface *pInterface)	CObjectInterface	static
DataObjectSet typedef	CDataObject
DependencyType enum name	CModel
destruct() override	CDataObject	virtual
DisplayName enum value	CDataObject
EmptyList	CDataContainer	static
findMetabByName(const std::string &name) const	CModel
findMoiety(const std::string &Target) const	CModel
Flag enum name	CDataObject
forceCompile(CProcessReport *pProcessReport)	CModel
freeMiriamInfo(CDataContainer *pParent)	CAnnotation	static
fromData(const CData &data, CUndoObjectInterface *pParent)	CModel	static
functionDefinitionChanged(const CFunction *pFunction)	CModel
generateUuid()	CUndoObjectInterface
getActiveModelParameterSet() const	CModel
getActiveModelParameterSet()	CModel
getAreaUnit() const	CModel
getAreaUnitName() const	CModel
getAvogadro() const	CModel
getChildObjectUnits(const CDataObject *pObject) const	CModel	virtual
getCN() const override	CDataObject	virtual
getCompartments()	CModel
getCompartments() const	CModel
getCorrespondingTransientObject(const CDataObject *pObject) const	CModel
getDataObject() const override	CDataObject	virtual
getDefaultNoiseExpression() const	CModelEntity
getDescendants(CDataObject::DataObjectSet &descendants, const bool &recursive=false) const	CDataContainer
getEvents()	CModel
getEvents() const	CModel
getExpression() const	CModelEntity
getExpressionPtr() const	CModelEntity
getExpressionPtr()	CModelEntity
getIndex(const CDataObject *pObject) const	CDataContainer	virtual
getInitialExpression() const	CModelEntity
getInitialExpressionPtr() const	CModelEntity
getInitialExpressionPtr()	CModelEntity
getInitialTime() const	CModel
getInitialValue() const	CModelEntity
getInitialValueReference() const	CModelEntity
getKey() const	CModel	virtual
getL() const	CModel
getL0() const	CModel
getLAnnotation() const	CModel
getLengthUnit() const	CModel
getLengthUnitName() const	CModel
getMathContainer() const	CModel
getMathContainer()	CModel
getMetabolites() const	CModel
getMetabolites()	CModel
getMetabolitesX() const	CModel
getMetabolitesX()	CModel
getMiriamAnnotation() const	CAnnotation
getModel() const	CModelEntity
getModelParameterSets() const	CModel
getModelParameterSets()	CModel
getModelType() const	CModel
getModelValues() const	CModel
getModelValues()	CModel
getMoieties() const	CModel
getNoiseExpression() const	CModelEntity
getNoiseExpressionPtr() const	CModelEntity
getNoiseExpressionPtr()	CModelEntity
getNoiseReference() const	CModelEntity
getNotes() const	CAnnotation
getNumAssignmentMetabs() const	CModel
getNumber2QuantityFactor() const	CModel
getNumDependentReactionMetabs() const	CModel
getNumIndependentReactionMetabs() const	CModel
getNumMetabs() const	CModel
getNumModelValues() const	CModel
getNumODEMetabs() const	CModel
getNumVariableMetabs() const	CModel
getObject(const CCommonName &cn) const override	CDataContainer	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	CDataObject
getObjectName() const	CDataObject
getObjectParent() const	CDataObject
getObjects() const	CDataContainer	virtual
getObjects()	CDataContainer	virtual
getObjectType() const	CDataObject
getParticleFlux() const	CModel
getPrerequisites() const override	CDataObject	virtual
getQuantity2NumberFactor() const	CModel
getQuantityUnit() const	CModel
getQuantityUnitName() const	CModel
getRate() const	CModelEntity
getRateReference() const	CModelEntity
getReactions()	CModel
getReactions() const	CModel
getReactionsPerSpecies(const CMetab *) const	CModel
getRedStoi() const	CModel
getRedStoiAnnotation() const	CModel
getSBMLId() const	CModelEntity
getStateTemplate() const	CModel
getStatus() const	CModelEntity
getStoi() const	CModel
getStoiAnnotation() const	CModel
getTime() const	CModel
getTimeUnit() const	CModel
getTimeUnitName() const	CModel
getTotSteps() const	CModel
getTreesWithDiscontinuities() const	CModel
getUnitExpression() const	CModelEntity	virtual
getUnits() const	CModel	virtual
getUnitSymbolUsage(std::string symbol) const	CModel
getUnsupportedAnnotations()	CAnnotation
getUnsupportedAnnotations() const	CAnnotation
getUsedUnits() const	CModel
getUuid() const	CUndoObjectInterface
getValidity() const override	CDataObject	virtual
getValue() const	CModelEntity
getValueObject() const override	CModelEntity	virtual
getValuePointer() const override	CModelEntity	virtual
getValueReference() const	CModelEntity
getVolumeUnit() const	CModel
getVolumeUnitName() const	CModel
Gui enum value	CDataObject
handleUnusedMetabolites()	CModel	private
hasFlag(const Flag &flag) const	CDataObject
hasNoise() const	CModelEntity
hasReversibleReaction() const	CModel
initial enum value	CModel
initializeAtolVector(const C_FLOAT64 &baseTolerance, const bool &reducedModel) const	CModel
initializeMetabolites()	CModel
initMiriamAnnotation(const std::string &newId)	CAnnotation
initObjects()	CModel	private
insert(const CData &data) override	CDataContainer	virtual
isAutonomous() const	CModel
isCompileNecessary() const	CModel
isFixed() const	CModelEntity	inline
isPrerequisiteForContext(const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override	CDataObject	virtual
isStateVariable(const CDataObject *pObject) const	CModel
isUsed() const	CModelEntity
isValidXML(const std::string &xml)	CAnnotation	privatestatic
length enum value	CModel
load(CReadConfig &configBuffer)	CModel
mActiveParameterSetKey	CModel	private
mAggregateValidity	CDataObject	private
mAreaUnit	CModel	private
Matrix enum value	CDataObject
mAvogadro	CModel	private
mBuildInitialSequence	CModel	private
mCompartments	CModel	private
mCompileIsNecessary	CModel	private
mElasticities	CModel	private
mEvents	CModel	private
mHasNoise	CModelEntity	protected
mIsAutonomous	CModel	private
mIValue	CModelEntity	protected
mJacobianPivot	CModel	private
mKey	CAnnotation	protected
mL	CModel	private
mLengthUnit	CModel	private
mLView	CModel	private
mMetabolites	CModel	private
mMetabolitesX	CModel	private
mMiriamAnnotation	CAnnotation	private
mMoieties	CModel	private
mNoise	CModelEntity	protected
mNotes	CAnnotation	private
mNumber2QuantityFactor	CModel	private
mNumMetabolitesAssignment	CModel	private
mNumMetabolitesODE	CModel	private
mNumMetabolitesReaction	CModel	private
mNumMetabolitesReactionIndependent	CModel	private
mNumMetabolitesUnused	CModel	private
mObjectDisplayName	CDataObject	mutableprivate
mObjectFlag	CDataObject	private
mObjectName	CDataObject	private
mObjects	CDataContainer	protected
mObjectType	CDataObject	private
ModelEntity enum value	CDataObject
ModelType enum name	CModel
ModelTypeNames	CModel	static
mParameterSet	CModel	private
mParameterSets	CModel	private
mParticleFluxes	CModel	private
mpAvogadroReference	CModel	private
mpExpression	CModelEntity	protected
mpInitialExpression	CModelEntity	protected
mpIValueReference	CModelEntity	protected
mpLinkMatrixAnnotation	CModel	private
mpMathContainer	CModel	private
mpModel	CModelEntity	mutableprotected
mpNoiseExpression	CModelEntity	protected
mpNoiseReference	CModelEntity	protected
mpObjectDisplayName	CDataObject	mutableprivate
mpObjectName	CDataObject	mutableprivate
mpObjectParent	CDataObject	private
mpProcessReport	CModel	private
mpQuantity2NumberFactorReference	CModel	private
mpRateReference	CModelEntity	protected
mpRedStoiAnnotation	CModel	private
mPrerequisits	CDataObject	protected
mpStoiAnnotation	CModel	private
mpUuid	CUndoObjectInterface	private
mpValueReference	CModelEntity	protected
mQuantity2NumberFactor	CModel	private
mQuantityUnit	CModel	private
mRate	CModelEntity	protected
mReactionsPerSpecies	CModel	private
mRedStoi	CModel	private
mReferencedValidities	CDataObject	private
mReferences	CDataObject	protected
mReorderNeeded	CModel	private
mSBMLId	CModelEntity	mutableprotected
mStateTemplate	CModel	private
mStatus	CModelEntity	private
mSteps	CModel	private
mStoi	CModel	private
mStructuralDependencies	CModel	private
mTimeUnit	CModel	private
mType	CModel	private
mUnitExpression	CModelEntity	protected
mUnsupportedAnnotations	CAnnotation	private
mUsed	CModelEntity	private
mUuidLocked	CUndoObjectInterface	private
mValidity	CObjectInterface	mutableprotected
mValue	CModelEntity	protected
mValues	CModel	private
mVolumeUnit	CModel	private
mXMLId	CAnnotation	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 CModel &src)	CModel	private
operator==(const CAnnotation &rhs) const	CAnnotation
physical enum value	CModel
prepareElasticity(const CReaction *pReaction, const CModelEntity *pVar, bool simplify)	CModel
prerequisitsContains(const DataObjectSet &objects) const	CDataObject
print(std::ostream *ostream) const override	CDataObject	virtual
quantity enum value	CModel
Reference enum value	CDataObject
refreshActiveParameterSet()	CModel
refreshAggregateValidity()	CDataObject	private
remove(CDataObject *pObject)	CDataContainer	virtual
removeCompartment(const size_t index, const bool &recursive=true)	CModel
removeCompartment(const std::string &key, const bool &recursive=true)	CModel
removeCompartment(const CCompartment *pCompartment, const bool &recursive=true)	CModel
removeDataObject(const CDataObject *pObject)	CModel	private
removeDependentModelObjects(const ObjectSet &deletedObjects, const bool &onlyStructural=false)	CModel
removeEvent(const size_t index, const bool &recursive=true)	CModel
removeEvent(const std::string &key, const bool &recursive=true)	CModel
removeEvent(const CEvent *pEvent, const bool &recursive=true)	CModel
removeFunction(const CFunction *pFunction, const bool &recursive=true)	CModel
removeIssue(const CIssue &issue)	CDataObject
removeLocalReactionParameter(const std::string &key, const bool &recursive=true)	CModel
removeMetabolite(const std::string &key, const bool &recursive=true)	CModel
removeMetabolite(const size_t index, const bool &recursive=true)	CModel
removeMetabolite(const CMetab *pMetabolite, const bool &recursive=true)	CModel
removeModelEntity(const CModelEntity *pModelEntity)	CModel
removeModelValue(const CModelValue *pModelValue, const bool &recursive=true)	CModel
removeModelValue(const std::string &key, const bool &recursive=true)	CModel
removeModelValue(const size_t index, const bool &recursive=true)	CModel
removeReaction(const CReaction *pReaction, const bool &recursive=true)	CModel
removeReaction(const std::string &key, const bool &recursive=true)	CModel
removeReaction(const size_t index, const bool &recursive=true)	CModel
removeReference(const CDataContainer *pReference)	CDataObject
removeUnsupportedAnnotation(const std::string &name)	CAnnotation
replaceInExpressions(const std::string &oldStr, const std::string &newStr)	CModel	private
replaceUnsupportedAnnotation(const std::string &name, const std::string &xml)	CAnnotation
Root enum value	CDataObject
sanitizeObjectName(std::string &name)	CDataObject	static
Separator enum value	CDataObject
setAreaUnit(const std::string &name)	CModel
setAvogadro(const C_FLOAT64 &avogadro, const CCore::Framework &frameWork)	CModel
setCompileFlag(bool flag=true)	CModel
setExpression(const std::string &expression)	CModelEntity
setExpressionPtr(CExpression *pExpression)	CModelEntity
setHasNoise(const bool &hasNoise)	CModelEntity
setInitialExpression(const std::string &expression)	CModelEntity
setInitialExpressionPtr(CExpression *pExpression)	CModelEntity
setInitialTime(const C_FLOAT64 &time)	CModel
setInitialValue(const C_FLOAT64 &initialValue)	CModelEntity	virtual
setLengthUnit(const std::string &name)	CModel
setMiriamAnnotation(const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)	CAnnotation
setModelType(const ModelType &modelType)	CModel
setNoiseExpression(const std::string &expression)	CModelEntity
setNoiseExpressionPtr(CExpression *pExpression)	CModelEntity
setNotes(const std::string &notes)	CAnnotation
setObjectName(const std::string &name)	CDataObject
setObjectParent(const CDataContainer *pParent)	CModel	virtual
setQuantityUnit(const std::string &name, const CCore::Framework &frameWork)	CModel
setRate(const C_FLOAT64 &rate)	CModelEntity
setSBMLId(const std::string &id) const	CModelEntity
setStatus(const CModelEntity::Status &status)	CModelEntity
setTime(const C_FLOAT64 &time)	CModel
setTimeUnit(const std::string &name)	CModel
setUnitExpression(std::string unitExpression)	CModelEntity	virtual
setUsed(const bool &used)	CModelEntity
setUuid(const xg::Guid &uuid)	CUndoObjectInterface
setUuid(const std::string &uuid)	CUndoObjectInterface
setValue(const C_FLOAT64 &value)	CModelEntity	virtual
setVolumeUnit(const std::string &name)	CModel
stateToIntialState()	CModel
StaticString enum value	CDataObject
Status enum name	CModelEntity
StatusName	CModelEntity	static
suitableForStochasticSimulation() const	CModel
time enum value	CModel
toData() const	CModel	virtual
transient enum value	CModel
UnitType enum name	CModel
UnsupportedAnnotation typedef	CAnnotation
updateIndex(const size_t &index, const CUndoObjectInterface *pUndoObject)	CUndoObjectInterface	virtual
updateInitialValues(const CCore::Framework &framework)	CModel
updateInitialValues(std::set< const CDataObject * > &changedObjects)	CModel
updateInitialValues(const CDataObject *changedObject)	CModel
updateMatrixAnnotations()	CModel	private
updateMoietyValues()	CModel	private
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
volume enum value	CModel
XMLStatus	CModelEntity	static
~CAnnotation()	CAnnotation	virtual
~CDataContainer()	CDataContainer	virtual
~CDataObject()	CDataObject	virtual
~CModel()	CModel
~CModelEntity()	CModelEntity
~CObjectInterface()	CObjectInterface	virtual
~CUndoObjectInterface()	CUndoObjectInterface	virtual