CReaction Member List

This is the complete list of members for CReaction, 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
addModifier(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)	CReaction
addObjectReference(const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)	CDataContainer	protected
addParameterObject(const size_t &index, const CDataObject *object)	CReaction
addParameterObject(const std::string &name, const CDataObject *object)	CReaction
addProduct(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)	CReaction
addReference(const CDataContainer *pReference)	CDataObject
addSubstrate(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)	CReaction
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
appendDeletedDependentData(CUndoData &undoData) const	CDataContainer	virtual
applyData(const CData &data, CUndoData::CChangeSet &changes)	CReaction	virtual
Array enum value	CDataObject
calculate()	CReaction	private
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
CObjectInterface()	CObjectInterface
CObjectInterface(const CObjectInterface &src)	CObjectInterface
compile()	CReaction
compileFunctionParameters(std::set< const CDataObject * > &Dependencies)	CReaction	private
Container enum value	CDataObject
Container2Info	CAnnotation	privatestatic
ContainerList typedef	CObjectInterface
CReaction(const std::string &name="NoName", const CDataContainer *pParent=NO_PARENT)	CReaction
CReaction(const CReaction &src, const CDataContainer *pParent)	CReaction
createFunctionFromExpression(const std::string &infix)	CReaction
createUndoData(CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const	CReaction	virtual
CUndoObjectInterface()	CUndoObjectInterface
CUndoObjectInterface(const CUndoObjectInterface &src)	CUndoObjectInterface
DataModel enum value	CDataObject
DataObject(const CObjectInterface *pInterface)	CObjectInterface	static
DataObjectSet typedef	CDataObject
destruct() override	CDataObject	virtual
DisplayName enum value	CDataObject
EmptyList	CDataContainer	static
escapeId(const std::string &id)	CReaction	private
Flag enum name	CDataObject
freeMiriamInfo(CDataContainer *pParent)	CAnnotation	static
fromData(const CData &data, CUndoObjectInterface *pParent)	CReaction	static
generateUuid()	CUndoObjectInterface
getCallParameters() const	CReaction
getChemEq() const	CReaction
getChemEq()	CReaction
getChildObjectUnits(const CDataObject *pObject) const	CReaction	virtual
getCN() const override	CDataObject	virtual
getCompartmentNumber() const	CReaction
getDataObject() const override	CDataObject	virtual
getDefaultNoiseExpression() const	CReaction
getDescendants(CDataObject::DataObjectSet &descendants, const bool &recursive=false) const	CDataContainer
getEffectiveKineticLawUnitType() const	CReaction
getExpressionTree()	CReaction
getFirstCModelOrDefault(std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	CReaction	private
getFlux() const	CReaction
getFluxReference()	CReaction
getFluxReference() const	CReaction
getFunction() const	CReaction
getFunctionParameters() const	CReaction
getIndex(const CDataObject *pObject) const	CDataContainer	virtual
getKey() const	CReaction	virtual
getKineticLawUnit() const	CReaction
getKineticLawUnitType() const	CReaction
getLargestCompartment() const	CReaction
getMap() const	CReaction
getMiriamAnnotation() const	CAnnotation
getNoiseExpression() const	CReaction
getNoiseExpressionPtr() const	CReaction
getNoiseExpressionPtr()	CReaction
getNoiseReference() const	CReaction
getNotes() const	CAnnotation
getObject(const CCommonName &cn) const	CReaction	virtual
getObjectAncestor(const std::string &type) const	CDataObject
getObjectDataModel() const	CDataObject
getObjectDisplayName() const	CReaction	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
getParameterCNs(const size_t &index) const	CReaction
getParameterCNs(const std::string &name) const	CReaction
getParameterCNs() const	CReaction
getParameterIndex(const std::string &parameterName, const CFunctionParameter **ppFunctionParameter=NULL) const	CReaction
getParameterObjects(const size_t &index) const	CReaction
getParameterObjects(const std::string &name) const	CReaction
getParameterObjects() const	CReaction
getParameters() const	CReaction
getParameters()	CReaction
getParameterValue(const std::string &parameterName) const	CReaction
getParticleFlux() const	CReaction
getParticleFluxReference()	CReaction
getParticleFluxReference() const	CReaction
getParticleNoiseReference() const	CReaction
getPrerequisites() const override	CDataObject	virtual
getPropensityReference()	CReaction
getPropensityReference() const	CReaction
getReactionScheme() const	CReaction
getSBMLId() const	CReaction
getScalingCompartment() const	CReaction
getScalingCompartmentCN() const	CReaction
getUnits() const override	CDataContainer	virtual
getUnsupportedAnnotations()	CAnnotation
getUnsupportedAnnotations() const	CAnnotation
getUuid() const	CUndoObjectInterface
getValidity() const override	CDataObject	virtual
getValueObject() const override	CDataContainer	virtual
getValuePointer() const override	CDataObject	virtual
Gui enum value	CDataObject
hasFlag(const Flag &flag) const	CDataObject
hasNoise() const	CReaction
initializeParameterMapping()	CReaction	private
initializeParameters()	CReaction	private
initMiriamAnnotation(const std::string &newId)	CAnnotation
initObjects()	CReaction	private
insert(const CData &data) override	CDataContainer	virtual
isFast() const	CReaction
isLocalParameter(const size_t &index) const	CReaction
isLocalParameter(const std::string &parameterName) const	CReaction
isPrerequisiteForContext(const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override	CDataObject	virtual
isReversible() const	CReaction
isValidXML(const std::string &xml)	CAnnotation	privatestatic
KineticLawUnit enum name	CReaction
KineticLawUnitTypeName	CReaction	static
load(CReadConfig &configbuffer)	CReaction
loadOld(CReadConfig &configbuffer)	CReaction	private
loadOneRole(CReadConfig &configbuffer, CFunctionParameter::Role role, C_INT32 n, const std::string &prefix)	CReaction	private
mAggregateValidity	CDataObject	private
Matrix enum value	CDataObject
mChemEq	CReaction	private
mFast	CReaction	private
mFlux	CReaction	private
mHasNoise	CReaction	private
mKey	CAnnotation	protected
mKineticLawUnit	CReaction	private
mMap	CReaction	private
mMiriamAnnotation	CAnnotation	private
mNoise	CReaction	private
mNotes	CAnnotation	private
mObjectDisplayName	CDataObject	mutableprivate
mObjectFlag	CDataObject	private
mObjectName	CDataObject	private
mObjects	CDataContainer	protected
mObjectType	CDataObject	private
ModelEntity enum value	CDataObject
mParameterIndexToCNs	CReaction	private
mParameterIndexToObjects	CReaction	private
mParameterNameToIndex	CReaction	private
mParameters	CReaction	private
mParticleFlux	CReaction	private
mParticleNoise	CReaction	private
mpFluxReference	CReaction	private
mpFunction	CReaction	private
mpNoiseExpression	CReaction	private
mpNoiseReference	CReaction	private
mpObjectDisplayName	CDataObject	mutableprivate
mpObjectName	CDataObject	mutableprivate
mpObjectParent	CDataObject	private
mpParticleFluxReference	CReaction	private
mpParticleNoiseReference	CReaction	private
mpPropensityReference	CReaction	private
mPrerequisits	CDataObject	protected
mPropensity	CReaction	private
mpScalingCompartment	CReaction	private
mpUuid	CUndoObjectInterface	private
mReferencedValidities	CDataObject	private
mReferences	CDataObject	protected
mSBMLId	CReaction	mutableprivate
mScalingCompartmentCN	CReaction	private
mUnsupportedAnnotations	CAnnotation	private
mUuidLocked	CUndoObjectInterface	private
mValidity	CObjectInterface	mutableprotected
mXMLId	CAnnotation	private
NameVector enum value	CDataObject
NonUniqueName enum value	CDataObject
object2variable(const CEvaluationNodeObject *objectNode, std::map< std::string, std::pair< CDataObject *, CFunctionParameter * > > &replacementMap, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	CReaction	private
objectMap typedef	CDataContainer
objectRenamed(CDataObject *pObject, const std::string &oldName)	CDataContainer
objects2variables(const CEvaluationNode *expression, std::map< std::string, std::pair< CDataObject *, CFunctionParameter * > > &replacementMap, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	CReaction	private
ObjectSet typedef	CObjectInterface
operator<<(std::ostream &os, const CReaction &d)	CReaction	friend
operator=(const CReaction &)	CReaction	private
operator==(const CAnnotation &rhs) const	CAnnotation
prerequisitsContains(const DataObjectSet &objects) const	CDataObject
print(std::ostream *ostream) const override	CDataObject	virtual
printDebug() const	CReaction
Reference enum value	CDataObject
refreshAggregateValidity()	CDataObject	private
remove(CDataObject *pObject)	CDataContainer	virtual
removeIssue(const CIssue &issue)	CDataObject
removeReference(const CDataContainer *pReference)	CDataObject
removeUnsupportedAnnotation(const std::string &name)	CAnnotation
replaceUnsupportedAnnotation(const std::string &name, const std::string &xml)	CAnnotation
resolveCN(const CModel *pModel, CCommonName cn)	CReaction	private
Root enum value	CDataObject
sanitizeObjectName(std::string &name)	CDataObject	static
sanitizeSBMLId(const std::string &id)	CReaction	privatestatic
Separator enum value	CDataObject
setFast(const bool &fast)	CReaction
setFunction(const std::string &functionName)	CReaction
setFunction(CFunction *pFunction)	CReaction
setFunctionFromExpressionTree(const CExpression &tree, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)	CReaction
setHasNoise(const bool &hasNoise)	CReaction
setKineticLawUnitType(const KineticLawUnit &kineticLawUnitType)	CReaction
setMiriamAnnotation(const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)	CAnnotation
setNoiseExpression(const std::string &expression)	CReaction
setNoiseExpressionPtr(CExpression *pExpression)	CReaction
setNotes(const std::string &notes)	CAnnotation
setObjectName(const std::string &name)	CDataObject
setObjectParent(const CDataContainer *pParent)	CReaction	virtual
setParameterCNs(const size_t &index, const std::vector< CRegisteredCommonName > &CNs)	CReaction
setParameterCNs(const std::string &name, const std::vector< CRegisteredCommonName > &CNs)	CReaction
setParameterObject(const size_t &index, const CDataObject *object)	CReaction
setParameterObject(const std::string &name, const CDataObject *object)	CReaction
setParameterObjects(const size_t &index, const std::vector< const CDataObject * > &objects)	CReaction
setParameterObjects(const std::string &name, const std::vector< const CDataObject * > &objects)	CReaction
setParameterValue(const std::string &parameterName, const C_FLOAT64 &value)	CReaction
setReactionScheme(const std::string &scheme, const std::string &newFunction="", bool createMetabolites=true, bool createOther=true)	CReaction
setReversible(bool reversible)	CReaction
setSBMLId(const std::string &id) const	CReaction
setScalingCompartment(const CCompartment *pCompartment)	CReaction
setScalingCompartmentCN(const std::string &compartmentCN)	CReaction
setScalingFactor()	CReaction	private
setUuid(const xg::Guid &uuid)	CUndoObjectInterface
setUuid(const std::string &uuid)	CUndoObjectInterface
StaticString enum value	CDataObject
toData() const	CReaction	virtual
UnsupportedAnnotation typedef	CAnnotation
updateIndex(const size_t &index, const CUndoObjectInterface *pUndoObject)	CUndoObjectInterface	virtual
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
variable2object(CEvaluationNodeVariable *pVariableNode)	CReaction	private
variables2objects(CEvaluationNode *expression)	CReaction	private
Vector enum value	CDataObject
~CAnnotation()	CAnnotation	virtual
~CDataContainer()	CDataContainer	virtual
~CDataObject()	CDataObject	virtual
~CObjectInterface()	CObjectInterface	virtual
~CReaction()	CReaction	virtual
~CUndoObjectInterface()	CUndoObjectInterface	virtual