CReaction Member List

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

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
addModifier(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)	CReaction
addObjectReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)	CCopasiContainer	inlineprotected
addParameterMapping(const size_t &index, const std::string &key)	CReaction
addParameterMapping(const std::string &parameterName, const std::string &key)	CReaction
addProduct(const std::string &metabKey, const C_FLOAT64 &multiplicity=1.0)	CReaction
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 unsigned C_INT32 &flag=0)	CCopasiContainer	inlineprotected
Array enum value	CCopasiObject	protected
buildUpdateSequence(const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())	CCopasiObject	static
calculate()	CReaction	private
calculateFlux()	CReaction
calculatePartialDerivative(C_FLOAT64 *pXi, const C_FLOAT64 &derivationFactor, const C_FLOAT64 &resolution)	CReaction
calculateParticleFlux()	CReaction
CAnnotation()	CAnnotation
CAnnotation(const CAnnotation &src)	CAnnotation
castObject(CCopasiObject *pObject)	CAnnotation	static
castObject(const CCopasiObject *pObject)	CAnnotation	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
cleanup()	CReaction
clearDirectDependencies()	CCopasiObject
clearParameterMapping(const std::string &parameterName)	CReaction
clearParameterMapping(const size_t &index)	CReaction
clearRefresh()	CCopasiObject
CObjectInterface()	CObjectInterface	inline
compile()	CReaction
Container enum value	CCopasiObject	protected
CReaction(const std::string &name="NoName", const CCopasiContainer *pParent=NULL)	CReaction
CReaction(const CReaction &src, const CCopasiContainer *pParent=NULL)	CReaction
DataModel enum value	CCopasiObject	protected
DataObjectSet typedef	CCopasiObject
DataUpdateSequence typedef	CCopasiObject
dependsOn(DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const	CCopasiObject
EmptyList	CCopasiContainer	static
escapeId(const std::string &id)	CReaction	private
Flag enum name	CCopasiObject	protected
getAllDependencies(DataObjectSet &dependencies, const DataObjectSet &context) const	CCopasiObject
getCallParameters() const	CReaction
getChemEq() const	CReaction
getChemEq()	CReaction
getChildObjectUnits(const CCopasiObject *pObject) const	CReaction	virtual
getCN() const	CCopasiObject	virtual
getCompartmentNumber() const	CReaction
getDeletedObjects() const	CReaction	virtual
getDirectDependencies(const DataObjectSet &context=DataObjectSet()) const	CCopasiObject	virtual
getExpressionTree()	CReaction
getFlux() const	CReaction
getFluxReference()	CReaction
getFluxReference() const	CReaction
getFunction() const	CReaction
getFunctionParameters() const	CReaction
getKey() const	CReaction	virtual
getLargestCompartment() const	CReaction
getMiriamAnnotation() const	CAnnotation
getNotes() const	CAnnotation
getObject(const CCopasiObjectName &cn) const	CReaction	virtual
getObjectAncestor(const std::string &type) const	CCopasiObject
getObjectDataModel()	CCopasiObject
getObjectDataModel() const	CCopasiObject
getObjectDisplayName(bool regular=true, bool richtext=false) const	CReaction	virtual
getObjectName() const	CCopasiObject
getObjectParent() const	CCopasiObject
getObjects() const	CCopasiContainer	virtual
getObjectType() const	CCopasiObject
getParameterIndex(const std::string &parameterName, CFunctionParameter::DataType *pType=NULL) const	CReaction
getParameterMapping(const size_t &index) const	CReaction
getParameterMapping(const std::string &parameterName) const	CReaction
getParameterMappings() const	CReaction	inline
getParameterMappings()	CReaction	inline
getParameters() const	CReaction
getParameters()	CReaction
getParameterValue(const std::string &parameterName) const	CReaction
getParticleFlux() const	CReaction
getParticleFluxReference()	CReaction
getParticleFluxReference() const	CReaction
getPrerequisites() const	CCopasiObject	virtual
getPropensityReference()	CReaction
getPropensityReference() const	CReaction
getRefresh() const	CCopasiObject	virtual
getSBMLId() const	CReaction
getUnits() const	CCopasiContainer	virtual
getUnsupportedAnnotations()	CAnnotation
getUnsupportedAnnotations() const	CAnnotation
getUpdateMethod() const	CCopasiObject
getValueObject() const	CCopasiContainer	virtual
getValuePointer() const	CCopasiObject	virtual
Gui enum value	CCopasiObject	protected
hasCircularDependencies(DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const	CCopasiObject
hasUpdateMethod() const	CCopasiObject
initializeMetaboliteKeyMap()	CReaction	private
initializeParameters()	CReaction	private
initObjects()	CReaction	private
isArray() const	CCopasiObject
isContainer() const	CCopasiObject
isDataModel() const	CCopasiObject
isFast() const	CReaction
isLocalParameter(const size_t &index) const	CReaction
isLocalParameter(const std::string &parameterName) const	CReaction
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
isReversible() const	CReaction
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
load(CReadConfig &configbuffer)	CReaction
loadOld(CReadConfig &configbuffer)	CReaction	private
loadOneRole(CReadConfig &configbuffer, CFunctionParameter::Role role, C_INT32 n, const std::string &prefix)	CReaction	private
Matrix enum value	CCopasiObject	protected
mChemEq	CReaction	private
mDefaultScalingFactor	CReaction	privatestatic
mFast	CReaction	private
mFlux	CReaction	private
mKey	CAnnotation	protected
mMap	CReaction	private
mMetabKeyMap	CReaction	private
mObjects	CCopasiContainer	protected
ModelEntity enum value	CCopasiObject	protected
mParameters	CReaction	private
mParticleFlux	CReaction	private
mpFluxReference	CReaction	private
mpFunction	CReaction	private
mpParticleFluxReference	CReaction	private
mpPropensityReference	CReaction	private
mPropensity	CReaction	private
mSBMLId	CReaction	private
mScalingFactor	CReaction	private
mUnitScalingFactor	CReaction	private
mustBeDeleted(const DataObjectSet &deletedObjects) const	CReaction	virtual
NameVector enum value	CCopasiObject	protected
NonUniqueName enum value	CCopasiObject	protected
object2variable(const CEvaluationNodeObject *objectNode, std::map< std::string, std::pair< CCopasiObject *, CFunctionParameter * > > &replacementMap, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap)	CReaction	private
objectMap typedef	CCopasiContainer
objects2variables(const CEvaluationNode *expression, std::map< std::string, std::pair< CCopasiObject *, CFunctionParameter * > > &replacementMap, std::map< CCopasiObject *, 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
print(std::ostream *ostream) const	CCopasiObject	virtual
printDebug() const	CReaction
Reference enum value	CCopasiObject	protected
remove(CCopasiObject *pObject)	CCopasiContainer	virtual
removeDirectDependency(const CCopasiObject *pObject)	CCopasiObject
removeUnsupportedAnnotation(const std::string &name)	CAnnotation
replaceUnsupportedAnnotation(const std::string &name, const std::string &xml)	CAnnotation
Root enum value	CCopasiObject	protected
Separator enum value	CCopasiObject	protected
setDirectDependencies(const DataObjectSet &directDependencies)	CCopasiObject
setFast(const bool &fast)	CReaction
setFunction(const std::string &functionName)	CReaction
setFunction(CFunction *pFunction)	CReaction
setFunctionFromExpressionTree(const CExpression &tree, std::map< CCopasiObject *, SBase * > &copasi2sbmlmap, CFunctionDB *pFunctionDB)	CReaction
setMiriamAnnotation(const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId)	CAnnotation
setNotes(const std::string &notes)	CAnnotation
setObjectName(const std::string &name)	CCopasiObject
setObjectParent(const CCopasiContainer *pParent)	CReaction	virtual
setObjectValue(const C_FLOAT64 &value)	CCopasiObject
setObjectValue(const C_INT32 &value)	CCopasiObject
setObjectValue(const bool &value)	CCopasiObject
setParameterMapping(const size_t &index, const std::string &key)	CReaction
setParameterMapping(const std::string &parameterName, const std::string &key)	CReaction
setParameterMappingVector(const std::string &parameterName, const std::vector< std::string > &keys)	CReaction
setParameterValue(const std::string &parameterName, const C_FLOAT64 &value, const bool &updateStatus=true)	CReaction
setRefresh(CType *pType, void(CType::*method)(void))	CCopasiObject	inline
setRenameHandler(CRenameHandler *rh)	CCopasiObject	inlinestatic
setReversible(bool reversible)	CReaction
setSBMLId(const std::string &id)	CReaction
setScalingFactor()	CReaction	private
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
smpRenameHandler	CCopasiObject	protectedstatic
StaticString enum value	CCopasiObject	protected
UnsupportedAnnotation typedef	CAnnotation
UpdateSequence typedef	CObjectInterface
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
variable2object(CEvaluationNodeVariable *pVariableNode)	CReaction	private
variables2objects(CEvaluationNode *expression)	CReaction	private
Vector enum value	CCopasiObject	protected
~CAnnotation()	CAnnotation	virtual
~CCopasiContainer()	CCopasiContainer	virtual
~CCopasiObject()	CCopasiObject	virtual
~CObjectInterface()	CObjectInterface	inlinevirtual
~CReaction()	CReaction	virtual