COPASI API  4.40.278
CReaction Member List

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

__SIZE enum valueCDataObject
add(CDataObject *pObject, const bool &adopt=true)CDataContainervirtual
addIssue(const CIssue &issue)CDataObject
addMatrixReference(const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)CDataContainerprotected
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)CDataContainerprotected
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)CDataContainerprotected
allocateMiriamInfo(CDataContainer *pParent)CAnnotationstatic
appendDeletedDependentData(CUndoData &undoData) constCDataContainervirtual
applyData(const CData &data, CUndoData::CChangeSet &changes)CReactionvirtual
Array enum valueCDataObject
calculate()CReactionprivate
calculateValue() overrideCDataObjectvirtual
CAnnotation()CAnnotation
CAnnotation(const CAnnotation &src)CAnnotation
castObject(CDataObject *pObject)CAnnotationstatic
castObject(const CDataObject *pObject)CAnnotationstatic
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
CObjectInterface()CObjectInterface
CObjectInterface(const CObjectInterface &src)CObjectInterface
compile()CReaction
compileFunctionParameters(std::set< const CDataObject * > &Dependencies)CReactionprivate
Container enum valueCDataObject
Container2InfoCAnnotationprivatestatic
ContainerList typedefCObjectInterface
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) constCReactionvirtual
CUndoObjectInterface()CUndoObjectInterface
CUndoObjectInterface(const CUndoObjectInterface &src)CUndoObjectInterface
DataModel enum valueCDataObject
DataObject(const CObjectInterface *pInterface)CObjectInterfacestatic
DataObjectSet typedefCDataObject
destruct() overrideCDataObjectvirtual
DisplayName enum valueCDataObject
EmptyListCDataContainerstatic
escapeId(const std::string &id)CReactionprivate
Flag enum nameCDataObject
freeMiriamInfo(CDataContainer *pParent)CAnnotationstatic
fromData(const CData &data, CUndoObjectInterface *pParent)CReactionstatic
generateUuid()CUndoObjectInterface
getCallParameters() constCReaction
getChemEq() constCReaction
getChemEq()CReaction
getChildObjectUnits(const CDataObject *pObject) constCReactionvirtual
getCN() const overrideCDataObjectvirtual
getCompartmentNumber() constCReaction
getDataObject() const overrideCDataObjectvirtual
getDefaultNoiseExpression() constCReaction
getDescendants(CDataObject::DataObjectSet &descendants, const bool &recursive=false) constCDataContainer
getEffectiveKineticLawUnitType() constCReaction
getExpressionTree()CReaction
getFirstCModelOrDefault(std::map< const CDataObject *, SBase * > &copasi2sbmlmap)CReactionprivate
getFlux() constCReaction
getFluxReference()CReaction
getFluxReference() constCReaction
getFunction() constCReaction
getFunctionParameters() constCReaction
getIndex(const CDataObject *pObject) constCDataContainervirtual
getKey() constCReactionvirtual
getKineticLawUnit() constCReaction
getKineticLawUnitType() constCReaction
getLargestCompartment() constCReaction
getMap() constCReaction
getMiriamAnnotation() constCAnnotation
getNoiseExpression() constCReaction
getNoiseExpressionPtr() constCReaction
getNoiseExpressionPtr()CReaction
getNoiseReference() constCReaction
getNotes() constCAnnotation
getObject(const CCommonName &cn) constCReactionvirtual
getObjectAncestor(const std::string &type) constCDataObject
getObjectDataModel() constCDataObject
getObjectDisplayName() constCReactionvirtual
GetObjectFromCN(const ContainerList &listOfContainer, const CCommonName &objName)CObjectInterfacestatic
getObjectFromCN(const CCommonName &cn) constCDataObject
getObjectName() constCDataObject
getObjectParent() constCDataObject
getObjects() constCDataContainervirtual
getObjects()CDataContainervirtual
getObjectType() constCDataObject
getParameterCNs(const size_t &index) constCReaction
getParameterCNs(const std::string &name) constCReaction
getParameterCNs() constCReaction
getParameterIndex(const std::string &parameterName, const CFunctionParameter **ppFunctionParameter=NULL) constCReaction
getParameterObjects(const size_t &index) constCReaction
getParameterObjects(const std::string &name) constCReaction
getParameterObjects() constCReaction
getParameters() constCReaction
getParameters()CReaction
getParameterValue(const std::string &parameterName) constCReaction
getParticleFlux() constCReaction
getParticleFluxReference()CReaction
getParticleFluxReference() constCReaction
getParticleNoiseReference() constCReaction
getPrerequisites() const overrideCDataObjectvirtual
getPropensityReference()CReaction
getPropensityReference() constCReaction
getReactionScheme() constCReaction
getSBMLId() constCReaction
getScalingCompartment() constCReaction
getScalingCompartmentCN() constCReaction
getUnits() const overrideCDataContainervirtual
getUnsupportedAnnotations()CAnnotation
getUnsupportedAnnotations() constCAnnotation
getUuid() constCUndoObjectInterface
getValidity() const overrideCDataObjectvirtual
getValueObject() const overrideCDataContainervirtual
getValuePointer() const overrideCDataObjectvirtual
Gui enum valueCDataObject
hasFlag(const Flag &flag) constCDataObject
hasNoise() constCReaction
initializeParameterMapping()CReactionprivate
initializeParameters()CReactionprivate
initMiriamAnnotation(const std::string &newId)CAnnotation
initObjects()CReactionprivate
insert(const CData &data) overrideCDataContainervirtual
isFast() constCReaction
isLocalParameter(const size_t &index) constCReaction
isLocalParameter(const std::string &parameterName) constCReaction
isPrerequisiteForContext(const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const overrideCDataObjectvirtual
isReversible() constCReaction
isValidXML(const std::string &xml)CAnnotationprivatestatic
KineticLawUnit enum nameCReaction
KineticLawUnitTypeNameCReactionstatic
load(CReadConfig &configbuffer)CReaction
loadOld(CReadConfig &configbuffer)CReactionprivate
loadOneRole(CReadConfig &configbuffer, CFunctionParameter::Role role, C_INT32 n, const std::string &prefix)CReactionprivate
mAggregateValidityCDataObjectprivate
Matrix enum valueCDataObject
mChemEqCReactionprivate
mFastCReactionprivate
mFluxCReactionprivate
mHasNoiseCReactionprivate
mKeyCAnnotationprotected
mKineticLawUnitCReactionprivate
mMapCReactionprivate
mMiriamAnnotationCAnnotationprivate
mNoiseCReactionprivate
mNotesCAnnotationprivate
mObjectDisplayNameCDataObjectmutableprivate
mObjectFlagCDataObjectprivate
mObjectNameCDataObjectprivate
mObjectsCDataContainerprotected
mObjectTypeCDataObjectprivate
ModelEntity enum valueCDataObject
mParameterIndexToCNsCReactionprivate
mParameterIndexToObjectsCReactionprivate
mParameterNameToIndexCReactionprivate
mParametersCReactionprivate
mParticleFluxCReactionprivate
mParticleNoiseCReactionprivate
mpFluxReferenceCReactionprivate
mpFunctionCReactionprivate
mpNoiseExpressionCReactionprivate
mpNoiseReferenceCReactionprivate
mpObjectDisplayNameCDataObjectmutableprivate
mpObjectNameCDataObjectmutableprivate
mpObjectParentCDataObjectprivate
mpParticleFluxReferenceCReactionprivate
mpParticleNoiseReferenceCReactionprivate
mpPropensityReferenceCReactionprivate
mPrerequisitsCDataObjectprotected
mPropensityCReactionprivate
mpScalingCompartmentCReactionprivate
mpUuidCUndoObjectInterfaceprivate
mReferencedValiditiesCDataObjectprivate
mReferencesCDataObjectprotected
mSBMLIdCReactionmutableprivate
mScalingCompartmentCNCReactionprivate
mUnsupportedAnnotationsCAnnotationprivate
mUuidLockedCUndoObjectInterfaceprivate
mValidityCObjectInterfacemutableprotected
mXMLIdCAnnotationprivate
NameVector enum valueCDataObject
NonUniqueName enum valueCDataObject
object2variable(const CEvaluationNodeObject *objectNode, std::map< std::string, std::pair< CDataObject *, CFunctionParameter * > > &replacementMap, std::map< const CDataObject *, SBase * > &copasi2sbmlmap)CReactionprivate
objectMap typedefCDataContainer
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)CReactionprivate
ObjectSet typedefCObjectInterface
operator<<(std::ostream &os, const CReaction &d)CReactionfriend
operator=(const CReaction &)CReactionprivate
operator==(const CAnnotation &rhs) constCAnnotation
prerequisitsContains(const DataObjectSet &objects) constCDataObject
print(std::ostream *ostream) const overrideCDataObjectvirtual
printDebug() constCReaction
Reference enum valueCDataObject
refreshAggregateValidity()CDataObjectprivate
remove(CDataObject *pObject)CDataContainervirtual
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)CReactionprivate
Root enum valueCDataObject
sanitizeObjectName(std::string &name)CDataObjectstatic
sanitizeSBMLId(const std::string &id)CReactionprivatestatic
Separator enum valueCDataObject
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)CReactionvirtual
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) constCReaction
setScalingCompartment(const CCompartment *pCompartment)CReaction
setScalingCompartmentCN(const std::string &compartmentCN)CReaction
setScalingFactor()CReactionprivate
setUuid(const xg::Guid &uuid)CUndoObjectInterface
setUuid(const std::string &uuid)CUndoObjectInterface
StaticString enum valueCDataObject
toData() constCReactionvirtual
UnsupportedAnnotation typedefCAnnotation
updateIndex(const size_t &index, const CUndoObjectInterface *pUndoObject)CUndoObjectInterfacevirtual
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
variable2object(CEvaluationNodeVariable *pVariableNode)CReactionprivate
variables2objects(CEvaluationNode *expression)CReactionprivate
Vector enum valueCDataObject
~CAnnotation()CAnnotationvirtual
~CDataContainer()CDataContainervirtual
~CDataObject()CDataObjectvirtual
~CObjectInterface()CObjectInterfacevirtual
~CReaction()CReactionvirtual
~CUndoObjectInterface()CUndoObjectInterfacevirtual