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PropertyReasoner.domains) and possible,
it sets the PropertyReasoner.propertyName values to "unknown".
Fetcher)Pathway and PhysicalEntity.PhysicalEntity pools are physically
transformed and become a member of one or more other PhysicalEntity pools.BioPAXIOHandler#convertToOWL(org.biopax.paxtools
.model.Model, Object), but
extracts a sub-model, converts it into BioPAX (OWL) format,
and writes it into the outputStream.
PropertyEditor.Entity if possible.
PropertyEditor.addMethod.
Fetcher) and adds them to a
new model.
Fetcher), although some of them
might have the same ID (are "clones" - for a purpose of due to a mistake)
Control interactions that this entity controls.
EntityReference.getEntityFeature()
SimplePhysicalEntity.getEntityReference()
PhysicalEntity.getFeature()
Contents of this set is generated automatically and should not be modified.
SimplePropertyAccessor.getMethod.
EntityReference.getMemberEntityReference()
EntityFeature.getMemberFeature()
EntityReferences of the member simple physical entities.
PhysicalEntity.getNotFeature()
Contents of this set is generated automatically and should not be modified.
Conversion.getLeft()) and right(Conversion.getRight()) participants.
PropertyEditor.removeMethod.
PropertyEditor.setMethod.
Stoichiometry.getPhysicalEntity() in
the context of the owner interaction or complex.
#getMethod.
SimplePropertyAccessor.getMethod.
PropertyReasoner.domains) and allowed,
it adds or sets the PropertyReasoner.propertyName from parents's
(if the top-most, a parent element that has this propertyName,
does not have any valueStack, then given valueStack will be set, and
children may inherit it)
PropertyReasoner.domains) and allowed,
it adds or sets the PropertyReasoner.propertyName from parents's
(if they have any valueStack)
BioPAXElement
or is an empty set or set of "unknown" values.
SimpleMerger.merge(Model, Model...))
NOTE: some applications, such as those dealing with persistence/transactions
or advanced BioPAX alignment/comparison algorithms (like the Patch),
may have to implement and use a more specific method instead.
Model.PropertyEditor.PropertyEditor.PropertyReasoner.traverse(BioPAXElement, Model) to call
PropertyReasoner.visit(Object, BioPAXElement, Model, PropertyEditor)
for each *object* property, except for 'nextStep'.
PropertyEditor.removeMethod.
PropertyEditor.removeValueFromBean(Object, BioPAXElement)
for each value in the set.
Model.contains(BioPAXElement) returns False)
- updates object properties (should refer to model's elements)
- repairs the internal map so that a object returned
by ModelImpl.getByID(String) does actually have this ID
PropertyReasoner.domains) and allowed (by BioPAX),
it forces the given PropertyReasoner.propertyName valueStack replace existing ones.
PropertyReasoner.propertyName valueStack of a BioPAX element
and its children.
PropertyReasoner.run(BioPAXElement, Object) method, although the
PropertyReasoner.propertyName property valueStack of every element (where apply)
can be still considered for its children (of the specified type).
PropertyReasoner.override mode.
Stoichiometry.getPhysicalEntity() in the context of the owner interaction or complex.
PropertyEditor.setMethod if
value is not null.
Fetcher)PropertyEditor.PropertyReasoner.propertyName we are interested in, then proceeds-
as the basic Traverser.traverse(BioPAXElement, Model)
would normally do (i.e., - delivering to the method
PropertyReasoner.visit(Object, BioPAXElement, Model, PropertyEditor)
for all properties without any predefined order).
Visitor all properties of the element.
PropertyReasoner.traverse(BioPAXElement, Model)
and goes deeper when the propertyName's range/valueStack is a BioPAX object.
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