Package org.biopax.paxtools.controller

Interface Summary

EditorMap	This class contains methods that eases to use editors for specific or a set of property.
ModelFilter
PropertyAccessor<D extends BioPAXElement,R>	Allows generic access to the properties or a path of properties from a bean.
PropertyFilterBilinked
Visitor	Basic visitor interface for classes using Traverser.

Class Summary

AbstractTraverser	This is a convenience all-in-one Traverser/Visitor that keeps track in the model and prevents infinite loops.
Cloner	Specifically "Clones" the BioPAX elements set (traverses to obtain dependent elements), puts them to the new model using the visitor and traverser framework; ignores elements that are not in the source list (compare to Fetcher)
Completer	This class is used for getting a valid subgraph from a set of BioPAX elements.
ConversionScore	Encapsulation of scores of conversions, and related information
DecoratingPropertyAccessor<D extends BioPAXElement,R>
EditorMapAdapter	This is the base adapter for all editor maps.
EnumeratedPropertyEditor<D extends BioPAXElement,R extends Enum>	Provides an ENUM class compatible editor by extending the PropertyEditor.
FeatureUtils	This class provides operations for comparing features of physical entities.
Fetcher	This class is used to fetch an element (traverse it to obtain its dependent elements) and to add this element into a model using the visitor and traverse functions.
FilteredPropertyAccessor<D extends BioPAXElement,R,F extends R>
Integrator	This class is intended to merge and to integrate biopax models not necessarily from the same resource - if models allow such a thing.
Merger	Utility class to merge multiple biopax models into one.
ModelUtils	An advanced BioPAX utility class that implements several useful algorithms to extract root or child BioPAX elements, remove dangling, replace elements or identifiers, etc.
ObjectPropertyEditor<D extends BioPAXElement,R extends BioPAXElement>	Provides an editor compatible with all value types other Primitive, ENUM, and String by extending the PropertyEditor.
PathAccessor	This class accepts an xPath like syntax to access a property path from a bean.
PrimitivePropertyEditor<D extends BioPAXElement,R>	Provides a primitive (int, float, double) class compatible editor by extending the PropertyEditor.
PropertyEditor<D extends BioPAXElement,R>	This is the base class for all property editors.
PropertyReasoner	A tool to set or infer a particular BioPAX property for an object and all its children.
ReusedPEPHelper	This class contains methods for handling reused PEPs.
ShallowCopy	Specifically "Clones" the BioPAX elements set (traverses to obtain dependent elements), puts them to the new model using the visitor and traverser framework; ignores elements that are not in the source list (compare to Fetcher)
SimpleMerger	This is a "simple" BioPAX merger, a utility class to merge 'source' BioPAX models or a set of elements into the target model, using the RDFId (URI) identity only.
SimplePropertyAccessor<D extends BioPAXElement,R>
StringPropertyEditor<D extends BioPAXElement>	Provides an String class compatible editor by extending the PropertyEditor.
TransitivePropertyAccessor<D extends BioPAXElement,R>	This class is a transitive decorator for PropertyAccessors
Traverser	This is a utility class for traversing over the dependent objects of a biopax element, based on property editors
TraverserBilinked
UnionPropertyAccessor<D extends BioPAXElement>

Enum Summary

ModelUtils.RelationshipType	Controlled vocabulary terms for the RelationshipType CV to be added with auto-generated/inferred comments and/or relationship xrefs.
SimpleEditorMap	Provides a simple editor map for a level with a given factory.