Package org.biopax.paxtools.controller

This package contains various methods and algorithms for traversing and manipulating the model.

See: Description

Interface Summary

Interface	Description
DataPropertyEditor<D extends BioPAXElement,R>	Created by igor on 13/08/15.
EditorMap	This class contains methods that eases to use editors for specific or a set of property.
ModelFilter	A generic filter interface for Models.
PropertyAccessor<D extends BioPAXElement,R>	Allows generic access to the properties or a path of properties from a bean.
PropertyEditor<D extends BioPAXElement,R>
PropertyFilterBilinked	A generic interface for bidirectional property filter
Visitor	Basic visitor interface for classes using Traverser.

Class Summary

Class	Description
AbstractPropertyEditor<D extends BioPAXElement,R>	This is the base class for all property editors.
AbstractTraverser	This is an all-in-one Traverser/Visitor combination to use when deep recursive visiting is required.
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>
EditorMapImpl	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.
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>	This class is a decorating property accessor that filters values with a given class.
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	Several useful algorithms and examples, e.g., to extract root or child BioPAX L3 elements, remove dangling, replace elements or URIs, fix/infer property values, etc.
ObjectPropertyEditor<D extends BioPAXElement,R extends BioPAXElement>	Provides an editor for all object value types, e.g.
PathAccessor	This class is a composite property accessor that allows users to chain multiple property accessors to define paths in the BioPAX object graph.
PrimitivePropertyEditor<D extends BioPAXElement,R>	Provides a primitive (int, float, double) class compatible editor by extending the PropertyEditor.
PropertyAccessorAdapter<D extends BioPAXElement,R>	Adapter class for all property accessors.
ReusedPEPHelper	This class contains methods for handling reused PEPs - a historically common problem in BioPAX L2 exports.
ShallowCopy	"Clones" a BioPAX element - using direct properties and dependent children only.
SimpleMerger	A "simple" BioPAX merger, a utility class to merge 'source' BioPAX models or a set of elements into the target model, using (URI) identity only.
SimplePropertyAccessor<D extends BioPAXElement,R>
StringPropertyEditor<D extends BioPAXElement>	Provides an String class compatible editor by extending the PropertyEditor.
TransitivePropertyAccessor<R extends BioPAXElement,D extends 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	A bi-directional BioPAX properties traverser.
UnionPropertyAccessor<D extends BioPAXElement,R>	In OWL a single property can have multiple domains.

Enum Summary

Enum	Description
SimpleEditorMap	Provides a simple editor map for a level with a given factory.

Package org.biopax.paxtools.controller Description

This package contains various methods and algorithms for traversing and manipulating the model.