Package org.biopax.paxtools.controller
package org.biopax.paxtools.controller
This package contains various methods and algorithms for traversing and manipulating the model.
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ClassDescriptionThis is the base class for all property editors.This is an all-in-one Traverser/Visitor combination to use when deep recursive visiting is required.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).This class is used for getting a valid subgraph from a set of BioPAX elements.Encapsulation of scores of conversions, and related informationCreated by igor on 13/08/15.This class contains methods that eases to use editors for specific or a set of property.This is the base adapter for all editor maps.Provides an ENUM class compatible editor by extending thePropertyEditor.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.This class is a decorating property accessor that filters the seed arguments, only accepts if they are assignable to filter class.This class is a decorating property accessor that filters values with a given class.Tries to get preferred type IDs of an entity reference.This class is intended to merge and to integrate BioPAX Level2 models not necessarily from the same resource - if models allow such a thing.Utility class to merge multiple biopax models into one.A generic filter interface for Models.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.Provides an editor for all object value types, e.g.This class is a composite property accessor that allows users to chain multiple property accessors to define paths in the BioPAX object graph.Provides a primitive (int, float, double) class compatible editor by extending thePropertyEditor.Allows generic access to the properties or a path of properties from a bean.Adapter class for all property accessors.A generic interface for bidirectional property filterThis class contains methods for handling reused PEPs - a historically common problem in BioPAX L2 exports."Clones" a BioPAX element - using direct properties and dependent children only.Provides a simple editor map for a level with a given factory.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.StringPropertyEditor<D extends BioPAXElement>Provides an String class compatible editor by extending thePropertyEditor.This class is a transitive decorator for PropertyAccessors.This is a utility class for traversing over the dependent objects of a biopax element, based on property editorsA bi-directional BioPAX properties traverser.In OWL a single property can have multiple domains.Basic visitor interface for classes using Traverser.