Uses of Package
org.biopax.paxtools.controller

Packages that use org.biopax.paxtools.controller

Package	Description
org.biopax.paxtools.command	This package contains classes for implementing undoable editing the model.
org.biopax.paxtools.controller	This package contains various methods and algorithms for traversing and manipulating the model.
org.biopax.paxtools.converter	This package contains a tools for upgrading BioPAX L1 and L2 to L3.
org.biopax.paxtools.examples	This package contains several examples that uses Paxtools to demonstrate basic functionality.
org.biopax.paxtools.impl	This package contains the default BioPAX Model implementations.
org.biopax.paxtools.io	This package contains classes that handle IO operations including reading and writing BioPAX from files and streams..
org.biopax.paxtools.io.jena	This package contains a Jena bases reader/writer for reading BioPAX files.
org.biopax.paxtools.pattern.constraint	Package for constraints.
org.biopax.paxtools.pattern.util	Package for several utility classes.
org.biopax.paxtools.query.wrapperL3	This package contains TODO annotate!

Classes in org.biopax.paxtools.controller used by org.biopax.paxtools.command

Class and Description
PropertyEditor

Classes in org.biopax.paxtools.controller used by org.biopax.paxtools.controller

Class and Description
AbstractPropertyEditor This is the base class for all property editors.
ConversionScore Encapsulation of scores of conversions, and related information
DataPropertyEditor Created by igor on 13/08/15.
DecoratingPropertyAccessor
EditorMap This class contains methods that eases to use editors for specific or a set of property.
ObjectPropertyEditor Provides an editor for all object value types, e.g.
PropertyAccessor Allows generic access to the properties or a path of properties from a bean.
PropertyAccessorAdapter Adapter class for all property accessors.
PropertyEditor
PropertyFilterBilinked A generic interface for bidirectional property filter
SimpleEditorMap Provides a simple editor map for a level with a given factory.
SimplePropertyAccessor
TransitivePropertyAccessor 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.
Visitor Basic visitor interface for classes using Traverser.

Classes in org.biopax.paxtools.controller used by org.biopax.paxtools.converter

Class and Description
AbstractTraverser This is an all-in-one Traverser/Visitor combination to use when deep recursive visiting is required.
ModelFilter A generic filter interface for Models.
PropertyEditor
Traverser This is a utility class for traversing over the dependent objects of a biopax element, based on property editors
Visitor Basic visitor interface for classes using Traverser.

Classes in org.biopax.paxtools.controller used by org.biopax.paxtools.examples

Class and Description
EditorMap This class contains methods that eases to use editors for specific or a set of property.
PropertyEditor
Visitor Basic visitor interface for classes using Traverser.

Classes in org.biopax.paxtools.controller used by org.biopax.paxtools.impl

Class and Description
ObjectPropertyEditor Provides an editor for all object value types, e.g.

Classes in org.biopax.paxtools.controller used by org.biopax.paxtools.io

Class and Description
EditorMap This class contains methods that eases to use editors for specific or a set of property.
PropertyEditor
ReusedPEPHelper This class contains methods for handling reused PEPs - a historically common problem in BioPAX L2 exports.
StringPropertyEditor Provides an String class compatible editor by extending the PropertyEditor.

Classes in org.biopax.paxtools.controller used by org.biopax.paxtools.io.jena

Class and Description
EditorMap This class contains methods that eases to use editors for specific or a set of property.
EditorMapImpl This is the base adapter for all editor maps.
PropertyEditor

Classes in org.biopax.paxtools.controller used by org.biopax.paxtools.pattern.constraint

Class and Description
PathAccessor This class is a composite property accessor that allows users to chain multiple property accessors to define paths in the BioPAX object graph.

Classes in org.biopax.paxtools.controller used by org.biopax.paxtools.pattern.util

Class and Description
PathAccessor This class is a composite property accessor that allows users to chain multiple property accessors to define paths in the BioPAX object graph.

Classes in org.biopax.paxtools.controller used by org.biopax.paxtools.query.wrapperL3

Class and Description
PathAccessor This class is a composite property accessor that allows users to chain multiple property accessors to define paths in the BioPAX object graph.