org.biopax.paxtools.controller
Class Completer

java.lang.Object
  org.biopax.paxtools.controller.Completer

All Implemented Interfaces:

Visitor

public class Completer
extends java.lang.Object
implements Visitor

This class is used for getting a valid subgraph from a set of BioPAX elements. For instance, if a BioPAX graph contains a complex with some members, but the subgraph contains the same complex without the members, then it is not valid. Similarly, an interaction is only valid with its participants; however, including its controls is optional.

Author:

Ozgun Babur

Field Summary

protected TraverserBilinked

traverser

Constructor Summary

Completer(EditorMap map)

Method Summary

java.util.Set<BioPAXElement>	complete(java.util.Collection<BioPAXElement> elements, Model model)
void	visit(BioPAXElement domain, java.lang.Object range, Model model, PropertyEditor editor) An implementation of this method should perform a BioPAX element and editor dependent operation on the model.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

traverser

protected TraverserBilinked traverser

Constructor Detail

Completer

public Completer(EditorMap map)

Method Detail

complete

public java.util.Set<BioPAXElement> complete(java.util.Collection<BioPAXElement> elements,
                                             Model model)

visit

public void visit(BioPAXElement domain,
                  java.lang.Object range,
                  Model model,
                  PropertyEditor editor)

Description copied from interface: Visitor

An implementation of this method should perform a BioPAX element and editor dependent operation on the model. Examples of uses of this method include adding a BioPAX element--with all its dependent elements that can be reached via the editor--into the model, or updating an element that is equivalent to the given BioPAX element using the latter's/former's values.

Specified by:

visit in interface Visitor

Parameters:

domain - BioPAXElement which is the domain of this property

range - Object which is the range of this property

model - model on which the visiting operation will be done

editor - editor