org.biopax.paxtools.controller

Class Completer

java.lang.Object

org.biopax.paxtools.controller.Completer

All Implemented Interfaces:

Visitor

public class Completer
extends 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

Fields

Modifier and Type	Field and Description
protected TraverserBilinked	traverser

Constructor Summary

Constructors

Constructor and Description
Completer(EditorMap map)

Method Summary

Modifier and Type	Method and Description
Set<BioPAXElement>	complete(Collection<BioPAXElement> elements)
Set<BioPAXElement>	complete(Collection<BioPAXElement> elements, Model model) Deprecated. use complete(Collection) instead (- model is never explicitly used there)
boolean	isSkipSubPathways()
void	setSkipSubPathways(boolean skipSubPathways) Use this property to optionally skip (if true) traversing into sub-pathways; i.e., when the value of BioPAX property 'pathwayComponent' or 'controlled' is a pathway.
void	visit(BioPAXElement domain, 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 Set<BioPAXElement> complete(Collection<BioPAXElement> elements,
                                   Model model)

Deprecated. use complete(Collection) instead (- model is never explicitly used there)

Parameters:

elements -

model -

Returns:

complete

public Set<BioPAXElement> complete(Collection<BioPAXElement> elements)

visit

public void visit(BioPAXElement domain,
                  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

setSkipSubPathways

public void setSkipSubPathways(boolean skipSubPathways)

Use this property to optionally skip (if true) traversing into sub-pathways; i.e., when the value of BioPAX property 'pathwayComponent' or 'controlled' is a pathway.

Parameters:

skipSubPathways - true/false (default is 'true' - do skip)

isSkipSubPathways

public boolean isSkipSubPathways()