org.biopax.paxtools.controller

Class AbstractTraverser

java.lang.Object

org.biopax.paxtools.controller.Traverser

org.biopax.paxtools.controller.AbstractTraverser

All Implemented Interfaces:

Visitor

Direct Known Subclasses:

LevelUpgrader

public abstract class AbstractTraverser
extends Traverser
implements Visitor

This is an all-in-one Traverser/Visitor combination to use when deep recursive visiting is required. Unlike Traverser, it keeps track of where current object is in the model and whether it's been already visited, which helps prevent infinite loops. Like it's for the Traverser, there is no any particular order in which it processes properties.

Author:

rodch

See Also:

Fetcher, Traverser, Visitor

Field Summary

Fields

Modifier and Type	Field and Description
protected Set<BioPAXElement>	visited

Fields inherited from class org.biopax.paxtools.controller.Traverser

editorMap, filters, visitor

Constructor Summary

Constructors

Constructor and Description
AbstractTraverser(EditorMap editorMap, Filter<PropertyEditor>... filters)

Method Summary

Modifier and Type	Method and Description
void	reset() Clears the internal set of traversed biopax objects.
<D extends BioPAXElement> void	traverse(D element, Model model) Traverse and visit Visitor all properties of the element.
void	visit(BioPAXElement domain, Object range, Model model, PropertyEditor<?,?> editor) Calls the protected abstract method visit that is to be implemented in subclasses of this abstract class.
protected abstract void	visit(Object range, BioPAXElement domain, Model model, PropertyEditor<?,?> editor) This is to implement a real action here: do something, return or even to continue (traverse) into the child (range) element's properties if it's a BioPAX object.

Methods inherited from class org.biopax.paxtools.controller.Traverser

filter, getVisitor, setVisitor, traverseElements

Methods inherited from class java.lang.Object

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

Field Detail

visited

protected final Set<BioPAXElement> visited

Constructor Detail

AbstractTraverser

public AbstractTraverser(EditorMap editorMap,
                         Filter<PropertyEditor>... filters)

Method Detail

visit

protected abstract void visit(Object range,
                              BioPAXElement domain,
                              Model model,
                              PropertyEditor<?,?> editor)

This is to implement a real action here: do something, return or even to continue (traverse) into the child (range) element's properties if it's a BioPAX object.

Parameters:

range - property value

domain - parent/owner BioPAX element

model - the BioPAX model of interest

editor - the property editor

visit

public void visit(BioPAXElement domain,
                  Object range,
                  Model model,
                  PropertyEditor<?,?> editor)

Calls the protected abstract method visit that is to be implemented in subclasses of this abstract class.

Specified by:

visit in interface Visitor

Parameters:

domain - BioPAX Element

range - property value (can be BioPAX element, primitive, enum, string)

model - the BioPAX model of interest

editor - parent's property PropertyEditor

traverse

public <D extends BioPAXElement> void traverse(D element,
                                               Model model)

Description copied from class: Traverser

Traverse and visit Visitor all properties of the element. This method does not traverse iteratively to the values.

Overrides:

traverse in class Traverser

Type Parameters:

D - actual BioPAX type which properties and inherited properties will be used

Parameters:

element - BioPAX element to be traversed

model - to be traversed, but not necessarily (depends on the Visitor implementation).

reset

public void reset()

Clears the internal set of traversed biopax objects. Apply if you're re-using the same traverser instance but start over from a different root biopax element.