Package org.biopax.paxtools.controller

Class Cloner

java.lang.Object

org.biopax.paxtools.controller.Cloner

All Implemented Interfaces:

Visitor

public class Cloner
extends Object
implements Visitor

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).

See Also:

• Visitor
• Traverser

Constructor Summary

Constructors

Constructor	Description
Cloner(EditorMap map, BioPAXFactory factory)

Method Summary

Modifier and Type	Method	Description
Model	clone(Set<BioPAXElement> toBeCloned)	For each element from the 'toBeCloned' list, it creates a copy in the new model, setting all the data properties; however, object property values that refer to BioPAX elements not in 'toBeCloned' list are ignored.
Model	clone(Model source, Set<BioPAXElement> toBeCloned)	Deprecated. use clone(Set) instead ('source' model was not used in previous versions)
void	visit(BioPAXElement domain, Object range, Model targetModel, 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

Constructor Details

Cloner

public Cloner(EditorMap map,
 BioPAXFactory factory)

Method Details

clone

public Model clone(Model source,
 Set<BioPAXElement> toBeCloned)

Deprecated.

use clone(Set) instead ('source' model was not used in previous versions)

For each element from the 'toBeCloned' list, it creates a copy in the new model, setting all the data properties; however, object property values that refer to BioPAX elements not in 'toBeCloned' list are ignored.

Parameters:

source - - actually, is never used... can be null all the same

toBeCloned - elements to clone

Returns:

a new model containing the cloned biopax objects

clone

public Model clone(Set<BioPAXElement> toBeCloned)

For each element from the 'toBeCloned' list, it creates a copy in the new model, setting all the data properties; however, object property values that refer to BioPAX elements not in 'toBeCloned' list are ignored. As the result, e.g., a Pathway can be incomplete, missing some or all its sub-processes, xrefs, pathway steps.

Parameters:

toBeCloned - elements to clone

Returns:

a new model containing the cloned biopax objects

visit

public void visit(BioPAXElement domain,
 Object range,
 Model targetModel,
 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

targetModel - model on which the visiting operation will be done

editor - editor