org.biopax.paxtools.controller

Class ShallowCopy

java.lang.Object

org.biopax.paxtools.controller.ShallowCopy

All Implemented Interfaces:

Visitor

public class ShallowCopy
extends Object
implements Visitor

"Clones" a BioPAX element - using direct properties and dependent children only. (shallow copy). Compare to Fetcher

See Also:

Visitor, Traverser

Constructor Summary

Constructors

Constructor and Description
ShallowCopy() Empty constructos that defaults to BioPAX L3.
ShallowCopy(BioPAXLevel level) BioPAXLevel based constructor
ShallowCopy(EditorMap map) Deprecated. use Level based constructor instead.

Method Summary

Modifier and Type	Method and Description
<T extends BioPAXElement> T	copy(Model model, T source, String newID) Creates a copy of the BioPAX object with all its properties are the same, and also adds it to a model.
<T extends BioPAXElement> T	copy(T source, String newID) Returns a copy of the BioPAX element (with all the property values are same)
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

Constructor Detail

ShallowCopy

public ShallowCopy(EditorMap map)

Deprecated. use Level based constructor instead.

Editor map based constructor.

Parameters:

map - that determines the BioPAX Level

ShallowCopy

public ShallowCopy(BioPAXLevel level)

BioPAXLevel based constructor

Parameters:

level - used for the cloning operation.

ShallowCopy

public ShallowCopy()

Empty constructos that defaults to BioPAX L3.

Method Detail

copy

public <T extends BioPAXElement> T copy(Model model,
                                        T source,
                                        String newID)

Creates a copy of the BioPAX object with all its properties are the same, and also adds it to a model.

Type Parameters:

T - BioPAX type/class of the source and copy elements

Parameters:

model - target biopax model

source - a biopax object to copy

newID - new (copy) biopax object's URI

Returns:

copy of the source biopax element

copy

public <T extends BioPAXElement> T copy(T source,
                                        String newID)

Returns a copy of the BioPAX element (with all the property values are same)

Type Parameters:

T - biopax type

Parameters:

source - biopax element to copy

newID - copy biopax element's absolute URI

Returns:

a copy of the source biopax element

visit

public 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. 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