Package org.pathvisio.libgpml.model

Class GPML2013aReader.PublicationXref

java.lang.Object

org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref

Enclosing class:

GPML2013aReader

public class GPML2013aReader.PublicationXref
extends java.lang.Object

Local class to help with reading gpml:Biopax:bp:PublicationXref.

Author:

finterly

Field Summary

Fields

Modifier and Type	Field	Description
(package private) org.jdom2.Element	element
(package private) java.lang.String	elementId
(package private) boolean	hasRef

Constructor Summary

Constructors

Constructor	Description
PublicationXref(org.jdom2.Element element, java.lang.String elementId)	Instantiates a PublicationXref object.

Method Summary

Modifier and Type	Method	Description
org.jdom2.Element	getElement()	Returns the jdom gpml:Biopax:PublicationXref element.
java.lang.String	getElementId()	Returns the assigned unique elementId for this PublicationXref.
boolean	getHasRef()	Returns true if there is at least one gpml:CommentGroup:BiopaxRef which refers to this gpml:Biopax:PublicationXref, false otherwise.
void	setHasRef(boolean hasRef)	Sets hasRef to true if at least one gpml:CommentGroup:BiopaxRef which refers to this gpml:Biopax:PublicationXref, false otherwise.

Methods inherited from class java.lang.Object

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

Field Details

element

org.jdom2.Element element

elementId

java.lang.String elementId

hasRef

boolean hasRef

Constructor Details

PublicationXref

public PublicationXref(org.jdom2.Element element,
java.lang.String elementId)

Instantiates a PublicationXref object. Stores the jdom gpml:Biopax:PublicationXref and the assigned elementId in GPML2013aReader.readPublicationXrefMap(org.jdom2.Element, java.util.Set<java.lang.String>, java.util.Map<java.lang.String, org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref>).

Parameters:

element - the jdom element.

elementId - the unique elementId, may or may not be the same string as the original biopax rdf:id.

Method Details

getElement

public org.jdom2.Element getElement()

Returns the jdom gpml:Biopax:PublicationXref element.

Returns:

element the jdom PublicationXref element.

getElementId

public java.lang.String getElementId()

Returns the assigned unique elementId for this PublicationXref.

Returns:

elementId;

getHasRef

public boolean getHasRef()

Returns true if there is at least one gpml:CommentGroup:BiopaxRef which refers to this gpml:Biopax:PublicationXref, false otherwise.

Returns:

true if referenced, false otherwise.

setHasRef

public void setHasRef(boolean hasRef)

Sets hasRef to true if at least one gpml:CommentGroup:BiopaxRef which refers to this gpml:Biopax:PublicationXref, false otherwise. Called in GPML2013aReader.readPublicationXrefs(org.pathvisio.libgpml.model.PathwayElement,org.jdom2.Element,java.util.Map<java.lang.String,org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref>).

Parameters:

hasRef - the boolean for whether referenced.