Uses of Class
org.pathvisio.libgpml.model.GPML2013aReader.PublicationXref

Packages that use GPML2013aReader.PublicationXref

Package	Description
org.pathvisio.libgpml.model	Classes representing the pathway "model".

Uses of GPML2013aReader.PublicationXref in org.pathvisio.libgpml.model

Method parameters in org.pathvisio.libgpml.model with type arguments of type GPML2013aReader.PublicationXref

Modifier and Type	Method	Description
protected void	GPML2013aReader.readCommentGroup(PathwayElement pathwayElement, org.jdom2.Element e, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads comment group (comment, biopaxref/citationRef, dynamic property) for pathway element from jdom element.
protected void	GPML2013aReader.readDataNodes(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads data node DataNode information for pathway model from root element.
protected void	GPML2013aReader.readGraphicalLines(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads graphical line GraphicalLine information for pathway model from root element.
protected void	GPML2013aReader.readGroups(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup, java.util.Map<java.lang.String,Group> graphIdToGroup)	Reads group Group information for pathway model from root element.
protected void	GPML2013aReader.readInteractions(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup, java.util.Map<org.jdom2.Element,LineElement.LinePoint> elementToPoint)	Reads interaction Interaction information for pathway model from root element.
protected void	GPML2013aReader.readLabels(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads label Label information for pathway model from root element.
protected void	GPML2013aReader.readLineElement(LineElement lineElement, org.jdom2.Element ln, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads line element LineElement information for interaction or graphical line from jdom element.
protected void	GPML2013aReader.readPublicationXrefMap(org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads gpml:Biopax:bp:PublicationXref and maps "id" to GPML2013aReader.PublicationXref in idToPublicationXref.
protected void	GPML2013aReader.readPublicationXrefs(PathwayElement pathwayElement, org.jdom2.Element e, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads gpml:Biopax:bp:PublicationXref and BiopaxRef information for pathway element from jdom element.
protected void	GPML2013aReader.readShapedElement(ShapedElement shapedElement, org.jdom2.Element se, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads shaped pathway element ShapedElement information: graphics and comment group (comments, biopaxRefs (equivalent to citationRefs), and dynamic properties).
protected void	GPML2013aReader.readShapes(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref, java.util.Map<java.lang.String,Group> groupIdToGroup)	Reads shape Shape information for pathway model from root element.
protected void	GPML2013aReader.readStates(PathwayModel pathwayModel, org.jdom2.Element root, java.util.Set<java.lang.String> elementIdSet, java.util.Map<java.lang.String,GPML2013aReader.PublicationXref> idToPublicationXref)	Reads state DataNode.State information for pathway model from root element.