Uses of Class
org.pathvisio.libgpml.model.Citation

Packages that use Citation

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

Uses of Citation in org.pathvisio.libgpml.model

Fields in org.pathvisio.libgpml.model declared as Citation

Modifier and Type	Field	Description
private Citation	TestCitation.a
private Citation	TestCitation.a2
private Citation	TestCopy.c
private Citation	TestReferenceable.c1
private Citation	PathwayElement.CitationRef.citation

Fields in org.pathvisio.libgpml.model with type parameters of type Citation

Modifier and Type	Field	Description
private java.util.List<Citation>	PathwayModel.citations

Methods in org.pathvisio.libgpml.model that return Citation

Modifier and Type	Method	Description
protected Citation	PathwayModel.addCitation(Citation citation)	Adds given citation to citations list.
Citation	Citation.copyRef()	Copies this citation.
Citation	PathwayElement.CitationRef.getCitation()	Returns the citation referenced.
private Citation	PathwayModel.hasEqualCitation(Citation citation)	Checks if given citation already exists for the pathway model.

Methods in org.pathvisio.libgpml.model that return types with arguments of type Citation

Modifier and Type	Method	Description
java.util.List<Citation>	PathwayModel.getCitations()	Returns the list of citations.

Methods in org.pathvisio.libgpml.model with parameters of type Citation

Modifier and Type	Method	Description
PathwayElement.CitationRef	PathwayElement.addCitation(Citation citation)	Creates and adds an citationRef to citationRefs list.
PathwayElement.CitationRef	PathwayElement.AnnotationRef.addCitation(Citation citation)	Creates and adds an citationRef to citationRefs list.
protected Citation	PathwayModel.addCitation(Citation citation)	Adds given citation to citations list.
PathwayElement.CitationRef	Referenceable.Citable.addCitation(Citation citation)	Creates and adds a citationRefs to citationRefs list.
void	Citation.copyValuesFrom(Citation src)	Copies values from the given source pathway element.
boolean	Citation.equalsCitation(Citation citation)	Compares this citation to the given citation.
private Citation	PathwayModel.hasEqualCitation(Citation citation)	Checks if given citation already exists for the pathway model.
void	PathwayModel.removeCitation(Citation citation)	Removes given citation from citations list and elementIdToPathwayObject map.
private void	PathwayElement.CitationRef.setCitation(Citation v)	Sets the source citation for this citationRef.
void	PathwayElement.CitationRef.setCitationTo(Citation citation)	Sets the source citation for this citationRef.

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

Modifier and Type	Method	Description
protected void	GPML2021Writer.writeCitations(java.util.List<Citation> citations, org.jdom2.Element root)	Writes citation Citation information.
protected void	GPML2013aWriter.writePublicationXref(java.util.List<Citation> citations, org.jdom2.Element bp)	Writes gpml:Biopax bp:PublicationXref Citation information.

Constructors in org.pathvisio.libgpml.model with parameters of type Citation

Constructor	Description
CitationRef(Citation citation)	Instantiates an CitationRef given source Citation and initializes annotationRefs lists.