Uses of Class
org.pathvisio.libgpml.model.PathwayElement.CitationRef

Packages that use PathwayElement.CitationRef

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

Uses of PathwayElement.CitationRef in org.pathvisio.libgpml.model

Fields in org.pathvisio.libgpml.model declared as PathwayElement.CitationRef

Modifier and Type	Field	Description
private PathwayElement.CitationRef	TestCitation.ar1
private PathwayElement.CitationRef	TestCitation.ar2
private PathwayElement.CitationRef	TestCopy.cr
private PathwayElement.CitationRef	TestReferenceable.cr1
private PathwayElement.CitationRef	TestReferenceable.cr2

Fields in org.pathvisio.libgpml.model with type parameters of type PathwayElement.CitationRef

Modifier and Type	Field	Description
private java.util.List<PathwayElement.CitationRef>	Citation.citationRefs	citationRefs with this citation as source
private java.util.List<PathwayElement.CitationRef>	PathwayElement.AnnotationRef.citationRefs
private java.util.List<PathwayElement.CitationRef>	PathwayElement.citationRefs

Methods in org.pathvisio.libgpml.model that return PathwayElement.CitationRef

Modifier and Type	Method	Description
PathwayElement.CitationRef	PathwayElement.addCitation(java.lang.String elementId, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a citation with given xref and urlLink, and adds citation to pathway model.
PathwayElement.CitationRef	PathwayElement.addCitation(org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a citation with given xref and urlLink, and adds citation to pathway model.
PathwayElement.CitationRef	PathwayElement.addCitation(Citation citation)	Creates and adds an citationRef to citationRefs list.
PathwayElement.CitationRef	PathwayElement.AnnotationRef.addCitation(java.lang.String elementId, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a citation with given xref and urlLink, and adds citation to pathway model.
PathwayElement.CitationRef	PathwayElement.AnnotationRef.addCitation(org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a citation with given xref and urlLink, and adds citation to pathway model.
PathwayElement.CitationRef	PathwayElement.AnnotationRef.addCitation(Citation citation)	Creates and adds an citationRef to citationRefs list.
PathwayElement.CitationRef	Referenceable.Citable.addCitation(java.lang.String elementId, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a citation with given xref and urlLink, and adds citation to pathway model.
PathwayElement.CitationRef	Referenceable.Citable.addCitation(org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a citation with given xref and urlLink, and adds citation to pathway model.
PathwayElement.CitationRef	Referenceable.Citable.addCitation(Citation citation)	Creates and adds a citationRefs to citationRefs list.

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

Modifier and Type	Method	Description
java.util.List<PathwayElement.CitationRef>	Citation.getCitationRefs()	Returns the list of citationRefs which reference this citation.
java.util.List<PathwayElement.CitationRef>	PathwayElement.AnnotationRef.getCitationRefs()	Returns the list of citation references.
java.util.List<PathwayElement.CitationRef>	PathwayElement.getCitationRefs()	Returns the list of citation references.
java.util.List<PathwayElement.CitationRef>	Referenceable.Citable.getCitationRefs()	Returns the list of citation references.

Methods in org.pathvisio.libgpml.model with parameters of type PathwayElement.CitationRef

Modifier and Type	Method	Description
protected void	Citation.addCitationRef(PathwayElement.CitationRef citationRef)	Adds the given citationRef to citationRefs list of this citation.
boolean	Citation.hasCitationRef(PathwayElement.CitationRef citationRef)	Check whether citationRefs has the given citationRef.
boolean	PathwayElement.AnnotationRef.hasCitationRef(PathwayElement.CitationRef citationRef)	Checks whether citationRefs has the given citationRef.
boolean	PathwayElement.hasCitationRef(PathwayElement.CitationRef citationRef)	Checks whether citationRefs has the given citationRef.
boolean	Referenceable.Citable.hasCitationRef(PathwayElement.CitationRef citationRef)	Check whether this citable has the given citationRef.
protected void	Citation.removeCitationRef(PathwayElement.CitationRef citationRef)	Removes the given citationRef from citationRefs list of the citation.
void	PathwayElement.AnnotationRef.removeCitationRef(PathwayElement.CitationRef citationRef)	Removes given citationRef from citationRefs list.
void	PathwayElement.removeCitationRef(PathwayElement.CitationRef citationRef)	Removes given citationRef from citationRefs list.
void	Referenceable.Citable.removeCitationRef(PathwayElement.CitationRef citationRef)	Removes given citationRef from citationRefs list.

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

Modifier and Type	Method	Description
private void	PathwayElement.copyCitationRefs(java.util.List<PathwayElement.CitationRef> citationRefs)	Copies citationsRefs and nested annotationRefs if applicable.
protected void	GPML2013aWriter.writeBiopaxRefs(java.util.List<PathwayElement.CitationRef> citationRefs, org.jdom2.Element e)	Writes BiopaxRef information from PathwayElement.getCitationRefs() for pathway or pathway element.
protected void	GPML2021Writer.writeCitationRefs(java.util.List<PathwayElement.CitationRef> citationRefs, org.jdom2.Element e)	Writes citation reference information for pathway or pathway element.