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

Packages that use PathwayElement.AnnotationRef

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

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

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

Modifier and Type	Field	Description
private PathwayElement.AnnotationRef	TestAnnotation.ar1
private PathwayElement.AnnotationRef	TestReferenceable.ar1
private PathwayElement.AnnotationRef	TestAnnotation.ar2
private PathwayElement.AnnotationRef	TestReferenceable.ar2

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

Modifier and Type	Field	Description
private java.util.List<PathwayElement.AnnotationRef>	Annotation.annotationRefs
private java.util.List<PathwayElement.AnnotationRef>	PathwayElement.annotationRefs
private java.util.List<PathwayElement.AnnotationRef>	PathwayElement.CitationRef.annotationRefs

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

Modifier and Type	Method	Description
PathwayElement.AnnotationRef	PathwayElement.addAnnotation(java.lang.String elementId, java.lang.String value, AnnotationType type, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a annotation with given properties, and adds annotation to pathway model.
PathwayElement.AnnotationRef	PathwayElement.addAnnotation(java.lang.String value, AnnotationType type, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a annotation with given properties, and adds annotation to pathway model.
PathwayElement.AnnotationRef	PathwayElement.addAnnotation(Annotation annotation)	Creates and adds an annotationRef to annotationRefs list.
PathwayElement.AnnotationRef	PathwayElement.CitationRef.addAnnotation(java.lang.String elementId, java.lang.String value, AnnotationType type, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a annotation with given properties, and adds annotation to pathway model.
PathwayElement.AnnotationRef	PathwayElement.CitationRef.addAnnotation(java.lang.String value, AnnotationType type, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a annotation with given properties, and adds annotation to pathway model.
PathwayElement.AnnotationRef	PathwayElement.CitationRef.addAnnotation(Annotation annotation)	Creates and adds an annotationRef to annotationRefs list.Sets annotable for the given annotationRef.
PathwayElement.AnnotationRef	Referenceable.Annotatable.addAnnotation(java.lang.String elementId, java.lang.String value, AnnotationType type, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a annotation with given properties, and adds annotation to pathway model.
PathwayElement.AnnotationRef	Referenceable.Annotatable.addAnnotation(java.lang.String value, AnnotationType type, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates a annotation with given properties, and adds annotation to pathway model.
PathwayElement.AnnotationRef	Referenceable.Annotatable.addAnnotation(Annotation annotation)	Creates and adds an annotationRef to annotationRefs list.

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

Modifier and Type	Method	Description
java.util.List<PathwayElement.AnnotationRef>	Annotation.getAnnotationRefs()	Returns the list of annotationRefs which reference the annotation.
java.util.List<PathwayElement.AnnotationRef>	PathwayElement.CitationRef.getAnnotationRefs()	Returns the list of annotation references.
java.util.List<PathwayElement.AnnotationRef>	PathwayElement.getAnnotationRefs()	Returns the list of annotation references.
java.util.List<PathwayElement.AnnotationRef>	Referenceable.Annotatable.getAnnotationRefs()	Returns the list of annotation references.

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

Modifier and Type	Method	Description
protected void	Annotation.addAnnotationRef(PathwayElement.AnnotationRef annotationRef)	Adds the given annotationRef to annotationRefs list of the annotation.
boolean	Annotation.hasAnnotationRef(PathwayElement.AnnotationRef annotationRef)	Check whether annotationRefs has the given annotationRef.
boolean	PathwayElement.CitationRef.hasAnnotationRef(PathwayElement.AnnotationRef annotationRef)	Checks whether annotationRefs has the given annotationRef.
boolean	PathwayElement.hasAnnotationRef(PathwayElement.AnnotationRef annotationRef)	Checks whether annotationRefs has the given annotationRef.
boolean	Referenceable.Annotatable.hasAnnotationRef(PathwayElement.AnnotationRef annotationRef)	Check whether this annotatable has the given annotationRef.
protected void	Annotation.removeAnnotationRef(PathwayElement.AnnotationRef annotationRef)	Removes the given annotationRef from annotationRefs list of this annotation.
void	PathwayElement.CitationRef.removeAnnotationRef(PathwayElement.AnnotationRef annotationRef)	Removes given annotationRef from annotationRefs list.
void	PathwayElement.removeAnnotationRef(PathwayElement.AnnotationRef annotationRef)	Removes given annotationRef from annotationRefs list.
void	Referenceable.Annotatable.removeAnnotationRef(PathwayElement.AnnotationRef annotationRef)	Removes given annotationRef from annotationRefs list.

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

Modifier and Type	Method	Description
private void	PathwayElement.copyAnnotationRefs(java.util.List<PathwayElement.AnnotationRef> annotationRefs)	Copies annotationRefs and nested citationRefs and evidenceRefs if applicable.
protected void	GPML2021Writer.writeAnnotationRefs(java.util.List<PathwayElement.AnnotationRef> annotationRefs, org.jdom2.Element e)	Writes annotation reference information for pathway or pathway element.