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

Packages that use Annotation

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

Uses of Annotation in org.pathvisio.libgpml.model

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

Modifier and Type	Field	Description
private Annotation	TestAnnotation.a
private Annotation	TestReferenceable.a1
private Annotation	TestAnnotation.a2
private Annotation	PathwayElement.AnnotationRef.annotation

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

Modifier and Type	Field	Description
private java.util.List<Annotation>	PathwayModel.annotations

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

Modifier and Type	Method	Description
protected Annotation	PathwayModel.addAnnotation(Annotation annotation)	Adds given annotation to annotations list.
Annotation	Annotation.copyRef()	Copies this annotation.
Annotation	PathwayElement.AnnotationRef.getAnnotation()	Returns the annotation referenced.
private Annotation	PathwayModel.hasEqualAnnotation(Annotation annotation)	Checks if given annotation already exists for the pathway model.

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

Modifier and Type	Method	Description
java.util.List<Annotation>	PathwayModel.getAnnotations()	Returns the list of annotations.

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

Modifier and Type	Method	Description
PathwayElement.AnnotationRef	PathwayElement.addAnnotation(Annotation annotation)	Creates and adds an annotationRef to annotationRefs list.
PathwayElement.AnnotationRef	PathwayElement.CitationRef.addAnnotation(Annotation annotation)	Creates and adds an annotationRef to annotationRefs list.Sets annotable for the given annotationRef.
protected Annotation	PathwayModel.addAnnotation(Annotation annotation)	Adds given annotation to annotations list.
PathwayElement.AnnotationRef	Referenceable.Annotatable.addAnnotation(Annotation annotation)	Creates and adds an annotationRef to annotationRefs list.
void	Annotation.copyValuesFrom(Annotation src)	Copies values from the given source pathway element.
boolean	Annotation.equalsAnnotation(Annotation annotation)	Compares this annotation to the given annotation.
private Annotation	PathwayModel.hasEqualAnnotation(Annotation annotation)	Checks if given annotation already exists for the pathway model.
void	PathwayModel.removeAnnotation(Annotation annotation)	Removes given annotation from annotations list and elementIdToPathwayObject map.
private void	PathwayElement.AnnotationRef.setAnnotation(Annotation v)	Sets the source annotation for this annotationRef.
void	PathwayElement.AnnotationRef.setAnnotationTo(Annotation annotation)	Sets the source annotation for this annotationRef.

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

Modifier and Type	Method	Description
protected void	GPML2021Writer.writeAnnotations(java.util.List<Annotation> annotations, org.jdom2.Element root)	Writes annotation Annotation information.

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

Constructor	Description
AnnotationRef(Annotation annotation)	Instantiates an AnnotationRef given source Annotation and initializes citationRefs and evidenceRefs lists.