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

Packages that use PathwayElement.EvidenceRef

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

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

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

Modifier and Type	Field	Description
private PathwayElement.EvidenceRef	TestEvidence.ar1
private PathwayElement.EvidenceRef	TestEvidence.ar2
private PathwayElement.EvidenceRef	TestReferenceable.er1
private PathwayElement.EvidenceRef	TestReferenceable.er2

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

Modifier and Type	Field	Description
private java.util.List<PathwayElement.EvidenceRef>	Evidence.evidenceRefs	evidenceRefs with this evidence as source
private java.util.List<PathwayElement.EvidenceRef>	PathwayElement.AnnotationRef.evidenceRefs
private java.util.List<PathwayElement.EvidenceRef>	PathwayElement.evidenceRefs

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

Modifier and Type	Method	Description
PathwayElement.EvidenceRef	PathwayElement.addEvidence(java.lang.String elementId, java.lang.String value, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates an evidence with given properties, and adds evidence to pathway model.
PathwayElement.EvidenceRef	PathwayElement.addEvidence(java.lang.String value, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates an evidence with given properties, and adds evidence to pathway model.
PathwayElement.EvidenceRef	PathwayElement.addEvidence(Evidence evidence)	Creates and adds an evidenceRef to evidenceRefs list.
PathwayElement.EvidenceRef	PathwayElement.AnnotationRef.addEvidence(java.lang.String elementId, java.lang.String value, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates an evidence with given properties, and adds evidence to pathway model.
PathwayElement.EvidenceRef	PathwayElement.AnnotationRef.addEvidence(java.lang.String value, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates an evidence with given properties, and adds evidence to pathway model.
PathwayElement.EvidenceRef	PathwayElement.AnnotationRef.addEvidence(Evidence evidence)	Creates and adds an evidenceRef to evidenceRefs list.
PathwayElement.EvidenceRef	Referenceable.Evidenceable.addEvidence(java.lang.String elementId, java.lang.String value, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates an evidence with given properties, and adds evidence to pathway model.
PathwayElement.EvidenceRef	Referenceable.Evidenceable.addEvidence(java.lang.String value, org.bridgedb.Xref xref, java.lang.String urlLink)	Creates an evidence with given properties, and adds evidence to pathway model.
PathwayElement.EvidenceRef	Referenceable.Evidenceable.addEvidence(Evidence evidence)	Creates and adds an evidenceRef to evidenceRefs list.

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

Modifier and Type	Method	Description
java.util.List<PathwayElement.EvidenceRef>	Evidence.getEvidenceRefs()	Returns the list of evidenceRefs which reference this evidence.
java.util.List<PathwayElement.EvidenceRef>	PathwayElement.AnnotationRef.getEvidenceRefs()	Returns the list of evidence references.
java.util.List<PathwayElement.EvidenceRef>	PathwayElement.getEvidenceRefs()	Returns the list of evidence references.
java.util.List<PathwayElement.EvidenceRef>	Referenceable.Evidenceable.getEvidenceRefs()	Returns the list of evidence references.

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

Modifier and Type	Method	Description
protected void	Evidence.addEvidenceRef(PathwayElement.EvidenceRef evidenceRef)	Adds the given evidenceRef to evidenceRefs list of this evidence.
boolean	Evidence.hasEvidenceRef(PathwayElement.EvidenceRef evidenceRef)	Check whether evidenceRefs has the given evidenceRef.
boolean	PathwayElement.AnnotationRef.hasEvidenceRef(PathwayElement.EvidenceRef evidenceRef)	Checks whether citationRefs has the given citationRef.
boolean	PathwayElement.hasEvidenceRef(PathwayElement.EvidenceRef evidenceRef)	Checks whether evidenceRefs has the given evidenceRef.
boolean	Referenceable.Evidenceable.hasEvidenceRef(PathwayElement.EvidenceRef evidenceRef)	Check whether this annotatable has the given evidenceRef.
protected void	Evidence.removeEvidenceRef(PathwayElement.EvidenceRef evidenceRef)	Removes the given evidenceRef from evidenceRefs list of this evidence.
void	PathwayElement.AnnotationRef.removeEvidenceRef(PathwayElement.EvidenceRef evidenceRef)	Removes given evidenceRef from evidenceRefs list.
void	PathwayElement.removeEvidenceRef(PathwayElement.EvidenceRef evidenceRef)	Removes given evidenceRef from evidenceRefs list.
void	Referenceable.Evidenceable.removeEvidenceRef(PathwayElement.EvidenceRef evidenceRef)	Removes given evidenceRef from evidenceRefs list.

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

Modifier and Type	Method	Description
private void	PathwayElement.copyEvidenceRefs(java.util.List<PathwayElement.EvidenceRef> evidenceRefs)	Copies evidenceRefs.
protected void	GPML2021Writer.writeEvidenceRefs(java.util.List<PathwayElement.EvidenceRef> evidenceRefs, org.jdom2.Element e)	Writes evidence reference information for pathway or pathway element , ElementInfo#getEvidenceRefs.