Package org.pathvisio.libgpml.model

Interface Referenceable.Evidenceable

All Superinterfaces:

Referenceable

All Known Implementing Classes:

DataNode, DataNode.State, GraphicalLine, Group, Interaction, Label, LineElement, Pathway, PathwayElement, PathwayElement.AnnotationRef, Shape, ShapedElement

Enclosing interface:

Referenceable

public static interface Referenceable.Evidenceable
extends Referenceable

Interface for classes which can hold a List of PathwayElement.EvidenceRef. These classes include PathwayElement and PathwayElement.AnnotationRef.

Author:

finterly

Nested Class Summary

Nested classes/interfaces inherited from interface org.pathvisio.libgpml.model.Referenceable

Referenceable.Annotatable, Referenceable.Citable, Referenceable.Evidenceable

Method Summary

Modifier and Type	Method	Description
PathwayElement.EvidenceRef	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	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	addEvidence(Evidence evidence)	Creates and adds an evidenceRef to evidenceRefs list.
java.util.List<PathwayElement.EvidenceRef>	getEvidenceRefs()	Returns the list of evidence references.
boolean	hasEvidenceRef(PathwayElement.EvidenceRef evidenceRef)	Check whether this annotatable has the given evidenceRef.
void	removeEvidenceRef(PathwayElement.EvidenceRef evidenceRef)	Removes given evidenceRef from evidenceRefs list.
void	removeEvidenceRefs()	Removes all evidenceRefs from evidenceRefs list.

Method Details

getEvidenceRefs

java.util.List<PathwayElement.EvidenceRef> getEvidenceRefs()

Returns the list of evidence references.

Returns:

evidenceRefs the list of annotation references, an empty list if no properties are defined.

hasEvidenceRef

boolean hasEvidenceRef(PathwayElement.EvidenceRef evidenceRef)

Check whether this annotatable has the given evidenceRef.

Parameters:

evidenceRef - the evidenceRef to look for.

Returns:

true if has evidenceRef, false otherwise.

addEvidence

PathwayElement.EvidenceRef addEvidence(Evidence evidence)

Creates and adds an evidenceRef to evidenceRefs list.

Parameters:

evidence - the evidenceRef for evidenceRef.

Returns:

the evidencRef for the evidence added.

addEvidence

PathwayElement.EvidenceRef 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. Creates a evidenceRef for evidence, and adds to evidenceRefs list for this evidenceable. Calls addEvidence(Evidence evidence).

Parameters:

value - the name, term, or text of the evidence.

xref - the evidence xref.

urlLink - the url link and description (optional) for a web address.

Returns:

the evidencRef for the evidence added.

addEvidence

PathwayElement.EvidenceRef 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. Creates a evidenceRef for evidence, and adds to evidenceRefs list for this evidenceable. Sets elementId for evidence. This method is used when reading gpml. Calls addEvidence(Evidence evidence).

Parameters:

elementId - the elementId to set.

value - the name, term, or text of the evidence.

xref - the evidence xref.

urlLink - the url link and description (optional) for a web address.

Returns:

the evidencRef for the evidence added.

removeEvidenceRef

void removeEvidenceRef(PathwayElement.EvidenceRef evidenceRef)

Removes given evidenceRef from evidenceRefs list.

Parameters:

evidenceRef - the evidenceRef to be removed.

removeEvidenceRefs

void removeEvidenceRefs()

Removes all evidenceRefs from evidenceRefs list.