Package org.pathvisio.libgpml.model

Interface Referenceable.Citable

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.Citable
extends Referenceable

Interface for classes which can hold a List of PathwayElement.CitationRef. These classes include Pathway, 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.CitationRef	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	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	addCitation(Citation citation)	Creates and adds a citationRefs to citationRefs list.
java.util.List<PathwayElement.CitationRef>	getCitationRefs()	Returns the list of citation references.
boolean	hasCitationRef(PathwayElement.CitationRef citationRef)	Check whether this citable has the given citationRef.
void	removeCitationRef(PathwayElement.CitationRef citationRef)	Removes given citationRef from citationRefs list.
void	removeCitationRefs()	Removes all citationRefs from citationRefs list.

Method Details

getCitationRefs

java.util.List<PathwayElement.CitationRef> getCitationRefs()

Returns the list of citation references.

Returns:

citationRefs the list of citations referenced, an empty list if no properties are defined.

hasCitationRef

boolean hasCitationRef(PathwayElement.CitationRef citationRef)

Check whether this citable has the given citationRef.

Parameters:

citationRef - the citationRef to look for.

Returns:

true if has citationRef, false otherwise.

addCitation

PathwayElement.CitationRef addCitation(Citation citation)

Creates and adds a citationRefs to citationRefs list.

Parameters:

citation - the citation for citationRef.

Returns:

the citationRef for the citation added.

addCitation

PathwayElement.CitationRef addCitation(org.bridgedb.Xref xref,
java.lang.String urlLink)

Creates a citation with given xref and urlLink, and adds citation to pathway model. Creates a citationRef for citation, and adds to citationRefs list for this citable. Calls addCitation(Citation citation).

Parameters:

xref - the citation xref.

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

Returns:

the citationRef for the citation added.

addCitation

PathwayElement.CitationRef 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. Creates a citationRef for citation, and adds to citationRefs list for this citable. Sets elementId for citation. This method is used when reading gpml. Calls addCitation(Citation citation).

Parameters:

elementId - the elementId to set.

xref - the citation xref.

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

Returns:

the citationRef for the citation added.

removeCitationRef

void removeCitationRef(PathwayElement.CitationRef citationRef)

Removes given citationRef from citationRefs list.

Parameters:

citationRef - the citationRef to be removed.

removeCitationRefs

void removeCitationRefs()

Removes all citationRefs from citationRefs list.