Uses of Class
cytoscape.data.annotation.Ontology

Packages that use Ontology

cytoscape.data.annotation	Classes used to represent generic annotation data in Cytoscape.
cytoscape.data.annotation.readers	Reader classes for generic annotation data.
cytoscape.data.servers	An interface for annotation data providers and various implementations of that interface, including both remote and in-process implementations.

Uses of Ontology in cytoscape.data.annotation

Fields in cytoscape.data.annotation declared as Ontology

protected Ontology

Annotation.ontology Deprecated.

Methods in cytoscape.data.annotation that return Ontology

Ontology

Annotation.getOntology() Deprecated. DOCUMENT ME!

Methods in cytoscape.data.annotation with parameters of type Ontology

boolean	OntologyTerm.isAncestorOf(Ontology ontology, OntologyTerm other) Deprecated.
void	Annotation.setOntology(Ontology newValue) Deprecated. DOCUMENT ME!

Constructors in cytoscape.data.annotation with parameters of type Ontology

Annotation(String species, String type, Ontology ontology)
Deprecated. Creates a new Annotation object.

Uses of Ontology in cytoscape.data.annotation.readers

Methods in cytoscape.data.annotation.readers that return Ontology

Ontology	OntologyXmlReader.getOntology() DOCUMENT ME!
Ontology	OntologyFlatFileReader.getOntology() DOCUMENT ME!

Uses of Ontology in cytoscape.data.servers

Methods in cytoscape.data.servers that return Ontology

protected Ontology	BioDataServer.pickOntology(Ontology[] ontologies, Annotation annotation)
Ontology[]	BioDataServer.readOntologyFlatFiles(String[] ontologyFilenames) DOCUMENT ME!
Ontology[]	BioDataServer.readOntologyFlatFiles2(String[] ontologyFilenames) DOCUMENT ME!

Methods in cytoscape.data.servers with parameters of type Ontology

protected Ontology

BioDataServer.pickOntology(Ontology[] ontologies, Annotation annotation)