cytoscape.data.servers
Class OntologyServer

java.lang.Object
  cytoscape.data.servers.OntologyServer

All Implemented Interfaces:

PropertyChangeListener, EventListener

public class OntologyServer
extends Object
implements PropertyChangeListener

Ontology Server which manages ontologies, aliases, and bookmarks.

Since:

Cytoscape 2.4

Version:

0.6

Author:

kono

Nested Class Summary

static class

OntologyServer.OntologyType

Constructor Summary

OntologyServer()
Constructor.
Create hash map for ontologies.

Method Summary

void	addOntology(Ontology onto)
void	addOntology(URL dataSource, OntologyServer.OntologyType type, String ontologyName, String description)
DBCrossReferences	getCrossReferences()
Aliases	getEdgeAliases()
Aliases	getNetworkAliases()
Aliases	getNodeAliases()
HashMap<String,Ontology>	getOntologies() Getter of the property ontologies
Set<String>	getOntologyNames()
Map<String,URL>	getOntologySources()
int	ontologyCount()
void	propertyChange(PropertyChangeEvent e)
void	setOntology(Ontology onto)
void	setOntologySources(Map<String,URL> newMap)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

OntologyServer

public OntologyServer()
               throws IOException,
                      JAXBException

Constructor.
Create hash map for ontologies.

Throws:

ConfigurationException

IOException

JAXBException

Method Detail

getCrossReferences

public DBCrossReferences getCrossReferences()

getOntologies

public HashMap<String,Ontology> getOntologies()

Getter of the property ontologies

Returns:

Returns the ontologies.

addOntology

public void addOntology(Ontology onto)

addOntology

public void addOntology(URL dataSource,
                        OntologyServer.OntologyType type,
                        String ontologyName,
                        String description)
                 throws IOException,
                        URISyntaxException

Throws:

IOException

URISyntaxException

ontologyCount

public int ontologyCount()

setOntology

public void setOntology(Ontology onto)

getOntologyNames

public Set<String> getOntologyNames()

getOntologySources

public Map<String,URL> getOntologySources()

setOntologySources

public void setOntologySources(Map<String,URL> newMap)

getNodeAliases

public Aliases getNodeAliases()

getEdgeAliases

public Aliases getEdgeAliases()

getNetworkAliases

public Aliases getNetworkAliases()

propertyChange

public void propertyChange(PropertyChangeEvent e)

Specified by:

propertyChange in interface PropertyChangeListener