Cytoscape 2.6.2 (c) 2006,2007 ISB, MSKCC, UCSD

cytoscape.data.servers
Class OntologyServer

java.lang.Object
  extended by 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.
 
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
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

OntologyServer

public OntologyServer()
               throws IOException,
                      javax.xml.bind.JAXBException
Constructor.
Create hash map for ontologies.

Throws:
ConfigurationException
IOException
javax.xml.bind.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

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