cytoscape.data.ontology
Class OntologyTerm

java.lang.Object
  org.biojava.utils.AbstractChangeable
      cytoscape.data.ontology.OntologyTerm

All Implemented Interfaces:

org.biojava.bio.Annotatable, org.biojava.ontology.OntologyTerm, org.biojava.ontology.Term, org.biojava.utils.Changeable

Direct Known Subclasses:

GOTerm

public class OntologyTerm
extends org.biojava.utils.AbstractChangeable
implements org.biojava.ontology.OntologyTerm

Simple in-memory implementation of an ontology term based on BioJava's interface.

This implementation uses CyNetwork and CyAttributes as its actual data storage. A term is equal to a CyNode and the node can have attributes like other regular nodes in CyNetwork. Synonyms, description, etc are stored in CyAttributes.

Since:

Cytoscape 2.4

Version:

0.8

Author:

kono

Nested Class Summary

static class

OntologyTerm.SynonymType

Nested classes/interfaces inherited from interface org.biojava.ontology.OntologyTerm

org.biojava.ontology.OntologyTerm.Impl

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

org.biojava.bio.Annotatable.AnnotationForwarder

Field Summary

protected static String

SYNONYM

Fields inherited from interface org.biojava.ontology.Term

ONTOLOGY

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Constructor Summary

OntologyTerm(String name, String ontologyName, String description)
Constructor.

Method Summary

void	addSynonym(Object synonym) In this implementation, key is the synonym name, and value is the synonym type.
void	addSynonym(Object synonym, OntologyTerm.SynonymType type) In this implementation, key is the synonym name, and value is the synonym type.
org.biojava.bio.Annotation	getAnnotation() Always return empty annotation object.
String	getDescription() Return a human-readable description of this term, or the empty string if none is available.
String	getName() Return name (ID) of this term.
org.biojava.ontology.Ontology	getOntology() Get ontology object which contains this term.
Object[]	getSynonyms() Return sysnonym attributes for this term.
void	removeSynonym(Object synonym) Remove a synonym for this term.

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Field Detail

SYNONYM

protected static final String SYNONYM

See Also:

Constant Field Values

Constructor Detail

OntologyTerm

public OntologyTerm(String name,
                    String ontologyName,
                    String description)

Constructor.

Parameters:

name - ID of this term. SHOULD NOT BE NULL.

ontologyName -

description -

Method Detail

getName

public String getName()

Return name (ID) of this term.

Specified by:

getName in interface org.biojava.ontology.Term

getOntology

public org.biojava.ontology.Ontology getOntology()

Get ontology object which contains this term.

Specified by:

getOntology in interface org.biojava.ontology.OntologyTerm

Specified by:

getOntology in interface org.biojava.ontology.Term

addSynonym

public void addSynonym(Object synonym)

In this implementation, key is the synonym name, and value is the synonym type.

Specified by:

addSynonym in interface org.biojava.ontology.Term

addSynonym

public void addSynonym(Object synonym,
                       OntologyTerm.SynonymType type)

In this implementation, key is the synonym name, and value is the synonym type.

getDescription

public String getDescription()

Return a human-readable description of this term, or the empty string if none is available.

Specified by:

getDescription in interface org.biojava.ontology.Term

getSynonyms

public Object[] getSynonyms()

Return sysnonym attributes for this term.

Specified by:

getSynonyms in interface org.biojava.ontology.Term

removeSynonym

public void removeSynonym(Object synonym)

Remove a synonym for this term.

Specified by:

removeSynonym in interface org.biojava.ontology.Term

getAnnotation

public org.biojava.bio.Annotation getAnnotation()

Always return empty annotation object. Instead of using this, use normal Cyattributes API.

Specified by:

getAnnotation in interface org.biojava.bio.Annotatable