cytoscape.data.ontology
Class GeneOntology

java.lang.Object
  org.biojava.utils.AbstractChangeable
      cytoscape.data.ontology.Ontology
          cytoscape.data.ontology.GeneOntology

All Implemented Interfaces:

org.biojava.ontology.Ontology, org.biojava.utils.Changeable

public class GeneOntology
extends Ontology

Gene Ontology object based on general Ontology.

Author:

kono

Nested Class Summary

static class

GeneOntology.GOAspect

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

org.biojava.ontology.Ontology.Impl

Field Summary

Fields inherited from class cytoscape.data.ontology.Ontology

IS_ONTOLOGY

Fields inherited from interface org.biojava.ontology.Ontology

TERM, TRIPLE

Constructor Summary

GeneOntology(String name, String curator, String description, CyNetwork dag)

Method Summary

GeneOntology.GOAspect	getAspect(String goID) Returns Aspect/name space of the GO term.
String	getCurator()
GOTerm	getGOTerm(String goID)
List<org.biojava.ontology.Term>	getTermsInNamespace(String namespace)

Methods inherited from class cytoscape.data.ontology.Ontology

add, containsTerm, containsTriple, createTerm, createTerm, createTriple, createVariable, deleteTerm, getDescription, getName, getOps, getTerm, getTerms, getTriples, importTerm, size, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Constructor Detail

GeneOntology

public GeneOntology(String name,
                    String curator,
                    String description,
                    CyNetwork dag)
             throws URISyntaxException,
                    MalformedURLException

Throws:

URISyntaxException

MalformedURLException

Method Detail

getCurator

public String getCurator()

Overrides:

getCurator in class Ontology

Returns:

Curator as string

getTermsInNamespace

public List<org.biojava.ontology.Term> getTermsInNamespace(String namespace)

getGOTerm

public GOTerm getGOTerm(String goID)

getAspect

public GeneOntology.GOAspect getAspect(String goID)

Returns Aspect/name space of the GO term.

Parameters:

goID - ID of the GO term (for example GO:000011)

Returns:

GOAspect of the given ID