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

cytoscape.data.ontology
Class GeneOntology

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

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