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

cytoscape.data.ontology
Class Ontology

java.lang.Object
  extended by org.biojava.utils.AbstractChangeable
      extended by cytoscape.data.ontology.Ontology
All Implemented Interfaces:
org.biojava.ontology.Ontology, org.biojava.utils.Changeable
Direct Known Subclasses:
GeneOntology

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

General Ontology class which implements Ontology interface from BioJava project.
This class representes a general and simple ontology class. This implementation uses
CyNetwork and CyAttributes for its actual data storage.

Since:
Cytoscape 2.4
Version:
0.8
Author:
kono
See Also:
org.biojava.ontology

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.biojava.ontology.Ontology
org.biojava.ontology.Ontology.Impl
 
Field Summary
static String IS_ONTOLOGY
           
 
Fields inherited from interface org.biojava.ontology.Ontology
TERM, TRIPLE
 
Constructor Summary
Ontology(String name)
          Constructor.
Ontology(String name, String curator, String description, CyNetwork dag)
          Constructor.
 
Method Summary
 void add(OntologyTerm newTerm)
          Add a new ontology term to the DAG.
 boolean containsTerm(String id)
           
 boolean containsTriple(org.biojava.ontology.Term subject, org.biojava.ontology.Term object, org.biojava.ontology.Term predicate)
          See if a triple exists in this ontology.
 org.biojava.ontology.Term createTerm(String name, String description)
          Create a new term in this ontology.
 org.biojava.ontology.Term createTerm(String arg0, String arg1, Object[] arg2)
          DOCUMENT ME!
 org.biojava.ontology.Triple createTriple(org.biojava.ontology.Term subject, org.biojava.ontology.Term object, org.biojava.ontology.Term predicate, String name, String description)
          DOCUMENT ME!
 org.biojava.ontology.Variable createVariable(String arg0, String arg1)
          DOCUMENT ME!
 void deleteTerm(org.biojava.ontology.Term arg0)
          Delete a term from DAG (CyNetwork)
 String getCurator()
           
 String getDescription()
          DOCUMENT ME!
 String getName()
          Returns name (actually, an ID).
 org.biojava.ontology.OntologyOps getOps()
          DOCUMENT ME!
 OntologyTerm getTerm(String id)
          Fetch the term with the specified name.
 Set getTerms()
          Return all the terms in this ontology.
 Set getTriples(org.biojava.ontology.Term arg0, org.biojava.ontology.Term arg1, org.biojava.ontology.Term arg2)
          returns set of Triples.
 org.biojava.ontology.Term importTerm(org.biojava.ontology.Term arg0, String arg1)
          DOCUMENT ME!
 int size()
           
 String 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
 

Field Detail

IS_ONTOLOGY

public static final String IS_ONTOLOGY
See Also:
Constant Field Values
Constructor Detail

Ontology

public Ontology(String name)
Constructor.

Creates null network for this ontology.

Parameters:
name - Name of this ontology. Will be used as ID.
Throws:
URISyntaxException

Ontology

public Ontology(String name,
                String curator,
                String description,
                CyNetwork dag)
Constructor.

Takes CyNetwork as its DAG.

Parameters:
name -
curator -
description -
dag -
Throws:
URISyntaxException
URISyntaxException
Method Detail

getName

public String getName()
Returns name (actually, an ID).

Specified by:
getName in interface org.biojava.ontology.Ontology
Returns:
Name of the ontology as string

getCurator

public String getCurator()
Returns:
Curator as string

add

public void add(OntologyTerm newTerm)
Add a new ontology term to the DAG.

Parameters:
newTerm -

size

public int size()
Returns:
Number of ontology terms in this ontology.

getTerms

public Set getTerms()
Return all the terms in this ontology.

Specified by:
getTerms in interface org.biojava.ontology.Ontology
Returns:
All ontology terms as Set object.

containsTerm

public boolean containsTerm(String id)
Specified by:
containsTerm in interface org.biojava.ontology.Ontology
Returns:
true if the term is in the DAG.

getTerm

public OntologyTerm getTerm(String id)
Fetch the term with the specified name.

Specified by:
getTerm in interface org.biojava.ontology.Ontology
Returns:
The term named name
Throws:
NoSuchElementException - if no term exists with that name

toString

public String toString()
Overrides:
toString in class Object

containsTriple

public boolean containsTriple(org.biojava.ontology.Term subject,
                              org.biojava.ontology.Term object,
                              org.biojava.ontology.Term predicate)
See if a triple exists in this ontology.

Specified by:
containsTriple in interface org.biojava.ontology.Ontology

createTerm

public org.biojava.ontology.Term createTerm(String name,
                                            String description)
                                     throws org.biojava.ontology.AlreadyExistsException,
                                            org.biojava.utils.ChangeVetoException,
                                            IllegalArgumentException
Create a new term in this ontology.

Specified by:
createTerm in interface org.biojava.ontology.Ontology
Throws:
org.biojava.ontology.AlreadyExistsException
org.biojava.utils.ChangeVetoException
IllegalArgumentException

createTerm

public org.biojava.ontology.Term createTerm(String arg0,
                                            String arg1,
                                            Object[] arg2)
                                     throws org.biojava.ontology.AlreadyExistsException,
                                            org.biojava.utils.ChangeVetoException,
                                            IllegalArgumentException
DOCUMENT ME!

Specified by:
createTerm in interface org.biojava.ontology.Ontology
Parameters:
arg0 - DOCUMENT ME!
arg1 - DOCUMENT ME!
arg2 - DOCUMENT ME!
Returns:
DOCUMENT ME!
Throws:
org.biojava.ontology.AlreadyExistsException - DOCUMENT ME!
org.biojava.utils.ChangeVetoException - DOCUMENT ME!
IllegalArgumentException - DOCUMENT ME!

createTriple

public org.biojava.ontology.Triple createTriple(org.biojava.ontology.Term subject,
                                                org.biojava.ontology.Term object,
                                                org.biojava.ontology.Term predicate,
                                                String name,
                                                String description)
                                         throws org.biojava.ontology.AlreadyExistsException,
                                                org.biojava.utils.ChangeVetoException
DOCUMENT ME!

Specified by:
createTriple in interface org.biojava.ontology.Ontology
Parameters:
subject - DOCUMENT ME!
object - DOCUMENT ME!
predicate - DOCUMENT ME!
name - DOCUMENT ME!
description - DOCUMENT ME!
Returns:
DOCUMENT ME!
Throws:
org.biojava.ontology.AlreadyExistsException - DOCUMENT ME!
org.biojava.utils.ChangeVetoException - DOCUMENT ME!

createVariable

public org.biojava.ontology.Variable createVariable(String arg0,
                                                    String arg1)
                                             throws org.biojava.ontology.AlreadyExistsException,
                                                    org.biojava.utils.ChangeVetoException,
                                                    IllegalArgumentException
DOCUMENT ME!

Specified by:
createVariable in interface org.biojava.ontology.Ontology
Parameters:
arg0 - DOCUMENT ME!
arg1 - DOCUMENT ME!
Returns:
DOCUMENT ME!
Throws:
org.biojava.ontology.AlreadyExistsException - DOCUMENT ME!
org.biojava.utils.ChangeVetoException - DOCUMENT ME!
IllegalArgumentException - DOCUMENT ME!

deleteTerm

public void deleteTerm(org.biojava.ontology.Term arg0)
                throws org.biojava.utils.ChangeVetoException
Delete a term from DAG (CyNetwork)

Specified by:
deleteTerm in interface org.biojava.ontology.Ontology
Throws:
org.biojava.utils.ChangeVetoException

getDescription

public String getDescription()
DOCUMENT ME!

Specified by:
getDescription in interface org.biojava.ontology.Ontology
Returns:
DOCUMENT ME!

getOps

public org.biojava.ontology.OntologyOps getOps()
DOCUMENT ME!

Specified by:
getOps in interface org.biojava.ontology.Ontology
Returns:
DOCUMENT ME!

getTriples

public Set getTriples(org.biojava.ontology.Term arg0,
                      org.biojava.ontology.Term arg1,
                      org.biojava.ontology.Term arg2)
returns set of Triples.
This is an expensive operation!

Specified by:
getTriples in interface org.biojava.ontology.Ontology

importTerm

public org.biojava.ontology.Term importTerm(org.biojava.ontology.Term arg0,
                                            String arg1)
                                     throws org.biojava.utils.ChangeVetoException,
                                            IllegalArgumentException
DOCUMENT ME!

Specified by:
importTerm in interface org.biojava.ontology.Ontology
Parameters:
arg0 - DOCUMENT ME!
arg1 - DOCUMENT ME!
Returns:
DOCUMENT ME!
Throws:
org.biojava.utils.ChangeVetoException - DOCUMENT ME!
IllegalArgumentException - DOCUMENT ME!

www.cytoscape.org