cytoscape.data.ontology
Class Ontology

java.lang.Object
  org.biojava.utils.AbstractChangeable
      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
protected MetadataParser	metaParser
protected String	name Name of this ontorogy.

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. This is an expensive operation!
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, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, equals, finalize, 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

name

protected String name

Name of this ontorogy. This will be used as the ID of this ontology.

metaParser

protected MetadataParser metaParser

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!