cytoscape.data.annotation
Class Ontology

java.lang.Object
  cytoscape.data.annotation.Ontology

All Implemented Interfaces:

Serializable

Deprecated. Use regular CyAttributes for annotation.

@Deprecated
public class Ontology
extends Object
implements Serializable

Contains a collection of OntologyTerms, each of which may have pointers to other terms, creating a hierarchical controlled vocabulary. The pointers may express either "parent/child" relationships, or "container/contained" relationships. Objects of this class each aggregate a full set of related terms, creating a distinct ontology of a certain type, like KEGG's metabolic pathways, or GeneOntology's biological processes. Extensive navigational methods are provided so that, for instance, the full leaf-to-root biological process hierarchies which may exist for a given gene are conveniently returned.

See Also:

Serialized Form

Field Summary

protected String	curator Deprecated.
protected String	ontologyType Deprecated.
protected HashMap	termHash Deprecated.

Constructor Summary

Ontology(String curator, String ontologyType)
Deprecated.

Method Summary

void	add(OntologyTerm newTerm) Deprecated. DOCUMENT ME!
boolean	containsTerm(int id) Deprecated. DOCUMENT ME!
int[][]	getAllHierarchyPaths(int termID) Deprecated. get all unique paths from the termID to the root of the ontology, in reverse order, with the most general classification first, and most specific last.
String[][]	getAllHierarchyPathsAsNames(int termID) Deprecated. DOCUMENT ME!
protected Vector	getAllHierarchyPathsAsVector(int termID) Deprecated.
String	getCurator() Deprecated. DOCUMENT ME!
OntologyDescription	getDescription() Deprecated. DOCUMENT ME!
OntologyTerm	getTerm(int id) Deprecated. DOCUMENT ME!
HashMap	getTerms() Deprecated. DOCUMENT ME!
String	getType() Deprecated. DOCUMENT ME!
protected Vector	oldRecursiveGetPath(int termID, Vector path) Deprecated.
protected Vector	recursiveGetPath(int termID, Vector path) Deprecated.
int	size() Deprecated. DOCUMENT ME!
String	toString() Deprecated. DOCUMENT ME!

Methods inherited from class java.lang.Object

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

Field Detail

curator

protected String curator

Deprecated.

ontologyType

protected String ontologyType

Deprecated.

termHash

protected HashMap termHash

Deprecated.

Constructor Detail

Ontology

public Ontology(String curator,
                String ontologyType)

Deprecated.

Parameters:

curator - The institute or group which maintains this ontology

ontolotyType - The nature of this ontology, eg, "metabolic pathway", "molecular function", or "cellular component"

Method Detail

getCurator

public String getCurator()

Deprecated.

DOCUMENT ME!

Returns:

DOCUMENT ME!

getType

public String getType()

Deprecated.

DOCUMENT ME!

Returns:

DOCUMENT ME!

add

public void add(OntologyTerm newTerm)

Deprecated.

DOCUMENT ME!

Parameters:

newTerm - DOCUMENT ME!

size

public int size()

Deprecated.

DOCUMENT ME!

Returns:

DOCUMENT ME!

getTerms

public HashMap getTerms()

Deprecated.

DOCUMENT ME!

Returns:

DOCUMENT ME!

containsTerm

public boolean containsTerm(int id)

Deprecated.

DOCUMENT ME!

Parameters:

id - DOCUMENT ME!

Returns:

DOCUMENT ME!

getTerm

public OntologyTerm getTerm(int id)

Deprecated.

DOCUMENT ME!

Parameters:

id - DOCUMENT ME!

Returns:

DOCUMENT ME!

getAllHierarchyPaths

public int[][] getAllHierarchyPaths(int termID)

Deprecated.

get all unique paths from the termID to the root of the ontology, in reverse order, with the most general classification first, and most specific last. for some terms, this will be a path, possibly with only one member. for other terms, which have be assigned to multiple categories, there will be multiple paths. furthermore, some categories belong to multiple pathways, further increasing the number of paths implicit in the termID.

getAllHierarchyPathsAsNames

public String[][] getAllHierarchyPathsAsNames(int termID)

Deprecated.

DOCUMENT ME!

Parameters:

termID - DOCUMENT ME!

Returns:

DOCUMENT ME!

getAllHierarchyPathsAsVector

protected Vector getAllHierarchyPathsAsVector(int termID)

Deprecated.

recursiveGetPath

protected Vector recursiveGetPath(int termID,
                                  Vector path)

Deprecated.

oldRecursiveGetPath

protected Vector oldRecursiveGetPath(int termID,
                                     Vector path)

Deprecated.

getDescription

public OntologyDescription getDescription()

Deprecated.

DOCUMENT ME!

Returns:

DOCUMENT ME!

toString

public String toString()

Deprecated.

DOCUMENT ME!

Overrides:

toString in class Object

Returns:

DOCUMENT ME!