cytoscape.data.annotation
Class Ontology

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

All Implemented Interfaces:

Serializable

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
protected String	ontologyType
protected HashMap	termHash

Constructor Summary

Ontology(String curator, String ontologyType)

Method Summary

void	add(OntologyTerm newTerm)
boolean	containsTerm(int id)
int[][]	getAllHierarchyPaths(int termID) 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) get all unique paths as a set of names, from termID to the root of the ontology, in reverse order, from most general to most specific.
protected Vector	getAllHierarchyPathsAsVector(int termID) assemble a Vector of Vectors of Integers, using a recursive traversal of the ontology hierarchy.
String	getCurator()
OntologyDescription	getDescription()
OntologyTerm	getTerm(int id)
HashMap	getTerms()
String	getType()
protected Vector	oldRecursiveGetPath(int termID, Vector path) traverse the ontology hierachy from leaf to root, adding a new vector with each recursive step.
protected Vector	recursiveGetPath(int termID, Vector path) traverse the ontology hierachy from leaf to root, adding a new vector with each recursive step.
int	size()
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

curator

protected String curator

ontologyType

protected String ontologyType

termHash

protected HashMap termHash

Constructor Detail

Ontology

public Ontology(String curator,
                String ontologyType)

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()

getType

public String getType()

add

public void add(OntologyTerm newTerm)

size

public int size()

getTerms

public HashMap getTerms()

containsTerm

public boolean containsTerm(int id)

getTerm

public OntologyTerm getTerm(int id)

getAllHierarchyPaths

public int[][] getAllHierarchyPaths(int termID)

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)

get all unique paths as a set of names, from termID to the root of the ontology, in reverse order, from most general to most specific. 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.

getAllHierarchyPathsAsVector

protected Vector getAllHierarchyPathsAsVector(int termID)

assemble a Vector of Vectors of Integers, using a recursive traversal of the ontology hierarchy. the recursive step often creates a multi-level list which is untangled into the desired simple list of lists by the FlattenIntVectors class.

recursiveGetPath

protected Vector recursiveGetPath(int termID,
                                  Vector path)

traverse the ontology hierachy from leaf to root, adding a new vector with each recursive step.

oldRecursiveGetPath

protected Vector oldRecursiveGetPath(int termID,
                                     Vector path)

traverse the ontology hierachy from leaf to root, adding a new vector with each recursive step.

getDescription

public OntologyDescription getDescription()

toString

public String toString()

Overrides:

toString in class Object