cytoscape.data.annotation
Class OntologyTerm

java.lang.Object
  cytoscape.data.annotation.OntologyTerm

All Implemented Interfaces:

Serializable

public class OntologyTerm
extends Object
implements Serializable

Represents one node in an ontology, which is a hierarchical classification of entities using a controlled vocabulary. Each term has a name, a unique integer identifier, a list of parent terms, and a list of containers. Parent terms capture the "is-child-of" relationship for this term. Container terms capture the "is-part-of" relationship. This data model was inspired by the three ontologies (biological process, molecular function, cellular component) of the Gene Ontology project. Other ontologies should work nicely with this class as well.

See Also:

Serialized Form

Constructor Summary

OntologyTerm(String name, int id)

Method Summary

void	addContainer(int newContainer)
void	addParent(int newParent)
int[]	getContainers()
int	getId()
String	getName()
int[]	getParents()
int[]	getParentsAndContainers()
boolean	isAncestorOf(Ontology ontology, OntologyTerm other)
boolean	isChildOf(OntologyTerm other)
boolean	isChildOfOrContainedIn(OntologyTerm other)
boolean	isContainedIn(OntologyTerm other)
boolean	isContainerOf(OntologyTerm other)
boolean	isParentOf(OntologyTerm other)
boolean	isParentOrContainerOf(OntologyTerm other)
int	numberOfContainers()
int	numberOfParents()
int	numberOfParentsAndContainers()
String	toString()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

OntologyTerm

public OntologyTerm(String name,
                    int id)

Method Detail

getName

public String getName()

getId

public int getId()

addParent

public void addParent(int newParent)

addContainer

public void addContainer(int newContainer)

numberOfParentsAndContainers

public int numberOfParentsAndContainers()

numberOfParents

public int numberOfParents()

numberOfContainers

public int numberOfContainers()

getParents

public int[] getParents()

getContainers

public int[] getContainers()

getParentsAndContainers

public int[] getParentsAndContainers()

isParentOf

public boolean isParentOf(OntologyTerm other)

isAncestorOf

public boolean isAncestorOf(Ontology ontology,
                            OntologyTerm other)

Parameters:

ontology - the Ontology that contains the terms

isChildOf

public boolean isChildOf(OntologyTerm other)

isContainerOf

public boolean isContainerOf(OntologyTerm other)

isContainedIn

public boolean isContainedIn(OntologyTerm other)

isChildOfOrContainedIn

public boolean isChildOfOrContainedIn(OntologyTerm other)

isParentOrContainerOf

public boolean isParentOrContainerOf(OntologyTerm other)

toString

public String toString()

Overrides:

toString in class Object