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)
Creates a new OntologyTerm object.

Method Summary

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

Methods inherited from class java.lang.Object

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

Constructor Detail

OntologyTerm

public OntologyTerm(String name,
                    int id)

Creates a new OntologyTerm object.

Parameters:

name - DOCUMENT ME!

id - DOCUMENT ME!

Method Detail

getName

public String getName()

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Returns:

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getId

public int getId()

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Returns:

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addParent

public void addParent(int newParent)

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Parameters:

newParent - DOCUMENT ME!

addContainer

public void addContainer(int newContainer)

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Parameters:

newContainer - DOCUMENT ME!

numberOfParentsAndContainers

public int numberOfParentsAndContainers()

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Returns:

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numberOfParents

public int numberOfParents()

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Returns:

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numberOfContainers

public int numberOfContainers()

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Returns:

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getParents

public int[] getParents()

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Returns:

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getContainers

public int[] getContainers()

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Returns:

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getParentsAndContainers

public int[] getParentsAndContainers()

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Returns:

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isParentOf

public boolean isParentOf(OntologyTerm other)

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Parameters:

other - DOCUMENT ME!

Returns:

DOCUMENT ME!

isAncestorOf

public boolean isAncestorOf(Ontology ontology,
                            OntologyTerm other)

Parameters:

ontology - the Ontology that contains the terms

isChildOf

public boolean isChildOf(OntologyTerm other)

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Parameters:

other - DOCUMENT ME!

Returns:

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isContainerOf

public boolean isContainerOf(OntologyTerm other)

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Parameters:

other - DOCUMENT ME!

Returns:

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isContainedIn

public boolean isContainedIn(OntologyTerm other)

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Parameters:

other - DOCUMENT ME!

Returns:

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isChildOfOrContainedIn

public boolean isChildOfOrContainedIn(OntologyTerm other)

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Parameters:

other - DOCUMENT ME!

Returns:

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isParentOrContainerOf

public boolean isParentOrContainerOf(OntologyTerm other)

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Parameters:

other - DOCUMENT ME!

Returns:

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toString

public String toString()

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Overrides:

toString in class Object

Returns:

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