ubic.basecode.ontology.model

Class OntologyTermImpl

java.lang.Object

ubic.basecode.ontology.model.AbstractOntologyResource

ubic.basecode.ontology.model.OntologyTermImpl

All Implemented Interfaces:

Serializable, Comparable<OntologyResource>, OntologyResource, OntologyTerm

Direct Known Subclasses:

OntologyRestrictionImpl, OntologyTermSimple

public class OntologyTermImpl
extends AbstractOntologyResource
implements OntologyTerm

Represents a class in an ontology

Author:

Paul

See Also:

Serialized Form

Field Summary

Fields inherited from class ubic.basecode.ontology.model.AbstractOntologyResource

log

Constructor Summary

Constructors

Constructor and Description
OntologyTermImpl(com.hp.hpl.jena.ontology.OntClass resource)

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj)
Collection<String>	getAlternativeIds()
Collection<AnnotationProperty>	getAnnotations()
Collection<OntologyTerm>	getChildren(boolean direct)
Collection<OntologyTerm>	getChildren(boolean direct, boolean includePartOf)
String	getComment()
Collection<OntologyIndividual>	getIndividuals()
Collection<OntologyIndividual>	getIndividuals(boolean direct)
String	getLabel()
String	getLocalName()
Object	getModel()
Collection<OntologyTerm>	getParents(boolean direct) Note that any restriction superclasses are not returned, unless they are has_proper_part
Collection<OntologyTerm>	getParents(boolean direct, boolean includePartOf)
Collection<OntologyRestriction>	getRestrictions()
String	getTerm()
String	getUri()
int	hashCode()
boolean	isRoot()
boolean	isTermObsolete() check to see if the term is obsolete, if it is it should not be used
String	toString()

Methods inherited from class ubic.basecode.ontology.model.AbstractOntologyResource

compareTo

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Comparable

compareTo

Constructor Detail

OntologyTermImpl

public OntologyTermImpl(com.hp.hpl.jena.ontology.OntClass resource)

Method Detail

equals

public boolean equals(Object obj)

Overrides:

equals in class AbstractOntologyResource

getAlternativeIds

public Collection<String> getAlternativeIds()

Specified by:

getAlternativeIds in interface OntologyTerm

getAnnotations

public Collection<AnnotationProperty> getAnnotations()

Specified by:

getAnnotations in interface OntologyTerm

getChildren

public Collection<OntologyTerm> getChildren(boolean direct)

Specified by:

getChildren in interface OntologyTerm

getChildren

public Collection<OntologyTerm> getChildren(boolean direct,
                                            boolean includePartOf)

Specified by:

getChildren in interface OntologyTerm

Parameters:

direct - return only the immediate children; if false, return all of them down to the leaves.

includePartOf - include terms matched via

Returns:

getComment

public String getComment()

Specified by:

getComment in interface OntologyTerm

getIndividuals

public Collection<OntologyIndividual> getIndividuals()

Specified by:

getIndividuals in interface OntologyTerm

getIndividuals

public Collection<OntologyIndividual> getIndividuals(boolean direct)

Specified by:

getIndividuals in interface OntologyTerm

getLabel

public String getLabel()

Specified by:

getLabel in interface OntologyResource

getLocalName

public String getLocalName()

Specified by:

getLocalName in interface OntologyTerm

getModel

public Object getModel()

Specified by:

getModel in interface OntologyTerm

getParents

public Collection<OntologyTerm> getParents(boolean direct)

Description copied from interface: OntologyTerm

Note that any restriction superclasses are not returned, unless they are has_proper_part

Specified by:

getParents in interface OntologyTerm

Returns:

getParents

public Collection<OntologyTerm> getParents(boolean direct,
                                           boolean includePartOf)

Specified by:

getParents in interface OntologyTerm

getRestrictions

public Collection<OntologyRestriction> getRestrictions()

Specified by:

getRestrictions in interface OntologyTerm

getTerm

public String getTerm()

Specified by:

getTerm in interface OntologyTerm

getUri

public String getUri()

Specified by:

getUri in interface OntologyResource

Specified by:

getUri in interface OntologyTerm

Specified by:

getUri in class AbstractOntologyResource

hashCode

public int hashCode()

Overrides:

hashCode in class AbstractOntologyResource

isRoot

public boolean isRoot()

Specified by:

isRoot in interface OntologyTerm

isTermObsolete

public boolean isTermObsolete()

Description copied from interface: OntologyTerm

check to see if the term is obsolete, if it is it should not be used

Specified by:

isTermObsolete in interface OntologyTerm

toString

public String toString()

Overrides:

toString in class Object