Package ubic.basecode.ontology.jena

Class OntologyTermImpl

java.lang.Object

ubic.basecode.ontology.jena.AbstractOntologyResource

ubic.basecode.ontology.jena.OntologyTermImpl

All Implemented Interfaces:

Serializable, Comparable<OntologyResource>, OntologyResource, OntologyTerm

Direct Known Subclasses:

OntologyRestrictionImpl

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.jena.AbstractOntologyResource

log

Constructor Summary

Constructors

Constructor	Description
OntologyTermImpl(com.hp.hpl.jena.ontology.OntClass resource, Set<com.hp.hpl.jena.ontology.Restriction> additionalRestrictions)
OntologyTermImpl(com.hp.hpl.jena.ontology.OntClass resource, Set<com.hp.hpl.jena.ontology.Restriction> additionalRestrictions, double score)

Method Summary

Modifier and Type	Method	Description
Collection<String>	getAlternativeIds()
Collection<AnnotationProperty>	getAnnotations()
Collection<OntologyTerm>	getChildren(boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)	Obtain the children of this term via subclass relationships and possibly some additional properties.
String	getComment()
Collection<OntologyIndividual>	getIndividuals(boolean direct)
String	getLocalName()
Object	getModel()
Collection<OntologyTerm>	getParents(boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
Collection<OntologyRestriction>	getRestrictions()
String	getTerm()
boolean	isObsolete()	Whether the resource is marked as obsolete.
boolean	isRoot()
boolean	isTermObsolete()	check to see if the term is obsolete, if it is it should not be used

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

compareTo, equals, getLabel, getScore, getUri, hashCode, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface ubic.basecode.ontology.model.OntologyResource

getLabel, getScore, getUri

Methods inherited from interface ubic.basecode.ontology.model.OntologyTerm

getChildren, getChildren, getIndividuals, getParents, getParents

Constructor Detail

OntologyTermImpl

public OntologyTermImpl(com.hp.hpl.jena.ontology.OntClass resource,
                        @Nullable
                        Set<com.hp.hpl.jena.ontology.Restriction> additionalRestrictions)

OntologyTermImpl

public OntologyTermImpl(com.hp.hpl.jena.ontology.OntClass resource,
                        Set<com.hp.hpl.jena.ontology.Restriction> additionalRestrictions,
                        double score)

Method Detail

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,
                                            boolean includeAdditionalProperties,
                                            boolean keepObsoletes)

Description copied from interface: OntologyTerm

Obtain the children of this term via subclass relationships and possibly some additional properties.

Specified by:

getChildren in interface OntologyTerm

Parameters:

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

includeAdditionalProperties - include terms matched via additional properties

getComment

public String getComment()

Specified by:

getComment in interface OntologyTerm

getIndividuals

public Collection<OntologyIndividual> getIndividuals(boolean direct)

Specified by:

getIndividuals in interface OntologyTerm

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,
                                           boolean includeAdditionalProperties,
                                           boolean keepObsoletes)

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

isObsolete

public boolean isObsolete()

Description copied from interface: OntologyResource

Whether the resource is marked as obsolete.

Specified by:

isObsolete in interface OntologyResource

Overrides:

isObsolete 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