Package ubic.basecode.ontology.simple

Class OntologyTermSimple

java.lang.Object

ubic.basecode.ontology.simple.AbstractOntologyResourceSimple

ubic.basecode.ontology.simple.OntologyTermSimple

All Implemented Interfaces:

Serializable, OntologyResource, OntologyTerm

public class OntologyTermSimple
extends AbstractOntologyResourceSimple
implements OntologyTerm

A light-weight version of OntologyTerms. Only supports a subset of the functionality of OntologyTermImpl (namely, it is missing the inference components)

Author:

Paul

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
OntologyTermSimple(@Nullable String uri, @Nullable String label)
OntologyTermSimple(@Nullable String uri, @Nullable String localName, @Nullable String label, @Nullable String comment, boolean isObsolete)

Method Summary

Modifier and Type	Method	Description
Collection<String>	getAlternativeIds()	Obtain alternative IDs for this term.
@Nullable AnnotationProperty	getAnnotation(String propertyUri)	Obtain an annotation by property URI.
Collection<AnnotationProperty>	getAnnotations()	Obtain all annotations for this term.
Collection<AnnotationProperty>	getAnnotations(String propertyUri)	Obtain all the annotations for a given property URI.
Collection<OntologyTerm>	getChildren(boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)	Obtain the children of this term via subclass relationships and possibly some additional properties.
@Nullable String	getComment()	A comment for the resource, if available, otherwise null.
Collection<OntologyIndividual>	getIndividuals(boolean direct)
Collection<OntologyTerm>	getParents(boolean direct, boolean includeAdditionalProperties, boolean keepObsoletes)
Collection<OntologyRestriction>	getRestrictions()
@Nullable 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boolean	isTermObsolete()	check to see if the term is obsolete, if it is it should not be used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.simple.AbstractOntologyResourceSimple

equals, getLabel, getLocalName, getUri, hashCode, unwrap

Methods inherited from class java.lang.Object

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

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

getLabel, getLocalName, getUri, unwrap

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

getChildren, getChildren, getIndividuals, getParents, getParents

Constructor Details

OntologyTermSimple

public OntologyTermSimple(@Nullable String uri,
 @Nullable String label)

OntologyTermSimple

public OntologyTermSimple(@Nullable String uri,
 @Nullable String localName,
 @Nullable String label,
 @Nullable String comment,
 boolean isObsolete)

Method Details

getAlternativeIds

public Collection<String> getAlternativeIds()

Description copied from interface: OntologyTerm

Obtain alternative IDs for this term.

Specified by:

getAlternativeIds in interface OntologyTerm

getAnnotations

public Collection<AnnotationProperty> getAnnotations()

Description copied from interface: OntologyTerm

Obtain all annotations for this term.

Specified by:

getAnnotations in interface OntologyTerm

getAnnotations

public Collection<AnnotationProperty> getAnnotations(String propertyUri)

Description copied from interface: OntologyTerm

Obtain all the annotations for a given property URI.

Specified by:

getAnnotations in interface OntologyTerm

getAnnotation

public @Nullable AnnotationProperty getAnnotation(String propertyUri)

Description copied from interface: OntologyTerm

Obtain an annotation by property URI.

Specified by:

getAnnotation 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 @Nullable String getComment()

Description copied from interface: OntologyResource

A comment for the resource, if available, otherwise null.

Specified by:

getComment in interface OntologyResource

getIndividuals

public Collection<OntologyIndividual> getIndividuals(boolean direct)

Specified by:

getIndividuals 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

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

getTerm

public @Nullable 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