ubic.basecode.ontology.model

Class OntologyTermSimple

java.lang.Object

ubic.basecode.ontology.model.AbstractOntologyResource

ubic.basecode.ontology.model.OntologyTermImpl

ubic.basecode.ontology.model.OntologyTermSimple

All Implemented Interfaces:

Serializable, Comparable<OntologyResource>, OntologyResource, OntologyTerm

public class OntologyTermSimple
extends OntologyTermImpl

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

Field Summary

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

log

Constructor Summary

Constructors

Constructor and Description
OntologyTermSimple(com.hp.hpl.jena.ontology.OntClass resource)
OntologyTermSimple(String uri, String term)
OntologyTermSimple(String uri, String term, String description, boolean isObsolete)

Method Summary

Modifier and Type	Method and Description
boolean	equals(Object obj)
Collection<String>	getAlternativeIds()
Collection<AnnotationProperty>	getAnnotations()
Collection<OntologyTerm>	getChildren(boolean direct)
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<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boolean	isTermObsolete() check to see if the term is obsolete, if it is it should not be used

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

fromOntClass, 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

OntologyTermSimple

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

OntologyTermSimple

public OntologyTermSimple(String uri,
                          String term)

OntologyTermSimple

public OntologyTermSimple(String uri,
                          String term,
                          String description,
                          boolean isObsolete)

Method Detail

equals

public boolean equals(Object obj)

Overrides:

equals in class OntologyTermImpl

getAlternativeIds

public Collection<String> getAlternativeIds()

Specified by:

getAlternativeIds in interface OntologyTerm

Overrides:

getAlternativeIds in class OntologyTermImpl

getAnnotations

public Collection<AnnotationProperty> getAnnotations()

Specified by:

getAnnotations in interface OntologyTerm

Overrides:

getAnnotations in class OntologyTermImpl

getChildren

public Collection<OntologyTerm> getChildren(boolean direct)

Specified by:

getChildren in interface OntologyTerm

Overrides:

getChildren in class OntologyTermImpl

Parameters:

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

Returns:

getComment

public String getComment()

Specified by:

getComment in interface OntologyTerm

Overrides:

getComment in class OntologyTermImpl

getIndividuals

public Collection<OntologyIndividual> getIndividuals()

Specified by:

getIndividuals in interface OntologyTerm

Overrides:

getIndividuals in class OntologyTermImpl

getIndividuals

public Collection<OntologyIndividual> getIndividuals(boolean direct)

Specified by:

getIndividuals in interface OntologyTerm

Overrides:

getIndividuals in class OntologyTermImpl

getLabel

public String getLabel()

Specified by:

getLabel in interface OntologyResource

Overrides:

getLabel in class OntologyTermImpl

getLocalName

public String getLocalName()

Specified by:

getLocalName in interface OntologyTerm

Overrides:

getLocalName in class OntologyTermImpl

getModel

public Object getModel()

Specified by:

getModel in interface OntologyTerm

Overrides:

getModel in class OntologyTermImpl

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

Overrides:

getParents in class OntologyTermImpl

Returns:

getRestrictions

public Collection<OntologyRestriction> getRestrictions()

Specified by:

getRestrictions in interface OntologyTerm

Overrides:

getRestrictions in class OntologyTermImpl

getTerm

public String getTerm()

Specified by:

getTerm in interface OntologyTerm

Overrides:

getTerm in class OntologyTermImpl

getUri

public String getUri()

Specified by:

getUri in interface OntologyResource

Specified by:

getUri in interface OntologyTerm

Overrides:

getUri in class OntologyTermImpl

hashCode

public int hashCode()

Overrides:

hashCode in class OntologyTermImpl

isRoot

public boolean isRoot()

Specified by:

isRoot in interface OntologyTerm

Overrides:

isRoot in class OntologyTermImpl

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

Overrides:

isTermObsolete in class OntologyTermImpl