Package ubic.basecode.ontology.providers

Class GenericOntologyService

java.lang.Object

ubic.basecode.ontology.jena.AbstractOntologyService

ubic.basecode.ontology.providers.AbstractOntologyService

ubic.basecode.ontology.providers.GenericOntologyService

All Implemented Interfaces:

OntologyService

public class GenericOntologyService
extends AbstractOntologyService

A way to create ad-hoc in-memory ontology services.

Author:

Paul

Nested Class Summary

Nested classes/interfaces inherited from interface ubic.basecode.ontology.providers.OntologyService

OntologyService.InferenceMode, OntologyService.LanguageLevel

Field Summary

Fields inherited from class ubic.basecode.ontology.jena.AbstractOntologyService

log

Constructor Summary

Constructors

Constructor	Description
GenericOntologyService(String name, String url)
GenericOntologyService(String name, String url, boolean cache)	Deprecated. use GenericOntologyService(String, String, String) with an explicit cache name instead
GenericOntologyService(String name, String url, boolean cache, boolean processImports)	Deprecated. use GenericOntologyService(String, String, String) with an explicit cache name instead and AbstractOntologyService.setProcessImports(boolean)
GenericOntologyService(String name, String url, String cacheName)

Method Summary

Modifier and Type	Method	Description
protected String	getCacheName()	A name for caching this ontology, or null to disable caching.
protected String	getOntologyName()	The simple getOntologyName() of the ontology.
protected String	getOntologyUrl()	Defines the location of the ontology eg: MGED
protected boolean	isOntologyEnabled()	Indicate if this ontology is enabled.

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

cancelInitializationThread, findIndividuals, findResources, findTerm, findUsingAlternativeId, getAdditionalPropertyUris, getAllURIs, getChildren, getDescription, getExcludedWordsFromStemming, getInferenceMode, getLanguageLevel, getName, getParents, getProcessImports, getResource, getTerm, getTermIndividuals, index, initialize, initialize, isEnabled, isInitializationThreadAlive, isInitializationThreadCancelled, isOntologyLoaded, isSearchEnabled, loadModel, loadModelFromStream, loadTermsInNameSpace, setAdditionalPropertyUris, setExcludedWordsFromStemming, setInferenceMode, setLanguageLevel, setProcessImports, setSearchEnabled, startInitializationThread, toString, waitForInitializationThread

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface ubic.basecode.ontology.providers.OntologyService

findIndividuals, findResources, findTerm, getChildren, getParents

Constructor Detail

GenericOntologyService

public GenericOntologyService(String name,
                              String url,
                              @Nullable
                              String cacheName)

GenericOntologyService

public GenericOntologyService(String name,
                              String url)

GenericOntologyService

@Deprecated
public GenericOntologyService(String name,
                              String url,
                              boolean cache)

Deprecated.

use GenericOntologyService(String, String, String) with an explicit cache name instead

GenericOntologyService

@Deprecated
public GenericOntologyService(String name,
                              String url,
                              boolean cache,
                              boolean processImports)

Deprecated.

use GenericOntologyService(String, String, String) with an explicit cache name instead and AbstractOntologyService.setProcessImports(boolean)

Method Detail

getOntologyName

protected String getOntologyName()

Description copied from class: AbstractOntologyService

The simple getOntologyName() of the ontology. Used for indexing purposes. (ie this will determine the getOntologyName() of the underlying index for searching the ontology)

Specified by:

getOntologyName in class AbstractOntologyService

getOntologyUrl

protected String getOntologyUrl()

Description copied from class: AbstractOntologyService

Defines the location of the ontology eg: MGED

Specified by:

getOntologyUrl in class AbstractOntologyService

isOntologyEnabled

protected boolean isOntologyEnabled()

Description copied from class: AbstractOntologyService

Indicate if this ontology is enabled.

Specified by:

isOntologyEnabled in class AbstractOntologyService

getCacheName

@Nullable
protected String getCacheName()

Description copied from class: AbstractOntologyService

A name for caching this ontology, or null to disable caching.

Note that if null is returned, the ontology will not have full-text search capabilities.

Specified by:

getCacheName in class AbstractOntologyService