Package ubic.basecode.ontology.providers

Class AbstractBaseCodeOntologyService

java.lang.Object

ubic.basecode.ontology.providers.AbstractDelegatingOntologyService

ubic.basecode.ontology.providers.AbstractBaseCodeOntologyService

All Implemented Interfaces:

AutoCloseable, OntologyService

Direct Known Subclasses:

CellLineOntologyService, CellTypeOntologyService, ChebiOntologyService, DiseaseOntologyService, ExperimentalFactorOntologyService, FMAOntologyService, HumanDevelopmentOntologyService, HumanPhenotypeOntologyService, MammalianPhenotypeOntologyService, MouseDevelopmentOntologyService, ObiService, SequenceOntologyService, UberonOntologyService, UnitsOntologyService

public abstract class AbstractBaseCodeOntologyService
extends AbstractDelegatingOntologyService

Base class for all ontologies built-in to the baseCode project.

The ontologies that subclass this will honor settings in the basecode.properties file for loading and locating the ontology.

Author:

poirigui

Nested Class Summary

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

OntologyService.InferenceMode, OntologyService.LanguageLevel

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	AbstractBaseCodeOntologyService(String name, String cacheName)	Intentionally package-private constructor.
	AbstractBaseCodeOntologyService(String name, String url, boolean isEnabled, String cacheName)

Method Summary

Methods inherited from class ubic.basecode.ontology.providers.AbstractDelegatingOntologyService

cancelInitializationThread, close, 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, 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

AbstractBaseCodeOntologyService

protected AbstractBaseCodeOntologyService(String name,
                                          String cacheName)

Intentionally package-private constructor.

AbstractBaseCodeOntologyService

public AbstractBaseCodeOntologyService(String name,
                                       String url,
                                       boolean isEnabled,
                                       String cacheName)