Package ubic.basecode.ontology.jena

Class AbstractOntologyMemoryBackedService

java.lang.Object

ubic.basecode.ontology.jena.AbstractOntologyService

ubic.basecode.ontology.jena.AbstractOntologyMemoryBackedService

All Implemented Interfaces:

OntologyService

Direct Known Subclasses:

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

public abstract class AbstractOntologyMemoryBackedService
extends AbstractOntologyService

This class has some stuff that's specific to in-memory ontologies. Unlike database backed ontologies we don't use a pool keeping only one instance of model in memory.

Author:

paul

Field Summary

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

log

Constructor Summary

Constructors

Constructor	Description
AbstractOntologyMemoryBackedService()

Method Summary

Modifier and Type	Method	Description
protected com.hp.hpl.jena.ontology.OntModel	loadModel()	Delegates the call as to load the model into memory or leave it on disk.
protected com.hp.hpl.jena.ontology.OntModel	loadModelFromStream(InputStream is)	Load a model from a given input stream.

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

cancelInitializationThread, closeIndex, findIndividuals, findResources, findTerm, findUsingAlternativeId, getAllURIs, getCacheName, getChildren, getOntologyName, getOntologyUrl, getParents, getResource, getTerm, getTermIndividuals, index, initialize, initialize, isEnabled, isInitializationThreadAlive, isInitializationThreadCancelled, isOntologyLoaded, loadTermsInNameSpace, 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

AbstractOntologyMemoryBackedService

public AbstractOntologyMemoryBackedService()

Method Detail

loadModel

protected com.hp.hpl.jena.ontology.OntModel loadModel()

Description copied from class: AbstractOntologyService

Delegates the call as to load the model into memory or leave it on disk. Simply delegates to either OntologyLoader.loadMemoryModel( url ); OR OntologyLoader.loadPersistentModel( url, spec );

Specified by:

loadModel in class AbstractOntologyService

loadModelFromStream

protected com.hp.hpl.jena.ontology.OntModel loadModelFromStream(InputStream is)

Description copied from class: AbstractOntologyService

Load a model from a given input stream.

Specified by:

loadModelFromStream in class AbstractOntologyService