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, MedicOntologyService, 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

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
AbstractOntologyMemoryBackedService()

Method Summary

Modifier and Type	Method	Description
protected String	getOntologyUrl()	Defines the location of the ontology eg: MGED
protected OntologyModel	loadModel(boolean processImports, OntologyService.LanguageLevel languageLevel, OntologyService.InferenceMode inferenceMode)	Delegates the call as to load the model into memory or leave it on disk.
protected OntologyModel	loadModelFromStream(InputStream is, boolean processImports, OntologyService.LanguageLevel languageLevel, OntologyService.InferenceMode inferenceMode)	Load a model from a given input stream.

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

cancelInitializationThread, findIndividuals, findResources, findTerm, findUsingAlternativeId, getAdditionalPropertyUris, getAllURIs, getCacheName, getChildren, getDescription, getInferenceMode, getLanguageLevel, getName, getOntologyName, getParents, getProcessImports, getResource, getTerm, getTermIndividuals, index, initialize, initialize, isEnabled, isInitializationThreadAlive, isInitializationThreadCancelled, isOntologyLoaded, isSearchEnabled, loadTermsInNameSpace, setAdditionalPropertyUris, 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

AbstractOntologyMemoryBackedService

public AbstractOntologyMemoryBackedService()

Method Detail

getOntologyUrl

protected String getOntologyUrl()

Description copied from class: AbstractOntologyService

Defines the location of the ontology eg: MGED

Specified by:

getOntologyUrl in class AbstractOntologyService

loadModel

protected OntologyModel loadModel(boolean processImports,
                                  OntologyService.LanguageLevel languageLevel,
                                  OntologyService.InferenceMode inferenceMode)
                           throws IOException

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

Throws:

IOException

loadModelFromStream

protected OntologyModel loadModelFromStream(InputStream is,
                                            boolean processImports,
                                            OntologyService.LanguageLevel languageLevel,
                                            OntologyService.InferenceMode inferenceMode)
                                     throws IOException

Description copied from class: AbstractOntologyService

Load a model from a given input stream.

Specified by:

loadModelFromStream in class AbstractOntologyService

Throws:

IOException