Package psidev.psi.mi.jami.bridges.ontologymanager.impl.ols

Class MIOlsOntology

java.lang.Object

psidev.psi.mi.jami.bridges.ontologymanager.impl.AbstractMIOntologyAccess

psidev.psi.mi.jami.bridges.ontologymanager.impl.ols.MIOlsOntology

All Implemented Interfaces:

MIOntologyAccess, psidev.psi.tools.ontology_manager.interfaces.OntologyAccessTemplate<MIOntologyTermI>

public class MIOlsOntology
extends AbstractMIOntologyAccess

jami extension for OlsOntology

Since:

01/11/11

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static org.apache.commons.logging.Log	log	Constant log

Constructor Summary

Constructors

Constructor	Description
MIOlsOntology()	Constructor for MIOlsOntology.
MIOlsOntology(String dbName, String dbIdentifier, Pattern dbRegexp, String parent)	Constructor for MIOlsOntology.
MIOlsOntology(OntologyTermFetcher termBuilder)	Constructor for MIOlsOntology.
MIOlsOntology(OntologyTermFetcher termBuilder, String dbName, String dbIdentifier, Pattern dbRegexp, String parent)	Constructor for MIOlsOntology.

Method Summary

Modifier and Type	Method	Description
boolean	isOntologyUpToDate()	isOntologyUpToDate.
void	loadOntology(String ontologyID, String name, String version, String format, URI uri)

Methods inherited from class psidev.psi.mi.jami.bridges.ontologymanager.impl.AbstractMIOntologyAccess

createNewOntologyTerm, getAllChildren, getAllParents, getDatabaseIdentifier, getDatabaseName, getDatabaseRegexp, getDirectChildren, getDirectParents, getOntologyID, getOntologyTermFetcher, getParentFromOtherOntology, getRootTerms, getTermForAccession, getValidTerms, isObsolete, isUseTermSynonyms, setOntologyDirectory, setOntologyID, setOntologyTermFetcher, setUseTermSynonyms

Methods inherited from class java.lang.Object

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

Field Detail

log

public static final org.apache.commons.logging.Log log

Constant log

Constructor Detail

MIOlsOntology

public MIOlsOntology()
              throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

Constructor for MIOlsOntology.

Throws:

psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException - if any.

MIOlsOntology

public MIOlsOntology(OntologyTermFetcher termBuilder)
              throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

Constructor for MIOlsOntology.

Parameters:

termBuilder - a OntologyTermFetcher object.

Throws:

psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException - if any.

MIOlsOntology

public MIOlsOntology(String dbName,
                     String dbIdentifier,
                     Pattern dbRegexp,
                     String parent)
              throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

Constructor for MIOlsOntology.

Parameters:

dbName - a String object.

dbIdentifier - a String object.

dbRegexp - a Pattern object.

parent - a String object.

Throws:

psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException - if any.

MIOlsOntology

public MIOlsOntology(OntologyTermFetcher termBuilder,
                     String dbName,
                     String dbIdentifier,
                     Pattern dbRegexp,
                     String parent)
              throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

Constructor for MIOlsOntology.

Parameters:

termBuilder - a OntologyTermFetcher object.

dbName - a String object.

dbIdentifier - a String object.

dbRegexp - a Pattern object.

parent - a String object.

Throws:

psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException - if any.

Method Detail

loadOntology

public void loadOntology(String ontologyID,
                         String name,
                         String version,
                         String format,
                         URI uri)
                  throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

Specified by:

loadOntology in interface psidev.psi.tools.ontology_manager.interfaces.OntologyAccessTemplate<MIOntologyTermI>

Specified by:

loadOntology in class AbstractMIOntologyAccess

Throws:

psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

isOntologyUpToDate

public boolean isOntologyUpToDate()
                           throws psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException

isOntologyUpToDate.

Specified by:

isOntologyUpToDate in interface psidev.psi.tools.ontology_manager.interfaces.OntologyAccessTemplate<MIOntologyTermI>

Specified by:

isOntologyUpToDate in class AbstractMIOntologyAccess

Returns:

a boolean.

Throws:

psidev.psi.tools.ontology_manager.impl.local.OntologyLoaderException - if any.