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

Class MILocalOntology

java.lang.Object

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

psidev.psi.mi.jami.bridges.ontologymanager.impl.local.MILocalOntology

All Implemented Interfaces:

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

public class MILocalOntology
extends AbstractMIOntologyAccess

JAMI implementation of LocalOntology access

Since:

08/11/11

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

Method Summary

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

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, setOntologyDirectory, setOntologyID, setOntologyTermFetcher

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

MILocalOntology

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

Constructor for MILocalOntology.

Throws:

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

MILocalOntology

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

Constructor for MILocalOntology.

Parameters:

termBuilder - a OntologyTermFetcher object.

Throws:

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

MILocalOntology

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

Constructor for MILocalOntology.

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.

MILocalOntology

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

Constructor for MILocalOntology.

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.

isUseTermSynonyms

public boolean isUseTermSynonyms()

isUseTermSynonyms.

Specified by:

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

Overrides:

isUseTermSynonyms in class AbstractMIOntologyAccess

Returns:

a boolean.

setUseTermSynonyms

public void setUseTermSynonyms(boolean useTermSynonyms)

Specified by:

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

Overrides:

setUseTermSynonyms in class AbstractMIOntologyAccess