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

Class AbstractMIOntologyAccess

java.lang.Object

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

All Implemented Interfaces:

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

Direct Known Subclasses:

MILocalOntology, MIOlsOntology

public abstract class AbstractMIOntologyAccess
extends Object
implements MIOntologyAccess

abstract class for OntologyAccess

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

Method Summary

Modifier and Type	Method	Description
protected MIOntologyTermI	createNewOntologyTerm(String identifier, String name)	createNewOntologyTerm.
Set<MIOntologyTermI>	getAllChildren(MIOntologyTermI term)	getAllChildren.
Set<MIOntologyTermI>	getAllParents(MIOntologyTermI term)	getAllParents.
String	getDatabaseIdentifier()	Getter for the field databaseIdentifier.
String	getDatabaseName()	Getter for the field databaseName.
Pattern	getDatabaseRegexp()	Getter for the field databaseRegexp.
Set<MIOntologyTermI>	getDirectChildren(MIOntologyTermI term)	getDirectChildren.
Set<MIOntologyTermI>	getDirectParents(MIOntologyTermI term)	getDirectParents.
String	getOntologyID()	Getter for the field ontologyID.
OntologyTermFetcher	getOntologyTermFetcher()	getOntologyTermFetcher.
String	getParentFromOtherOntology()	getParentFromOtherOntology.
Collection<MIOntologyTermI>	getRootTerms()	getRootTerms.
MIOntologyTermI	getTermForAccession(String accession)
Set<MIOntologyTermI>	getValidTerms(String accession, boolean allowChildren, boolean useTerm)	Method that is used by the validator to determine a Set of Ontology terms that are valid terms for a particular rule.
boolean	isObsolete(MIOntologyTermI term)	isObsolete.
abstract boolean	isOntologyUpToDate()	isOntologyUpToDate.
boolean	isUseTermSynonyms()	isUseTermSynonyms.
abstract void	loadOntology(String ontologyID, String name, String version, String format, URI uri)
void	setOntologyDirectory(File directory)
protected void	setOntologyID(String ontologyID)	Setter for the field ontologyID.
protected void	setOntologyTermFetcher(OntologyTermFetcher termFetcher)	setOntologyTermFetcher.
void	setUseTermSynonyms(boolean useTermSynonyms)

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

AbstractMIOntologyAccess

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

Constructor for AbstractMIOntologyAccess.

Throws:

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

AbstractMIOntologyAccess

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

Constructor for AbstractMIOntologyAccess.

Parameters:

termBuilder - a OntologyTermFetcher object.

Throws:

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

AbstractMIOntologyAccess

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

Constructor for AbstractMIOntologyAccess.

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.

AbstractMIOntologyAccess

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

Constructor for AbstractMIOntologyAccess.

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

createNewOntologyTerm

protected MIOntologyTermI createNewOntologyTerm(String identifier,
                                                String name)
                                         throws BridgeFailedException

createNewOntologyTerm.

Parameters:

identifier - a String object.

name - a String object.

Returns:

a MIOntologyTermI object.

Throws:

BridgeFailedException - if any.

getOntologyID

public String getOntologyID()

Getter for the field ontologyID.

Specified by:

getOntologyID in interface MIOntologyAccess

Returns:

a String object.

getDatabaseIdentifier

public String getDatabaseIdentifier()

Getter for the field databaseIdentifier.

Specified by:

getDatabaseIdentifier in interface MIOntologyAccess

Returns:

a String object.

getParentFromOtherOntology

public String getParentFromOtherOntology()

getParentFromOtherOntology.

Specified by:

getParentFromOtherOntology in interface MIOntologyAccess

Returns:

a String object.

getRootTerms

public Collection<MIOntologyTermI> getRootTerms()

getRootTerms.

Specified by:

getRootTerms in interface MIOntologyAccess

Returns:

a Collection object.

getDatabaseRegexp

public Pattern getDatabaseRegexp()

Getter for the field databaseRegexp.

Specified by:

getDatabaseRegexp in interface MIOntologyAccess

Returns:

a Pattern object.

getOntologyTermFetcher

public OntologyTermFetcher getOntologyTermFetcher()

getOntologyTermFetcher.

Specified by:

getOntologyTermFetcher in interface MIOntologyAccess

Returns:

a OntologyTermFetcher object.

loadOntology

public abstract 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>

Throws:

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

setOntologyDirectory

public void setOntologyDirectory(File directory)

Specified by:

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

getValidTerms

public Set<MIOntologyTermI> getValidTerms(String accession,
                                          boolean allowChildren,
                                          boolean useTerm)

Method that is used by the validator to determine a Set of Ontology terms that are valid terms for a particular rule. E.g. according to the flags, this can be the term corresponding to the provided accession or its children or both.

Specified by:

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

getTermForAccession

public MIOntologyTermI getTermForAccession(String accession)

Specified by:

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

isObsolete

public boolean isObsolete(MIOntologyTermI term)

isObsolete.

Specified by:

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

Parameters:

term - a MIOntologyTermI object.

Returns:

a boolean.

getDirectParents

public Set<MIOntologyTermI> getDirectParents(MIOntologyTermI term)

getDirectParents.

Specified by:

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

Parameters:

term - a MIOntologyTermI object.

Returns:

a Set object.

getDirectChildren

public Set<MIOntologyTermI> getDirectChildren(MIOntologyTermI term)

getDirectChildren.

Specified by:

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

Parameters:

term - a MIOntologyTermI object.

Returns:

a Set object.

getAllParents

public Set<MIOntologyTermI> getAllParents(MIOntologyTermI term)

getAllParents.

Specified by:

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

Parameters:

term - a MIOntologyTermI object.

Returns:

a Set object.

getAllChildren

public Set<MIOntologyTermI> getAllChildren(MIOntologyTermI term)

getAllChildren.

Specified by:

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

Parameters:

term - a MIOntologyTermI object.

Returns:

a Set object.

isOntologyUpToDate

public abstract 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>

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>

Returns:

a boolean.

setUseTermSynonyms

public void setUseTermSynonyms(boolean useTermSynonyms)

Specified by:

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

getDatabaseName

public String getDatabaseName()

Getter for the field databaseName.

Specified by:

getDatabaseName in interface MIOntologyAccess

Returns:

a String object.

setOntologyID

protected void setOntologyID(String ontologyID)

Setter for the field ontologyID.

Parameters:

ontologyID - a String object.

setOntologyTermFetcher

protected void setOntologyTermFetcher(OntologyTermFetcher termFetcher)

setOntologyTermFetcher.

Parameters:

termFetcher - a OntologyTermFetcher object.