Package psidev.psi.mi.jami.bridges.obo

Class OboFetcherTemplate<T extends CvTerm>

java.lang.Object

psidev.psi.mi.jami.bridges.obo.OboFetcherTemplate<T>

All Implemented Interfaces:

CvTermFetcher<T>

Direct Known Subclasses:

OboCvTermFetcher, OboOntologyTermFetcher, OboSourceFetcher

public class OboFetcherTemplate<T extends CvTerm>
extends Object
implements CvTermFetcher<T>

Template fetcher for OBO files

Since:

17/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
OboFetcherTemplate(String databaseName, AbstractOboLoader<T> oboLoader, String filePath)	Constructor for OboFetcherTemplate.
OboFetcherTemplate(CvTerm database, AbstractOboLoader<T> oboLoader, String filePath)	Constructor for OboFetcherTemplate.

Method Summary

Modifier and Type	Method	Description
T	fetchByIdentifier(String termIdentifier, String ontologyDatabaseName)	Uses the identifier and the name of the database to search for a complete form of the cvTerm.
T	fetchByIdentifier(String termIdentifier, CvTerm ontologyDatabase)	fetchByIdentifier.
Collection<T>	fetchByIdentifiers(Collection<String> termIdentifiers, String ontologyDatabaseName)	fetchByIdentifiers.
Collection<T>	fetchByIdentifiers(Collection<String> termIdentifiers, CvTerm ontologyDatabase)	Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.
Collection<T>	fetchByName(String searchName)	Uses the name of the term and the name of the database to search for a complete form of the term.
T	fetchByName(String searchName, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
Collection<T>	fetchByNames(Collection<String> searchNames)	Finds the CvTerms which match the exact names provided.
Collection<T>	fetchByNames(Collection<String> searchNames, String ontologyDatabaseName)	Uses the name of the term and the name of the database to search for a complete form of the term.
protected Map<String,T>	getId2Term()	Getter for the field id2Term.
protected Map<String,T>	getName2Term()	Getter for the field name2Term.
protected CvTerm	getOntologyDatabase()	Getter for the field ontologyDatabase.
protected void	initialiseLocalMaps()	initialiseLocalMaps.

Methods inherited from class java.lang.Object

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

Constructor Detail

OboFetcherTemplate

public OboFetcherTemplate(CvTerm database,
                          AbstractOboLoader<T> oboLoader,
                          String filePath)

Constructor for OboFetcherTemplate.

Parameters:

database - a CvTerm object.

oboLoader - a AbstractOboLoader object.

filePath - a String object.

OboFetcherTemplate

public OboFetcherTemplate(String databaseName,
                          AbstractOboLoader<T> oboLoader,
                          String filePath)

Constructor for OboFetcherTemplate.

Parameters:

databaseName - a String object.

oboLoader - a AbstractOboLoader object.

filePath - a String object.

Method Detail

fetchByIdentifier

public T fetchByIdentifier(String termIdentifier,
                           String ontologyDatabaseName)
                    throws BridgeFailedException

Uses the identifier and the name of the database to search for a complete form of the cvTerm.

Specified by:

fetchByIdentifier in interface CvTermFetcher<T extends CvTerm>

Parameters:

termIdentifier - The identifier for the CvTerm to fetch.

ontologyDatabaseName - The name of the ontology to search for. Eg, psi-mi, psi-mod, go. Must not be Null.

Returns:

A full cvTerm which matches the search term or null if one cannot be found.

Throws:

BridgeFailedException - if any.

fetchByIdentifier

public T fetchByIdentifier(String termIdentifier,
                           CvTerm ontologyDatabase)
                    throws BridgeFailedException

fetchByIdentifier.

Specified by:

fetchByIdentifier in interface CvTermFetcher<T extends CvTerm>

Parameters:

termIdentifier - a String object.

ontologyDatabase - a CvTerm object.

Returns:

a T object.

Throws:

BridgeFailedException - if any.

fetchByName

public T fetchByName(String searchName,
                     String ontologyDatabaseName)
              throws BridgeFailedException

Uses the name of the term and the name of the database to search for a complete form of the term.

Specified by:

fetchByName in interface CvTermFetcher<T extends CvTerm>

Parameters:

searchName - A full or short name for the term to be searched for.

ontologyDatabaseName - The ontology to search for the term in.

Returns:

A fully enriched cvTerm which matches the search term or null if one cannot be found.

Throws:

BridgeFailedException - if any.

fetchByName

public Collection<T> fetchByName(String searchName)
                          throws BridgeFailedException

Uses the name of the term and the name of the database to search for a complete form of the term.

If the term can not be resolved to a database, then this method may return null.

Specified by:

fetchByName in interface CvTermFetcher<T extends CvTerm>

Parameters:

searchName - A full or short name for the term to be searched for.

Returns:

A fully enriched cvTerm which matches the search term or null if one cannot be found.

Throws:

BridgeFailedException - if any.

fetchByIdentifiers

public Collection<T> fetchByIdentifiers(Collection<String> termIdentifiers,
                                        String ontologyDatabaseName)
                                 throws BridgeFailedException

fetchByIdentifiers.

Specified by:

fetchByIdentifiers in interface CvTermFetcher<T extends CvTerm>

Parameters:

termIdentifiers - a Collection object.

ontologyDatabaseName - a String object.

Returns:

a Collection object.

Throws:

BridgeFailedException - if any.

fetchByIdentifiers

public Collection<T> fetchByIdentifiers(Collection<String> termIdentifiers,
                                        CvTerm ontologyDatabase)
                                 throws BridgeFailedException

Uses the identifier and a cvTerm denoting the database to search to fetch a complete from of the term.

Specified by:

fetchByIdentifiers in interface CvTermFetcher<T extends CvTerm>

Parameters:

termIdentifiers - The identifier for the CvTerms to fetch.

ontologyDatabase - The name of the ontology to search for the terms in.

Returns:

A fully enriched cvTerm which matches the search term or null if one cannot be found.

Throws:

BridgeFailedException - if any.

fetchByNames

public Collection<T> fetchByNames(Collection<String> searchNames,
                                  String ontologyDatabaseName)
                           throws BridgeFailedException

Uses the name of the term and the name of the database to search for a complete form of the term.

Specified by:

fetchByNames in interface CvTermFetcher<T extends CvTerm>

Parameters:

searchNames - A full or short name for the term to be searched for.

ontologyDatabaseName - The name of the database to search for the names in.

Returns:

A fully enriched cvTerm which matches the search term or null if one cannot be found.

Throws:

BridgeFailedException - if any.

fetchByNames

public Collection<T> fetchByNames(Collection<String> searchNames)
                           throws BridgeFailedException

Finds the CvTerms which match the exact names provided.

If the a term found by the search can not be resolved to a database, this method may return null.

Specified by:

fetchByNames in interface CvTermFetcher<T extends CvTerm>

Parameters:

searchNames - A collection full or short names for the term to be searched for.

Returns:

A collection of cvTerms which matched a search term.

Throws:

BridgeFailedException - if any.

initialiseLocalMaps

protected void initialiseLocalMaps()

initialiseLocalMaps.

getId2Term

protected Map<String,T> getId2Term()

Getter for the field id2Term.

Returns:

a Map object.

getName2Term

protected Map<String,T> getName2Term()

Getter for the field name2Term.

Returns:

a Map object.

getOntologyDatabase

protected CvTerm getOntologyDatabase()

Getter for the field ontologyDatabase.

Returns:

a CvTerm object.