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

Class OboOntologyTermFetcher

java.lang.Object

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

psidev.psi.mi.jami.bridges.obo.OboOntologyTermFetcher

All Implemented Interfaces:

CvTermFetcher<OntologyTerm>, OntologyTermFetcher

public class OboOntologyTermFetcher
extends OboFetcherTemplate<OntologyTerm>
implements OntologyTermFetcher

The ontology fetcher based on OBO file

Since:

17/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
OboOntologyTermFetcher(String databaseName, String filePath)	Constructor for OboOntologyTermFetcher.
OboOntologyTermFetcher(CvTerm database, String filePath)	Constructor for OboOntologyTermFetcher.

Method Summary

Modifier and Type	Method	Description
Set<OntologyTerm>	fetchRootTerms(String database)	fetchRootTerms.
Set<OntologyTerm>	fetchRootTerms(CvTerm database)	fetchRootTerms.

Methods inherited from class psidev.psi.mi.jami.bridges.obo.OboFetcherTemplate

fetchByIdentifier, fetchByIdentifier, fetchByIdentifiers, fetchByIdentifiers, fetchByName, fetchByName, fetchByNames, fetchByNames, getId2Term, getName2Term, getOntologyDatabase, initialiseLocalMaps

Methods inherited from class java.lang.Object

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

Methods inherited from interface psidev.psi.mi.jami.bridges.fetcher.CvTermFetcher

fetchByIdentifier, fetchByIdentifier, fetchByIdentifiers, fetchByIdentifiers, fetchByName, fetchByName, fetchByNames, fetchByNames

Constructor Detail

OboOntologyTermFetcher

public OboOntologyTermFetcher(CvTerm database,
                              String filePath)

Constructor for OboOntologyTermFetcher.

Parameters:

database - a CvTerm object.

filePath - a String object.

OboOntologyTermFetcher

public OboOntologyTermFetcher(String databaseName,
                              String filePath)

Constructor for OboOntologyTermFetcher.

Parameters:

databaseName - a String object.

filePath - a String object.

Method Detail

fetchRootTerms

public Set<OntologyTerm> fetchRootTerms(String database)
                                 throws BridgeFailedException

fetchRootTerms.

Specified by:

fetchRootTerms in interface OntologyTermFetcher

Parameters:

database - : ontology database name

Returns:

a set of root terms for the ontology matching this database name

Throws:

BridgeFailedException - if any.

fetchRootTerms

public Set<OntologyTerm> fetchRootTerms(CvTerm database)
                                 throws BridgeFailedException

fetchRootTerms.

Specified by:

fetchRootTerms in interface OntologyTermFetcher

Parameters:

database - a CvTerm object.

Returns:

a Set object.

Throws:

BridgeFailedException - if any.