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

Class OlsOntologyTermFetcher

java.lang.Object

psidev.psi.mi.jami.bridges.ols.AbstractOlsFetcher<OntologyTerm>

psidev.psi.mi.jami.bridges.ols.OlsOntologyTermFetcher

All Implemented Interfaces:

CvTermFetcher<OntologyTerm>, OntologyTermFetcher

public class OlsOntologyTermFetcher
extends AbstractOlsFetcher<OntologyTerm>
implements OntologyTermFetcher

Finds ontology terms in the Ontology Lookup Service as well as having options to recursively find parents and or children.

Implements CvTermFetcher, returning the results as OntologyTerms. Further to this, the OntologyTermFetcher is implemented to include methods for finding children and parents.

Since:

03/07/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Field Summary

Fields inherited from class psidev.psi.mi.jami.bridges.ols.AbstractOlsFetcher

dbMap, olsClient

Constructor Summary

Constructors

Constructor	Description
OlsOntologyTermFetcher()	Constructor for OlsOntologyTermFetcher.

Method Summary

Modifier and Type	Method	Description
Set<OntologyTerm>	fetchRootTerms(String databaseName)	fetchRootTerms.
Set<OntologyTerm>	fetchRootTerms(CvTerm database)	fetchRootTerms.
protected OntologyTerm	instantiateCvTerm(String termName, Xref identity, String ontologyName)	instantiateCvTerm.

Methods inherited from class psidev.psi.mi.jami.bridges.ols.AbstractOlsFetcher

createXref, fetchByIdentifier, fetchByIdentifier, fetchByIdentifiers, fetchByIdentifiers, fetchByName, fetchByName, fetchByNames, fetchByNames, initialiseDbMap

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

OlsOntologyTermFetcher

public OlsOntologyTermFetcher()
                       throws BridgeFailedException

Constructor for OlsOntologyTermFetcher.

Throws:

BridgeFailedException - if any.

Method Detail

instantiateCvTerm

protected OntologyTerm instantiateCvTerm(String termName,
                                         Xref identity,
                                         String ontologyName)

instantiateCvTerm.

Specified by:

instantiateCvTerm in class AbstractOlsFetcher<OntologyTerm>

Parameters:

termName - a String object.

identity - a Xref object.

ontologyName - a String object.

Returns:

a T object.

fetchRootTerms

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

fetchRootTerms.

Specified by:

fetchRootTerms in interface OntologyTermFetcher

Parameters:

databaseName - : 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.