Package psidev.psi.mi.jami.bridges.uniprot

Class UniprotGeneFetcher

java.lang.Object

psidev.psi.mi.jami.bridges.uniprot.UniprotGeneFetcher

All Implemented Interfaces:

GeneFetcher, InteractorFetcher<Gene>

Direct Known Subclasses:

CachedUniprotGeneFetcher

public class UniprotGeneFetcher
extends Object
implements GeneFetcher

Created with IntelliJ IDEA.

Since:

22/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
UniprotGeneFetcher()	Constructor for UniprotGeneFetcher.

Method Summary

Modifier and Type	Method	Description
Collection<Gene>	fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Gene>	fetchByIdentifier(String identifier, int taxID)	fetchByIdentifier.
Collection<Gene>	fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Collection<Gene>	fetchByIdentifiers(Collection<String> identifiers, int taxID)	fetchByIdentifiers.

Methods inherited from class java.lang.Object

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

Constructor Detail

UniprotGeneFetcher

public UniprotGeneFetcher()

Constructor for UniprotGeneFetcher.

Method Detail

fetchByIdentifier

public Collection<Gene> fetchByIdentifier(String identifier,
                                          int taxID)
                                   throws BridgeFailedException

fetchByIdentifier.

Finds a gene in uniprot using with the ensembl ID, the refseq ID or the ensemblGenomes ID. The organism is optional, a taxid of 0 or less

Specified by:

fetchByIdentifier in interface GeneFetcher

Parameters:

identifier - The identifier of the gene

taxID - The organism the gene is from.

Returns:

The genes matching the search terms.

Throws:

BridgeFailedException - if any.

fetchByIdentifiers

public Collection<Gene> fetchByIdentifiers(Collection<String> identifiers)
                                    throws BridgeFailedException

Takes a collection of string identifiers and returns the interactors which match. Returns an empty collection of no entries are returned.

Specified by:

fetchByIdentifiers in interface InteractorFetcher<Gene>

Parameters:

identifiers - The identifiers to search for.

Returns:

The proteins which match the search term. Empty if no matches.

Throws:

BridgeFailedException - if any.

fetchByIdentifiers

public Collection<Gene> fetchByIdentifiers(Collection<String> identifiers,
                                           int taxID)
                                    throws BridgeFailedException

fetchByIdentifiers.

Specified by:

fetchByIdentifiers in interface GeneFetcher

Parameters:

identifiers - The identifiers of the gene

taxID - The organism the gene is from.

Returns:

The genes matching the search terms.

Throws:

BridgeFailedException - if any.

fetchByIdentifier

public Collection<Gene> fetchByIdentifier(String identifier)
                                   throws BridgeFailedException

Takes a string identifier and returns the interactors which match. Returns an empty collection of no entries are returned

Specified by:

fetchByIdentifier in interface InteractorFetcher<Gene>

Parameters:

identifier - The identifier to search for.

Returns:

The proteins which match the search term. Empty if no matches.

Throws:

BridgeFailedException - A problem has been encountered when contacting the service