Package psidev.psi.mi.jami.bridges.fetcher.mock

Class MockGeneFetcher

java.lang.Object

psidev.psi.mi.jami.bridges.fetcher.mock.AbstractMockFetcher<Collection<Gene>>

psidev.psi.mi.jami.bridges.fetcher.mock.MockGeneFetcher

All Implemented Interfaces:

GeneFetcher, InteractorFetcher<Gene>, MockFetcher<Collection<Gene>>

public class MockGeneFetcher
extends AbstractMockFetcher<Collection<Gene>>
implements GeneFetcher

A mock fetcher for testing. It extends all the methods of the true fetcher, but does not access an external service. Instead, it holds a map which can be loaded with objects and keys. which are then returned. It attempts to replicate the responses of the fetcher in most scenarios.

Since:

23/05/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from class psidev.psi.mi.jami.bridges.fetcher.mock.AbstractMockFetcher

localMap

Constructor Summary

Constructors

Constructor	Description
MockGeneFetcher()

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.
protected Collection<Gene>	getEntry(String identifier)	getEntry.

Methods inherited from class psidev.psi.mi.jami.bridges.fetcher.mock.AbstractMockFetcher

addEntry, clearEntries, removeEntry

Methods inherited from class java.lang.Object

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

Constructor Detail

MockGeneFetcher

public MockGeneFetcher()

Method Detail

getEntry

protected Collection<Gene> getEntry(String identifier)
                             throws BridgeFailedException

getEntry.

Overrides:

getEntry in class AbstractMockFetcher<Collection<Gene>>

Parameters:

identifier - a String object.

Returns:

a T object.

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

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.

fetchByIdentifier

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

fetchByIdentifier.

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,
                                           int taxID)
                                    throws BridgeFailedException

Description copied from interface: GeneFetcher

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.