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

Class FailingGeneFetcher

java.lang.Object

psidev.psi.mi.jami.bridges.fetcher.mock.AbstractMockFetcher<T>

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

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

All Implemented Interfaces:

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

public class FailingGeneFetcher
extends AbstractFailingFetcher<Collection<Gene>>
implements GeneFetcher

A mock fetcher for testing exceptions. It extends the functionality of the mock fetcher but can also throw exceptions. Upon initialisation, an integer is given which sets how many times a query is made before returning the result. If the current query matches the last query and the counter of the number of times is less than the maxQuery set at initialisation, then an exception will be thrown. Additionally, if the maxQuery is set to -1, the fetcher will always throw an exception.

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
FailingGeneFetcher(int maxQuery)	Constructor for FailingProteinFetcher.

Method Summary

Modifier and Type	Method	Description
void	addEntry(String identifier, Gene gene)	addEntry.
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.AbstractFailingFetcher

getEntries

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

FailingGeneFetcher

public FailingGeneFetcher(int maxQuery)

Constructor for FailingProteinFetcher.

Parameters:

maxQuery - a int.

Method Detail

getEntry

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

getEntry.

Used to retrieve an entry from the internal list. will throw exceptions if the required number of queries has not been made.

Overrides:

getEntry in class AbstractFailingFetcher<Collection<Gene>>

Parameters:

identifier - a String object.

Returns:

a T object.

Throws:

BridgeFailedException - if any.

addEntry

public void addEntry(String identifier,
                     Gene gene)

addEntry.

Parameters:

identifier - a String object.

gene - a Protein object.

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

Description copied from interface: GeneFetcher

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.