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

Class UniprotProteinFetcher

java.lang.Object

psidev.psi.mi.jami.bridges.uniprot.UniprotProteinFetcher

All Implemented Interfaces:

InteractorFetcher<Protein>, ProteinFetcher

public class UniprotProteinFetcher
extends Object
implements ProteinFetcher

Created with IntelliJ IDEA.

Since:

14/05/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
UniprotProteinFetcher()	Constructor for UniprotProteinFetcher.

Method Summary

Modifier and Type	Method	Description
Collection<Protein>	fetchByIdentifier(String identifier)	Takes a string identifier and returns the interactors which match.
Collection<Protein>	fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.
Map<uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType,CvTerm>	getSelectedDatabases()	Getter for the field selectedDatabases.
void	setSelectedDatabases(Map<uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType,CvTerm> selectedDatabases)	Setter for the field selectedDatabases.

Methods inherited from class java.lang.Object

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

Constructor Detail

UniprotProteinFetcher

public UniprotProteinFetcher()

Constructor for UniprotProteinFetcher.

Method Detail

getSelectedDatabases

public Map<uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType,CvTerm> getSelectedDatabases()

Getter for the field selectedDatabases.

Returns:

a Map object.

setSelectedDatabases

public void setSelectedDatabases(Map<uk.ac.ebi.kraken.interfaces.uniprot.DatabaseType,CvTerm> selectedDatabases)

Setter for the field selectedDatabases.

Parameters:

selectedDatabases - a Map object.

fetchByIdentifier

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

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

Takes the various type of uniprot protein identifier and uses the uniprotJAPI to retrieve the matching proteins.

Specified by:

fetchByIdentifier in interface InteractorFetcher<Protein>

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<Protein> 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.

Takes the various type of uniprot protein identifier and uses the uniprotJAPI to retrieve the matching proteins.

Specified by:

fetchByIdentifiers in interface InteractorFetcher<Protein>

Parameters:

identifiers - The identifiers to search for.

Returns:

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

Throws:

BridgeFailedException - if any.