Package psidev.psi.mi.jami.bridges.chebi

Class ChebiFetcher

java.lang.Object

psidev.psi.mi.jami.bridges.chebi.ChebiFetcher

All Implemented Interfaces:

BioactiveEntityFetcher, InteractorFetcher<BioactiveEntity>

public class ChebiFetcher
extends Object
implements BioactiveEntityFetcher

Accesses Chebi entries using the WSDL SOAP service.

Since:

07/08/13

Author:

Gabriel Aldam (galdam@ebi.ac.uk)

Field Summary

Fields

Modifier and Type	Field	Description
static String	CHEBI_POLYSACCHARYDE_PARENT	Constant CHEBI_POLYSACCHARYDE_PARENT="CHEBI:18154"

Constructor Summary

Constructors

Constructor	Description
ChebiFetcher()	Constructor for ChebiFetcher.

Method Summary

Modifier and Type	Method	Description
Collection<BioactiveEntity>	fetchByIdentifier(String identifier)	Searches Chebi for an entry matching the identifier.
Collection<BioactiveEntity>	fetchByIdentifiers(Collection<String> identifiers)	Takes a collection of string identifiers and returns the interactors which match.

Methods inherited from class java.lang.Object

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

Field Detail

CHEBI_POLYSACCHARYDE_PARENT

public static final String CHEBI_POLYSACCHARYDE_PARENT

Constant CHEBI_POLYSACCHARYDE_PARENT="CHEBI:18154"

See Also:

Constant Field Values

Constructor Detail

ChebiFetcher

public ChebiFetcher()

Constructor for ChebiFetcher.

Method Detail

fetchByIdentifier

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

Searches Chebi for an entry matching the identifier. If it's found, the record is used to create a bioactiveEntity with: ChebiAsciiName = Full name, Short name with Inchi, InchiKey, Smile, ChebiId matched to the corresponding fields.

Specified by:

fetchByIdentifier in interface InteractorFetcher<BioactiveEntity>

Parameters:

identifier - The identifier of the CHEBI entry to find.

Returns:

A completed bioactiveEntity for the given identifier. May be null.

Throws:

BridgeFailedException - Thrown if the fetcher encounters a problem.

fetchByIdentifiers

public Collection<BioactiveEntity> 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<BioactiveEntity>

Parameters:

identifiers - The identifiers to search for.

Returns:

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

Throws:

BridgeFailedException - if any.