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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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NAME

Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor

SYNOPSIS

DESCRIPTION

Provides database interaction for the Bio::EnsEMBL::Map::Marker object

METHODS

fetch_all

Arg [1]    : none
Example    : @all_markers = @{$marker_adaptor->fetch_all};
Description: Retrieves all markers from the database
Returntype : listref of Bio::EnsEMBL::Map::Markers
Exceptions : none
Caller     : general
Status     : stable

fetch_by_dbID

Arg [1]    : int $dbID
             The internal identifier of the Marker to retrieve
Example    : $marker = $marker_adaptor->fetch_by_dbID(123);
Description: Retrieves a marker object from the database via its internal
             identifier.
Returntype : Bio::EnsEMBL::Map::Marker
Exceptions : thrown if no marker with $dbID is present in the database
Caller     : general
Status     : stable

fetch_all_by_synonym

Arg [1]    : string $synonym
             An name of this marker
Arg [2]    : (opional) string $source
             The source of this name
Example    : @markers = @{$marker_adaptor->fetch_all_by_synonym($id)};
Description: Retrieves a list of markers with the synonym (alias) $synonym
             and from source $source.  In most cases the list will have a 
             single element, however it is possible that multiple markers 
             with the same synonym exist.
Returntype : listref of Bio::EnsEMBL::Map::Markers
Exceptions : none
Caller     : general
Status     : stable

fetch_attributes

Arg [1]    : Bio::EnsEMBL::Map::Marker $marker
Example    : $marker_adaptor->fetch_attributes($marker);
Description: Fetches the marker_synonym and map_location attributes of
             a marker.  This is done so that these attributes can be
             lazy-loaded on request. 
Returntype : none
Exceptions : none
Caller     : Bio::EnsEMBL::Map::Marker::marker
Status     : stable

store

Arg [1]    : Bio::EnsEMBL::Map::Marker
Example    : $marker_adaptor->store(@markers);
Description: Stores a list of markers in this database.
             The dbID and adaptor of each marker will be set on successful
             storing.
Returntype : 1 on success
Exceptions : thrown if not all data needed for storing is populated in the
             marker
Caller     : general
Status     : stable

_store_MarkerSynonym

Arg [1]    : Bio::EnsEMBL::Map::Marker
Arg [2]    : Bio::EnsEMBL::Map::MarkerSynonym
Example    : $marker_adaptor->_store_MarkerSynonym($marker,$ms);
Description: Stores a marker synonym attached to the marker in the database
             The dbID of each MarkerSynonym will be set on successful
             storing.
Returntype : dbID of the MarkerSynonym
Exceptions : thrown if not all data needed for storing is populated
Caller     : $self->store
Status     : stable