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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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     http://www.apache.org/licenses/LICENSE-2.0

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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