LICENSE

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::MarkerFeature

SYNOPSIS

DESCRIPTION

Represents a marker feature in the EnsEMBL database. A marker feature is a marker which has been mapped to the genome by ePCR. Each marker has one marker feature per mapped location.

METHODS

new

  Arg [1]    : (optional) int $dbID
  Arg [2]    : (optional) Bio::EnsEMBL::Adaptor $adaptor
  Arg [3]    : (optional) int $start
  Arg [4]    : (optional) int $end
  Arg [5]    : (optional) Bio::EnsEMBL::Slice $slice
  Arg [6]    : (optional) Bio::EnsEMBL::Analysis
  Arg [7]    : (optional) int $marker_id
  Arg [8]    : (optional) int $map_weight
  Arg [9]    : (optional) Bio::EnsEMBL::Map::Marker $marker 
  Example    : $marker = Bio::EnsEMBL::Map::MarkerFeature->new(123, $adaptor,
                                                               100, 200, 
                                                               $ctg, 123);
  Description: Creates a new MarkerFeature
  Returntype : Bio::EnsEMBL::Map::MarkerFeature
  Exceptions : none
  Caller     : general
  Status     : stable

_marker_id

  Arg [1]    : (optional) int $marker_id
  Example    : none
  Description: PRIVATE Getter/Setter for the internal identifier of the marker
               associated with this marker feature
  Returntype : int
  Exceptions : none
  Caller     : internal
  Status     : stable

marker

  Arg [1]    : (optional) Bio::EnsEMBL::Map::Marker $marker
  Example    : $marker = $marker_feature->marker;
  Description: Getter/Setter for the marker associated with this marker feature
               If the marker has not been set and the database is available
               the marker will automatically be retrieved (lazy-loaded).
  Returntype : Bio::EnsEMBL::Map::Marker
  Exceptions : none
  Caller     : general
  Status     : stable

map_weight

  Arg [1]    : (optional) int $map_weight
  Example    : $map_weight = $marker_feature->map_weight;
  Description: Getter/Setter for the map weight of this marker.  This is the
               number of times that this marker has been mapped to the genome.
               E.g.  a marker iwth map weight 3 has been mapped to 3 locations
               in the genome.
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : stable

display_id

  Arg [1]    : none
  Example    : print $mf->display_id();
  Description: This method returns a string that is considered to be
               the 'display' identifier.  For marker features this is the
               name of the display synonym or '' if it is not defined.
  Returntype : string
  Exceptions : none
  Caller     : web drawing code
  Status     : stable