MarkerFeature documentation.

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.

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

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

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

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

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

sub _marker_id {

  my $self = shift;

  if(@_) {
    $self->{'marker_id'} = shift;
  }

  return $self->{'marker_id'};

}

sub display_id {

  my $self = shift;
  my $marker = $self->{'marker'};

  return '' if(!$marker);
  my $ms = $marker->display_MarkerSynonym();
  return '' if(!$ms);
  return $ms->name() || '';
}


1;

}

sub map_weight {

  my $self = shift;

  if(@_) {
    $self->{'map_weight'} = shift;
  }

  return $self->{'map_weight'};

}

sub marker {

  my $self = shift;

  if(@_) {
    $self->{'marker'} = shift;
  } elsif(!$self->{'marker'} && $self->{'adaptor'} && $self->{'marker_id'}) {
    #lazy load the marker if it is not already loaded
    my $ma = $self->{'adaptor'}->db->get_MarkerAdaptor;
    $self->{'marker'} = $ma->fetch_by_dbID($self->{'marker_id'});
  }

  return $self->{'marker'};

}

sub new {

  my ($caller, $dbID, $adaptor, $start, $end, $slice, $analysis,
      $marker_id, $map_weight, $marker) = @_;

  my $class = ref($caller) || $caller;

  return bless( {
		 'dbID'        => $dbID,
		 'adaptor'     => $adaptor,
		 'start'       => $start,
		 'end'         => $end,
		 'strand'      => 0,
		 'slice'       => $slice,
		 'analysis'    => $analysis,
		 'marker_id'   => $marker_id,
		 'marker'      => $marker,
     'map_weight'  => $map_weight }, $class);

}

  Copyright (c) 1999-2009 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    /info/about/code_licence.html

  Please email comments or questions to the public Ensembl
  developers list at <ensembl-dev@ebi.ac.uk>.

  Questions may also be sent to the Ensembl help desk at
  <helpdesk@ensembl.org>.

_marker_id	Description	Code
display_id	Description	Code
map_weight	Description	Code
marker	Description	Code
new	Description	Code