Bio::EnsEMBL::Map::MarkerFeature Class Reference

Inheritance diagram for Bio::EnsEMBL::Map::MarkerFeature:

Public Member Functions
public Bio::EnsEMBL::Map::MarkerFeature	new ()
protected Int	_marker_id ()
public Bio::EnsEMBL::Map::Marker	marker ()
public Int	map_weight ()
public String	display_id ()
Public Member Functions inherited from Bio::EnsEMBL::Feature
public Bio::EnsEMBL::Feature	new ()
public Int	start ()
public Int	end ()
public Int	strand ()
public void	move ()
public Int	length ()
public Bio::EnsEMBL::Analysis	analysis ()
public Bio::EnsEMBL::Slice	slice ()
public Boolean Or Undef	equals ()
public Bio::EnsEMBL::Feature	transform ()
public Bio::EnsEMBL::Feature	transfer ()
public Listref	project_to_slice ()
public Listref	project ()
public String	seqname ()
public String	display_id ()
public String	version ()
public Bio::EnsEMBL::Slice	feature_Slice ()
public String	seq_region_name ()
public Int	seq_region_length ()
public Boolean	seq_region_strand ()
public Int	seq_region_start ()
public Int	seq_region_end ()
public String	coord_system_name ()
public String	seq ()
public Listref	get_all_alt_locations ()
public Boolean	overlaps ()
public Boolean	overlaps_local ()
public List	get_overlapping_Genes ()
public Bio::EnsEMBL::Gene	get_nearest_Gene ()
public String	feature_so_acc ()
public String	feature_so_term ()
public Hashref	summary_as_hash ()
public String	species ()
public	sub_SeqFeature ()
public	add_sub_SeqFeature ()
public	flush_sub_SeqFeature ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

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.

Definition at line 16 of file MarkerFeature.pm.

Member Function Documentation

_marker_id()

protected Int Bio::EnsEMBL::Map::MarkerFeature::_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

Code:

display_id()

public String Bio::EnsEMBL::Map::MarkerFeature::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

Code:

map_weight()

public Int Bio::EnsEMBL::Map::MarkerFeature::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

Code:

marker()

public Bio::EnsEMBL::Map::Marker Bio::EnsEMBL::Map::MarkerFeature::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

Code:

new()

public Bio::EnsEMBL::Map::MarkerFeature Bio::EnsEMBL::Map::MarkerFeature::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

Code:

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The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/Map/MarkerFeature.pm