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Bio-EnsEMBL-113.0.0
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/ Bio::EnsEMBL::Map::Marker

LICENSE

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

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

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

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NAME

Bio::EnsEMBL::Map::Marker

SYNOPSIS

DESCRIPTION

Represents a marker in the EnsEMBL database. The marker object is unpositioned on the genome. Markers which are positioned are represented by the MarkerFeature object.

METHODS

new

  Arg [1]    : (optional) int $dbID
  Arg [2]    : (optional) Bio::EnsEMBL::Map::DBSQL::MarkerAdaptor $adaptor
  Arg [3]    : (optional) string $left_primer
  Arg [4]    : (optional) string $right_primer
  Arg [5]    : (optional) int $primer_distance
  Arg [6]    : (optional) int $priority
  Arg [7]    : (optional) string $type
  Arg [8]    : (optional) Bio::EnsEMBL::Map::MarkerSynonym $display_synonym
  Arg [9]    : (optional) listref of Bio::EnsEMBL::Map::MarkerSynonyms $syns
  Arg [10]   : (optional) listref of Bio::EnsEMBL::Map::MapLocations $locs
  Example    : $marker = Bio::EnsEMBL::Map::MarkerSynonym->new
                            (123, $adaptor,
			     $left_primer, $right_primer, 400,
			     80, $ms1, [$ms1, $ms2], [$mloc1, $mloc2]);
  Description: Creates a new Marker
  Returntype : Bio::EnsEMBL::Map::Marker
  Exceptions : none
  Caller     : general
  Status     : stable

left_primer

Arg [1]    : (optional) string $left_primer
Example    : $left_primer = $marker->left_primer;
Description: Getter/Setter for the left primer sequence of this marker
Returntype : string
Exceptions : none
Caller     : general
Status     : stable

right_primer

Arg [1]    : (optional) string $right_primer
Example    : $right_primer = $marker->right_primer;
Description: Getter/Setter for the right primer sequence of this marker
Returntype : string
Exceptions : none
Caller     : general
Status     : stable

min_primer_dist

Arg [1]    : (optional) string $min
Example    : $dist = $marker->min_primer_dist;
Description: Getter/Setter for the minimum seperation distance between the 
             left and right primers of this marker
Returntype : int
Exceptions : none
Caller     : general
Status     : stable

max_primer_dist

Arg [1]    : (optional) string $max
Example    : $dist = $marker->max_primer_dist;
Description: Getter/Setter for the maximum seperation distance between the 
             left and right primers of this marker
Returntype : int
Exceptions : none
Caller     : general
Status     : stable

priority

Arg [1]    : (optional) int $priority
Example    : $priority = $marker->priority;
Description: Getter/Setter for priority of this marker which can be used to 
             determine which markers are displayed.
Returntype : int
Exceptions : none
Caller     : general
Status     : stable

type

Arg [1]    : (optional) string $type
Example    : $type = $marker->type;
Description: Getter/Setter for type of this marker. Rat markers are typed
             as 'est' or 'microsatellite'.  Other markers may not have 
             defined types.
Returntype : string
Exceptions : none
Caller     : general
Status     : stable

get_all_MarkerSynonyms

Arg [1]    : none
Example    : @synonyms = @{$marker->get_all_MarkerSynonyms};
Description: Retrieves a list of marker synonyms associated with this
             marker.  If this marker is connected to the datbase (i.e. it
             has an adaptor and 
Returntype : listref of Bio::EnsEMBL::Map::MarkerSynonyms
Exceptions : none
Caller     : general
Status     : stable

add_MarkerSynonyms

Arg [1]    : Bio::EnsEMBL::MarkerSynonym $ms
Example    : $marker->add_MarkerSynonym($ms);
Description: Associates a new synonym with this marker.  Adding marker 
             synonyms to a marker which has not yet retrieved its
             synonyms from the database will prevent the loading of these
             from the database at request time (unless flush_MarkerSynonyms
             is called first).
Returntype : none
Exceptions : thrown if incorrect argument is passed
Caller     : general
Status     : stable

flush_MarkerSynonyms

Arg [1]    : none
Example    : $marker->flush_MarkerSynonyms;
Description: clears all of the marker sysnonyms which have been added to 
             this marker.
Returntype : none
Exceptions : none
Caller     : general
Status     : stable

display_MarkerSynonym

Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::MarkerSynonym $ms
Example    : none
Description: Getter/Setter for the 'display' synonym of this marker
Returntype : Bio::EnsEMBL::Map::MarkerSynonym
Exceptions : thrown if the argument is invalid
Caller     : general
Status     : stable

get_all_MarkerFeatures

Arg [1]    : none
Example    : @marker_features = @{$marker->get_all_MarkerFeatures};
Description: Retrieves the marker features which are associated with this
             marker.  I.e. locations where this marker has been mapped to
             the genome via e-PCR
Returntype : listref of Bio::EnsEMBL::Map::MarkerFeatures
Exceptions : none
Caller     : general
Status     : stable

get_all_MapLocations

Arg [1]    : none
Example    : @map_locations = @{$marker->get_all_MapLocations};
Description: Retrieves all map locations which are associated with this 
             marker. 
Returntype : listref of Bio::EnsEMBL::Map::MapLocations
Exceptions : none
Caller     : general
Status     : stable

get_MapLocation

Arg [1]    : string $map_name 
Example    : $map_location = $marker->get_MapLocation('genethon');
Description: Retrieves the location of this marker in a specified map.
             If this marker is not defined in the specified map then 
             undef is returned.
Returntype : Bio::EnsEMBL::Map::MapLocation
Exceptions : thrown if the map_name arg is not provided
Caller     : general
Status     : stable

add_MapLocations

Arg [1..n] : @mlocs list of Bio::EnsEMBL::MapLocations
Example    : $marker->add_MapLocations(@mlocs);
Description: Associates 1 or more map locations with this marker
             using this function to manually load map locations will prevent
             lazy-loading of locations from the database. 
Returntype : listref of Bio::EnsEMBL::MapLocations
Exceptions : throws if map location has no name
Caller     : general
Status     : stable

flush_MapLocations

Arg [1]    : none
Example    : $marker->get_all_MapLocations;
Description: Removes map locations associated with this marker.  Markers may
             be lazy-loaded from the database (again) after this.
Returntype : none
Exceptions : 
Caller     : 
Status     : stable