The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
Bio-EnsEMBL-112.0.0_58
River stage zero No dependents
/ 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

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

  Questions may also be sent to the Ensembl help desk at
  <http://www.ensembl.org/Help/Contact>.

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