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Bio::EnsEMBL::Map::Marker Class Reference
Inheritance diagram for Bio::EnsEMBL::Map::Marker:

List of all members.


Class Summary

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.
 

Definition at line 17 of file Marker.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public Listref add_MapLocations ()
public void add_MarkerSynonyms ()
public Int dbID ()
public
Bio::EnsEMBL::Map::MarkerSynonym 
display_MarkerSynonym ()
public void flush_MapLocations ()
public void flush_MarkerSynonyms ()
public get_all_DAS_Features ()
public Listref get_all_MapLocations ()
public Listref get_all_MarkerFeatures ()
public Listref get_all_MarkerSynonyms ()
public
Bio::EnsEMBL::Map::MapLocation 
get_MapLocation ()
public Boolean is_stored ()
public String left_primer ()
public Int max_primer_dist ()
public Int min_primer_dist ()
public Bio::EnsEMBL::Map::Marker new ()
public Int priority ()
public String right_primer ()
public String type ()

Method Documentation

public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
  Example    : none
  Description: get/set for this objects Adaptor
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
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public Listref Bio::EnsEMBL::Map::Marker::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
 
Code:
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public void Bio::EnsEMBL::Map::Marker::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
 
Code:
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public Int Bio::EnsEMBL::Storable::dbID ( ) [inherited]
  Arg [1]    : int $dbID
  Example    : none
  Description: getter/setter for the database internal id
  Returntype : int
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public Bio::EnsEMBL::Map::MarkerSynonym Bio::EnsEMBL::Map::Marker::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
 
Code:
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public void Bio::EnsEMBL::Map::Marker::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
 
Code:
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public void Bio::EnsEMBL::Map::Marker::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
 
Code:
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public Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

Code:
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Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.

public Listref Bio::EnsEMBL::Map::Marker::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
 
Code:
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public Listref Bio::EnsEMBL::Map::Marker::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
 
Code:
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public Listref Bio::EnsEMBL::Map::Marker::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
 
Code:
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public Bio::EnsEMBL::Map::MapLocation Bio::EnsEMBL::Map::Marker::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
 
Code:
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public Boolean Bio::EnsEMBL::Storable::is_stored ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection 
             : or Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : do_something if($object->is_stored($db));
  Description: Returns true if this object is stored in the provided database.
               This works under the assumption that if the adaptor and dbID are
               set and the database of the adaptor shares the port, dbname and
               hostname with the provided database, this object is stored in
               that database.
  Returntype : 1 or 0
  Exceptions : throw if dbID is set but adaptor is not
               throw if adaptor is set but dbID is not
               throw if incorrect argument is passed
  Caller     : store methods
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::Map::Marker::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
 
Code:
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public Int Bio::EnsEMBL::Map::Marker::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
 
Code:
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public Int Bio::EnsEMBL::Map::Marker::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
 
Code:
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public Bio::EnsEMBL::Map::Marker Bio::EnsEMBL::Map::Marker::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
 
Code:
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Reimplemented from Bio::EnsEMBL::Storable.

public Int Bio::EnsEMBL::Map::Marker::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
 
Code:
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public String Bio::EnsEMBL::Map::Marker::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
 
Code:
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public String Bio::EnsEMBL::Map::Marker::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
 
Code:
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The documentation for this class was generated from the following file: