NAME

       Bio::Map::LinkageMap - A representation of a genetic linkage map.

SYNOPSIS

           use Bio::Map::LinkageMap;
               # create a new map
           my $map = Bio::Map::LinkageMap->new(-name => 'Chads Superterriffic Map',
                                             -type => 'Linkage',
                                             -units=> 'cM');
               # create the location of a marker for that map
           my $position = Bio::Map::LinkagePosition->new( -positions => 1,
                       -distance => "22.3");
               # create a marker and place it at that position
           my $marker = Bio::Map::Marker::Microsatellite->new(
                               -name => 'SuuuperMarker',
                               -position => $position);
               # place that marker on that map
           $map->add_element($marker);

               # done!

DESCRIPTION

       This object describes the basic functionality of a genetic linkage map in Bioperl. Each
       'position' can have one or more markers that map some number of units from the markers at
       the previous position.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Chad Matsalla

       Email bioinformatics1@dieselwurks.com

CONTRIBUTORS

       Lincoln Stein       lstein@cshl.org Heikki Lehvaslaiho  heikki-at-bioperl-dot-org Jason
       Stajich       jason@bioperl.org Sendu Bala          bix@sendu.me.uk

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are
       usually preceded with a _

   new
        Title   : new
        Usage   : my $linkage_map = Bio::Map::LinkageMap->new();
        Function: Builds a new Bio::Map::LinkageMap object
        Returns : Bio::Map::LinkageMap
        Args    : -name    => the name of the map (string) [optional]
                      -type    => the type of this map (string, defaults to Linkage) [optional]
                  -species => species for this map (Bio::Species) [optional]
                  -units   => the map units (string, defaults to cM) [optional]
                  -elements=> elements to initialize with
                              (arrayref of Bio::Map::MappableI objects) [optional]
                  -uid      => Unique ID of this map

   length
        Title   : length
        Usage   : my $length = $map->length();
        Function: Retrieves the length of the map. In the case of a LinkageMap, the
                      length is the sum of all marker distances.
        Returns : An integer representing the length of this LinkageMap. Will return
                      0 if length is not calculateable
        Args    : None.

   add_element($marker)
        Title   : add_element($marker)
        Usage   : $map->add_element($marker)
        Function: Add a Bio::Map::MappableI object to the Map
        Returns : none
        Args    : Bio::Map::MappableI object
        Notes   : It is strongly recommended that you use a
                  Bio::Map::LinkagePosition as the position in any
                  Bio::Map::Mappable that you create to place on this
                  map. Using some other Bio::Map::Position might work but might
                  be unpredictable.
                  N.B. I've added Bio::Map::OrderedPosition which should achieve
                       similar things from LinkagePosition and will work for
                       RH markers too.