Provided by: libbio-perl-perl_1.6.901-2_all bug


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


           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

               # done!


       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.


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AUTHOR - Chad Matsalla



       Lincoln Stein Heikki Lehvaslaiho  heikki-at-bioperl-dot-org Jason
       Stajich Sendu Bala


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

        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

        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.

        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.