Provided by: libbio-perl-perl_1.7.2-2_all bug


       Bio::Map::Marker - An central map object representing a generic marker that can have
       multiple location in several maps.


         # get map objects somehow

         # a marker with complex localisation
         $o_usat = Bio::Map::Marker->new(-name=>'Chad Super Marker 2',
                                         -positions => [ [$map1, $position1],
                                                         [$map1, $position2]
                                                       ] );

         # The markers deal with Bio::Map::Position objects which can also
         # be explicitly created and passed on to markers as an array ref:
         $o_usat2 = Bio::Map::Marker->new(-name=>'Chad Super Marker 3',
                                         -positions => [ $pos1,
                                                       ] );

         # a marker with unique position in a map
         $marker1 = Bio::Map::Marker->new(-name=>'hypervariable1',
                                          -map => $map1,
                                          -position => 100

         # another way of creating a marker with unique position in a map:
         $marker2 = Bio::Map::Marker->new(-name=>'hypervariable2');

         # position method is a short cut for get/setting unique positions
         # which overwrites previous values
         # to place a marker to other maps or to have multiple positions
         # for a map within the same map use add_position()

         $marker2->add_position(200);  # new position in the same map
         $marker2->add_position($map2,200); # new map

         # setting a map() in a marker or adding a marker into a map are
         # identical mathods. Both set the bidirectional connection which is
         # used by the marker to remember its latest, default map.

         # Regardes of how marker positions are created, they are stored and
         # returned as Bio::Map::PositionI objects:

         # unique position
         print $marker1->position->value, "\n";
         # several positions
         foreach $pos ($marker2->each_position($map1)) {
            print $pos->value, "\n";

       See Bio::Map::Position and Bio::Map::PositionI for more information.


       A Marker is a Bio::Map::Mappable with some properties particular to markers.  It also
       offers a number of convienience methods to make dealing with map elements easier.


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AUTHOR - Chad Matsalla



       Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein 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 $marker = Bio::Map::Marker->new( -name => 'Whizzy marker',
                                                         -position => $position);
        Function: Builds a new Bio::Map::Marker object
        Returns : Bio::Map::Marker
        Args    :
                  -name    => name of this microsatellite
                              [optional], string,default 'Unknown'
                  -default_map => the default map for this marker, a Bio::Map::MapI
                  -position => map position for this marker, a Bio::Map::PositionI
                  -positions => array ref of Bio::Map::PositionI objects

                  position and positions can also take as values anything the
                  corresponding methods can take

        Title   : default_map
        Usage   : my $map = $marker->default_map();
        Function: Get/Set the default map for the marker.
        Returns : L<Bio::Map::MapI>
        Args    : [optional] new L<Bio::Map::MapI>

        Title   : map
        Function: This is a synonym of the default_map() method

                          *** does not actually add this marker to the map! ***

        Status  : deprecated, will be removed in next version

        Title   : get_position_class
        Usage   : my $position = $marker->get_position_object();
        Function: To get an object of the default Position class
                  for this Marker. Subclasses should redefine this method.
                  The Position returned needs to be a L<Bio::Map::PositionI> with
                          -element set to self.
        Returns : L<Bio::Map::PositionI>
        Args    : none for an 'empty' PositionI object, optionally
                  Bio::Map::MapI and value string to set the Position's -map and -value

        Title   : position
        Usage   : my $position = $mappable->position();
        Function: Get/Set the Position of this Marker (where it is on which map),
                  purging all other positions before setting.
        Returns : L<Bio::Map::PositionI>
        Args    : Bio::Map::PositionI
                  Bio::Map::MapI AND
                  scalar, but only if the marker has a default map

        Title   : add_position
        Usage   : $marker->add_position($position);
        Function: Add a Position to this marker
        Returns : n/a
        Args    : Bio::Map::PositionI
                  Bio::Map::MapI AND
                  scalar, but only if the marker has a default map

        Title   : positions
        Usage   : $marker->positions([$pos1, $pos2, $pos3]);
        Function: Add multiple Bio::Map::PositionI to this marker
        Returns : n/a
        Args    : array ref of $map/value tuples or array ref of Bio::Map::PositionI

        Title   : in_map
        Usage   : if ( $marker->in_map($map) ) {}
        Function: Tests if this marker is found on a specific map
        Returns : boolean
        Args    : a map unique id OR Bio::Map::MapI