Bio::Map::Marker(3pm)					User Contributed Perl Documentation				     Bio::Map::Marker(3pm)

NAME

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

SYNOPSIS

	 # 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,
							 $pos2
						       ] );

	 # 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');
	 $map1->add_element($marker2);
	 $marker2->position(100);

	 # 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, "
";
	 # several positions
	 foreach $pos ($marker2->each_position($map1)) {
	    print $pos->value, "
";
	 }

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

DESCRIPTION

       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.

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

       Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein      lstein@cshl.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 $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

   default_map
	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>

   map
	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

   get_position_object
	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
		  attributes.

   position
	Title	: position
	Usage	: my $position = $mappable->position();
			  $mappable->position($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
		   OR
		  Bio::Map::MapI AND
		  scalar
		   OR
		  scalar, but only if the marker has a default map

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

   positions
	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

   in_map
	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

perl v5.14.2							    2012-03-02						     Bio::Map::Marker(3pm)