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

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

       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://github.com/bioperl/bioperl-live/issues

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 v5.24.1			  2017-07-08		   Bio::Map::Marker(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Chad Matsalla | CONTRIBUTORS | APPENDIX

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