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

NAME
       Bio::Map::MarkerI - Interface for basic marker functionality

SYNOPSIS
	   # do	not use	this module directly
	   # See Bio::Map::Marker for an example of
	   # implementation.

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 - Jason Stajich
       Email jason@bioperl.org

CONTRIBUTORS
       Heikki Lehvaslaiho heikki-at-bioperl-dot-org Lincoln Stein
       lstein@cshl.org Jason Stajich	  jason@bioperl.org Chad Matsalla
       bioinformatics1@dieselwurks.com 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 _

   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

   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

   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>

   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::MarkerI(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Jason Stajich | CONTRIBUTORS | APPENDIX

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