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Bio::Map::PositionHandUser3Contributed Perl DocumeBio::Map::PositionHandler(3)

NAME
       Bio::Map::PositionHandler - A Position Handler Implementation

SYNOPSIS
	   # This is used by modules when they want to implement being a
	   # Position or being something that has Positions (when they are
	   # a L<Bio::Map::EntityI>)

	   # Make a PositionHandler that knows about you
	   my $ph = Bio::Map::PositionHandler->new($self);

	   # Register with it so that it handles your Position-related needs
	   $ph->register;

	   # If	you are	a position, get/set the	map you	are on and the marker you are
	   # for
	   $ph->map($map);
	   $ph->element($marker);
	   my $map = $ph->map;
	   my $marker =	$ph->element;

	   # If	you are	a marker, add a	new position to	yourself
	   $ph->add_positions($pos);

	   # And then get all your positions on	a particular map
	   foreach my $pos ($ph->get_positions($map)) {
	       # do something with this	Bio::Map::PositionI
	   }

	   # Or	find out what maps you exist on
	   my @maps = $ph->get_other_entities;

	   # The same applies if you were a map

DESCRIPTION
       A Position Handler copes	with the coordination of different
       Bio::Map::EntityI objects, adding and removing them from	each other and
       knowning	who belongs to who. These relationships	between	objects	are
       based around shared Positions, hence PositionHandler.

       This PositionHandler is able to cope with Bio::Map::PositionI objects,
       Bio::Map::MappableI objects and Bio::Map::MapI objects.

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 - Sendu Bala
       Email bix@sendu.me.uk

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

   General methods
   new
	Title	: new
	Usage	: my $position_handler = Bio::Map::PositionHandler->new(-self => $self);
	Function: Get a	Bio::Map::PositionHandler that knows who you are.
	Returns	: Bio::Map::PositionHandler object
	Args	: -self	=> Bio::Map::EntityI that is you

   register
	Title	: register
	Usage	: $position_handler->register();
	Function: Ask this Position Handler to look after your entity relationships.
	Returns	: n/a
	Args	: none

   index
	Title	: index
	Usage	: my $index = $position_handler->index();
	Function: Get the unique registry index	for yourself, generated	during the
		  resistration process.
	Returns	: int
	Args	: none

   get_entity
	Title	: get_entity
	Usage	: my $entity = $position_handler->get_entity($index);
	Function: Get the entity that corresponds to the supplied registry index.
	Returns	: Bio::Map::EntityI object
	Args	: int

   Methods for Bio::Map::PositionI objects
   map
	Title	: map
	Usage	: my $map = $position_handler->map();
		  $position_handler->map($map);
	Function: Get/Set the map you are on. You must be a Position.
	Returns	: L<Bio::Map::MapI>
	Args	: none to get, OR
		  new L<Bio::Map::MapI>	to set

   element
	Title	: element
	Usage	: my $element =	$position_handler->element();
		  $position_handler->element($element);
	Function: Get/Set the map element you are for. You must	be a Position.
	Returns	: L<Bio::Map::MappableI>
	Args	: none to get, OR
		  new L<Bio::Map::MappableI> to	set

   Methods for all other Bio::Map::EntityI objects
   add_positions
	Title	: add_positions
	Usage	: $position_handler->add_positions($pos1, $pos2, ...);
	Function: Add some positions to	yourself. You can't be a position.
	Returns	: n/a
	Args	: Array	of Bio::Map::PositionI objects

   get_positions
	Title	: get_positions
	Usage	: my @positions	= $position_handler->get_positions();
	Function: Get all your positions. You can't be a Position.
	Returns	: Array	of Bio::Map::PositionI objects
	Args	: none for all,	OR
		  Bio::Map::EntityI object to limit the	Positions to those that
		  are shared by	you and	this other entity.

   purge_positions
	Title	: purge_positions
	Usage	: $position_handler->purge_positions();
	Function: Remove all positions from yourself. You can't	be a Position.
	Returns	: n/a
	Args	: none to remove all, OR
		  Bio::Map::PositionI object to	remove only that entity, OR
		  Bio::Map::EntityI object to limit the	removal	to those Positions that
		  are shared by	you and	this other entity.

   get_other_entities
	Title	: get_other_entities
	Usage	: my @entities = $position_handler->get_other_entities();
	Function: Get all the entities that share your Positions. You can't be a
		  Position.
	Returns	: Array	of Bio::Map::EntityI objects
	Args	: none

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

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Sendu Bala | APPENDIX

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