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

NAME

       Bio::Map::PositionHandlerI - A Position Handler Interface

SYNOPSIS

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

DESCRIPTION

       This interface describes the basic methods required for Position Handlers. 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.

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