Provided by: libbio-perl-perl_1.7.2-2_all
Bio::Map::PositionHandlerI - A Position Handler Interface
# do not use this module directly # See Bio::Map::PositionHandler for an example of # implementation.
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.
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AUTHOR - Sendu Bala
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