Bio::Map::PositionHandler(3pm) | User Contributed Perl Documentation | Bio::Map::PositionHandler(3pm) |
Bio::Map::PositionHandler - A Position Handler Implementation
# 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
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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : register Usage : $position_handler->register(); Function: Ask this Position Handler to look after your entity relationships. Returns : n/a Args : none
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
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
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
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
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
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.
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.
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
2018-10-27 | perl v5.26.2 |