Provided by: libbio-perl-perl_1.7.2-2_all bug


       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

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

           # If you are a marker, add a new position to yourself

           # 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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AUTHOR - Sendu Bala



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

   General methods
        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

   Methods for Bio::Map::PositionI objects
        Title   : map
        Usage   : my $map = $position_handler->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();
        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
        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
        Returns : Array of Bio::Map::EntityI objects
        Args    : none