Christopher Fields > BioPerl-1.6.901 > Bio::Map::PositionHandler



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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924


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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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.                  - General discussion  - About the mailing lists


Please direct usage questions or support issues to the mailing list:

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:

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
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