Reference

Bio::Map::PositionHandler(3pm)

A Position Handler Implementation

NAME

Bio::Map::PositionHandler - A Position Handler Implementation

SYNOPSIS

    # 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

DESCRIPTION

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.

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Sendu Bala

Email [email protected]

APPENDIX

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

General methods

new

 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

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

History