/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Map::PositionHandler

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.

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

bioperl-l@bioperl.org

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 bix@sendu.me.uk

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