Bio::Map::PositionHandlerI(3pm) User Contributed Perl Documentation Bio::Map::PositionHandlerI(3pm)
NAME
Bio::Map::PositionHandlerI - A Position Handler Interface
SYNOPSIS
# do not use this module directly
# See Bio::Map::PositionHandler for an example of
# implementation.
DESCRIPTION
This interface describes the basic methods required for Position Handlers. 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.
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://redmine.open-bio.org/projects/bioperl/
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
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
perl v5.14.2 2012-03-02 Bio::Map::PositionHandlerI(3pm)