SYNOPSIS
use Bio::Map::OrderedPosition;
# the first marker in the sequence
my $position = Bio::Map::OrderedPosition->new(-order => 1,
-positions => [ [ $map, 22.3] ] );
# the second marker in the sequence, 15.6 units from the fist one
my $position2 = Bio::Map::OrderedPosition->new(-order => 2,
-positions => [ [ $map, 37.9] ] );
# the third marker in the sequence, coincidental with the second
# marker
my $position3 = Bio::Map::OrderedPosition->new(-order => 3,
-posititions => [ [ $map, 37.9]] );
DESCRIPTION
This object is an implementation of the PositionI interface and the Position object handles the specific values of a position. OrderedPosition is intended to be slightly more specific then Position but only specific enough for a parser from the MarkerIO subsystem to create and then pass to a client application to bless into the proper type. For an example of how this is intended to work, see the Mapmaker.pm.No units are assumed here - units are handled by context of which Map a position is placed in.
Se Bio::Map::Position for additional information.
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: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 - Chad Matsalla
Email [email protected]CONTRIBUTORS
Lincoln Stein, [email protected] Heikki Lehvaslaiho, heikki-at-bioperl-dot-org Jason Stajich, [email protected] Sendu Bala, [email protected]APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
Title : new Usage : my $obj = Bio::Map::OrderedPosition->new(); Function: Builds a new Bio::Map::OrderedPosition object Returns : Bio::Map::OrderedPosition Args : -order : The order of this position
order
Title : order Usage : $o_position->order($new_order); my $order = $o_position->order(); Function: Get/set the order position of this position in a map. Returns : int, the order of this position Args : none to get, OR int to set
sortable
Title : sortable Usage : my $num = $position->sortable(); Function: Read-only method that is guaranteed to return a value suitable for correctly sorting this kind of position amongst other positions of the same kind on the same map. Note that sorting different kinds of position together is unlikely to give sane results. Returns : numeric Args : none
equals
Title : equals Usage : if ($mappable->equals($mapable2)) {...} Function: Test if a position is equal to another position. Returns : boolean Args : Bio::Map::PositionI
less_than
Title : less_than Usage : if ($mappable->less_than($m2)) {...} Function: Tests if a position is less than another position It is assumed that 2 positions are in the same map. Returns : boolean Args : Bio::Map::PositionI
greater_than
Title : greater_than Usage : if ($mappable->greater_than($m2)) {...} Function: Tests if position is greater than another position. It is assumed that 2 positions are in the same map. Returns : boolean Args : Bio::Map::PositionI