NAME¶
Bio::Map::OrderedPosition - Abstracts the notion of a member of an ordered list
of markers. Each marker is a certain distance from the one in the ordered
list before it.
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.
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 - Chad Matsalla¶
Email bioinformatics1@dieselwurks.com
CONTRIBUTORS¶
Lincoln Stein, lstein@cshl.org Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
Jason Stajich, jason@bioperl.org Sendu Bala, bix@sendu.me.uk
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