NAME¶
Bio::Map::OrderedPositionWithDistance - 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::OrderedPositionWithDistance;
# the first marker in the sequence
my $position = Bio::Map::OrderedPositionWithDistance->new(-positions => 1,
-distance => 22.3 );
# the second marker in the sequence, 15.6 units from the fist one
my $position2 = Bio::Map::OrderedPositionWithDistance->new(-positions => 2,
-distance => 15.6 );
# the third marker in the sequence, coincidental with the second
# marker
my $position3 = Bio::Map::OrderedPositionWithDistance->new(-positions => 3,
-distance => 0 );
DESCRIPTION¶
This object is an implementation of the PositionI interface and the Position
object handles the specific values of a position. OrderedPositionWithDistance
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
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
new¶
Title : new
Usage : my $obj = Bio::Map::OrderedPositionWithDistance->new();
Function: Builds a new Bio::Map::OrderedPositionWithDistance object
Returns : Bio::Map::OrderedPositionWithDistance
Args : -positions - Should be a single value representing the order
of this marker within the list of markers
-distance - The distance this marker is from the marker before it.
0 reflects coincidentality.
distance($new_distance)¶
Title : distance($new_distance)
Usage : $position->distance(new_distance) _or_
$position->distance()
Function: get/set the distance of this position from the previous marker
Returns : A scalar representing the current distance for this position.
Args : If $new_distance is provided the distance of this Position will
be set to $new_distance