Bio::Location::CoordinatePolicyI(3pm) User Contributed Perl Documentation Bio::Location::CoordinatePolicyI(3pm)
NAME
Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing a certain policy of computing integer-valued coordinates of
a Location
SYNOPSIS
# get a location, e.g., from a SeqFeature
$location = $feature->location();
# examine its coordinate computation policy
print "Location of feature ", $feature->primary_tag(), " employs a ",
ref($location->coordinate_policy()),
" instance for coordinate computation
";
# change the policy, e.g. because the user chose to do so
$location->coordinate_policy(Bio::Location::NarrowestCoordPolicy->new());
DESCRIPTION
Objects implementing this interface are used by Bio::LocationI implementing objects to determine integer-valued coordinates when asked for
it. While this may seem trivial for simple locations, there are different ways to do it for fuzzy or compound (split) locations. Classes
implementing this interface implement a certain policy, like 'always widest range', 'always smallest range', 'mean for BETWEEN locations',
etc. By installing a different policy object in a Location object, the behaviour of coordinate computation can be changed on-the-fly, and
with a single line of code client-side.
FEEDBACK
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Hilmar Lapp, Jason Stajich
Email hlapp@gmx.net, jason@bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
start
Title : start
Usage : $start = $policy->start($location);
Function: Get the integer-valued start coordinate of the given location as
computed by this computation policy.
Returns : A positive integer number.
Args : A Bio::LocationI implementing object.
end
Title : end
Usage : $end = $policy->end($location);
Function: Get the integer-valued end coordinate of the given location as
computed by this computation policy.
Returns : A positive integer number.
Args : A Bio::LocationI implementing object.
perl v5.14.2 2012-03-02 Bio::Location::CoordinatePolicyI(3pm)