/ 
bioperl-1.2.3
/ Bio::Location::CoordinatePolicyI

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\n";
# 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://bio.perl.org/MailList.html - About the mailing lists

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 email or the web:

bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/

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.