Christopher Fields > BioPerl-1.6.901 > Bio::Location::CoordinatePolicyI

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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924

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://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.
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