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Summary

Bio::Location::CoordinatePolicyI - Abstract interface for objects implementing
a certain policy of computing integer-valued coordinates of a Location

Package variables

Included modules

Inherit

Bio::Root::RootI

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.

Methods

Methods description

  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.

  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.

Methods code

sub end {

    my ($self) = @_;
    $self->throw_not_implemented();
}

1;

}

sub start {

    my ($self) = @_;
    $self->throw_not_implemented();

}

General documentation

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
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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/

Email hlapp@gmx.net, jason@bioperl.org

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _