Raw content of Bio::Location::AvWithinCoordPolicy
<![CDATA[# $Id: AvWithinCoordPolicy.pm,v 1.4 2002/12/01 00:05:20 jason Exp $
#
# BioPerl module for Bio::Location::AvWithinCoordPolicy
#
# Cared for by Hilmar Lapp <hlapp@gmx.net>
# and Jason Stajich <jason@bioperl.org>
#
# Copyright Hilmar Lapp, Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Location::AvWithinCoordPolicy - class implementing
Bio::Location::CoordinatePolicy as the average for WITHIN and the widest possible and reasonable range otherwise
=head1 SYNOPSIS
See Bio::Location::CoordinatePolicyI
=head1 DESCRIPTION
CoordinatePolicyI implementing objects are used by Bio::LocationI
implementing objects to determine integer-valued coordinates when
asked for it.
This class will compute the coordinates such that for fuzzy locations
of type WITHIN and BETWEEN the average of the two limits will be
returned, and for all other locations it will return the widest
possible range, but by using some common sense. This means that
e.g. locations like "E<lt>5..100" (start before position 5) will return 5
as start (returned values have to be positive integers).
=head1 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
=head2 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/
=head1 AUTHOR - Hilmar Lapp, Jason Stajich
Email E<lt>hlapp@gmx.netE<gt>, E<lt>jason@bioperl.orgE<gt>
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Location::AvWithinCoordPolicy;
use vars qw(@ISA);
use strict;
use Bio::Location::WidestCoordPolicy;
@ISA = qw(Bio::Location::WidestCoordPolicy);
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
return $self;
}
=head2 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.
=cut
sub start {
my ($self,$loc) = @_;
if(($loc->start_pos_type() eq 'WITHIN') ||
($loc->start_pos_type() eq 'BETWEEN')) {
my ($min, $max) = ($loc->min_start(), $loc->max_start());
return int(($min+$max)/2) if($min && $max);
}
return $self->SUPER::start($loc);
}
=head2 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.
=cut
sub end {
my ($self,$loc) = @_;
if(($loc->end_pos_type() eq 'WITHIN') ||
($loc->end_pos_type() eq 'BETWEEN')) {
my ($min, $max) = ($loc->min_end(), $loc->max_end());
return int(($min+$max)/2) if($min && $max);
}
return $self->SUPER::end($loc);
}
1;
]]>