comparison variant_effect_predictor/Bio/Location/WidestCoordPolicy.pm @ 0:1f6dce3d34e0

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# $Id: WidestCoordPolicy.pm,v 1.6 2002/12/01 00:05:20 jason Exp $
#
# BioPerl module for Bio::Location::WidestCoordPolicy
#
# Cared for by Hilmar Lapp <[e-mail]>
#          and Jason Stajich <[e-mail]>
#
# 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::WidestCoordPolicy - class implementing 
Bio::Location::CoordinatePolicy as the widest possible and reasonable range

=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 always the widest possible
range is returned, 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.

  [e-mail]             - 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:

  [e-mail]
  http://bugzilla.bioperl.org/

=head1 AUTHOR - Hilmar Lapp, Jason Stajich

Email [e-mail], [e-mail]

=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::WidestCoordPolicy;
use vars qw(@ISA);
use strict;

use Bio::Root::Root;
use Bio::Location::CoordinatePolicyI;

@ISA = qw(Bio::Root::Root Bio::Location::CoordinatePolicyI);

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) = @_;

    # For performance reasons we don't check that it's indeed a Bio::LocationI
    # object. Hopefully, Location-object programmers are smart enough.
    my $pos = $loc->min_start();
    # if min is not defined or equals 0 we resort to max
    $pos = $loc->max_start() if(! $pos);
    return $pos;
}

=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) = @_;

    # For performance reasons we don't check that it's indeed a Bio::LocationI
    # object. Hopefully, Location-object programmers are smart enough.
    my $pos = $loc->max_end();
    # if max is not defined or equals 0 we resort to min
    $pos = $loc->min_end() if(! $pos);
    return $pos;
}

1;