Raw content of Bio::Graphics::Util
<![CDATA[package Bio::Graphics::Util;
# $Id: Util.pm,v 1.2.2.2 2003/07/06 21:53:55 heikki Exp $
# Non object-oriented utilities used here-and-there in Bio::Graphics modules
use strict;
require Exporter;
use vars '@ISA','@EXPORT','@EXPORT_OK';
@ISA = 'Exporter';
@EXPORT = 'frame_and_offset';
=over 4
=item ($frame,$offset) = frame_and_offset($pos,$strand,$phase)
Calculate the reading frame for a given genomic position, strand and
phase. The offset is the offset from $pos to the first nucleotide
of the reading frame.
In a scalar context, returns the frame only.
=back
=cut
sub frame_and_offset {
my ($pos,$strand,$phase) = @_;
$strand ||= +1;
$phase ||= 0;
my $frame = $strand >= 0
? ($pos - $phase - 1) % 3
: (1 - $pos - $phase) % 3;
my $offset = -$phase % 3;
$offset *= -1 if $strand < 0;
return wantarray ? ($frame,$offset) : $frame;
}
1;
]]>