[Bioperl-l] Bio::Graphics off by one?

Lincoln Stein lstein at cshl.edu
Tue Feb 21 10:55:30 EST 2006


Hi,

When you are looking at the resolution of individual bases, a base pair at 
position one occupies the half-open interval from 1->2, meaning that it comes 
up to, but doesn't quite touch, the 2. For the purposes of display, 
Bio::Graphics draws the end of the half-open interval.

Lincoln

On Tuesday 21 February 2006 05:47, Dave Howorth wrote:
> I'm drawing a simple graphic and seeing something I didn't expect. I'm
> not sure whether I've misunderstood the docs or found a bug. If I run a
> program containing:
>
>      my $name   = 'O68601';
>      my $length = 44;
>      my $panel  = Bio::Graphics::Panel->new(
>                  -length    => $length,
>                  -width     => 800,
>                  -pad_left  => 10,
>                  -pad_right => 10,
>                  -key_style => 'between',
>                  );
>
>      my $feature = new Bio::SeqFeature::Generic(
>                  -start  => 1,
>                  -end    => $length,
>                  -display_name => $name . " ($length)",
>                  );
>
>      $panel->add_track($feature,
>                  -glyph   => 'arrow',
>                  -tick    =>  1,
>                  -fgcolor => 'black',
>                  -double  => 1,
>                  -label   => 1,
>                  );
>
> Then I see a tick strip labelled at its left end with '1' and at its
> right end with '45'. I expected to see '44'. Should I be looking for a
> bug in Bio::Graphics or fixing my program?
>
> Thanks, Dave
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
FOR URGENT MESSAGES & SCHEDULING, 
PLEASE CONTACT MY ASSISTANT, 
SANDRA MICHELSEN, AT michelse at cshl.edu


More information about the Bioperl-l mailing list