[Bioperl-l] Bio::Graphics::Panel, -spacing => 0 constructor problem.

[Lincoln Stein]

Spacing adds additional padding between tracks.  You cannot get them to overly 
each other.  Possibly -start and -end are not doing what you think they 
should do.

Lincoln

On Friday 22 August 2003 06:23 pm, Philip MacMenamin wrote:
> Hi,
>
> Am I right in thinking that the '-spacing' constructor for
> Bio::Graphics::Panel, if set to 0, should result in no space between
> tracks? ie That the tracks are either over-laying eachother, or squashed
> down onto the same plane as the previous one.
>
> I cannot get this to happen if this is its purpose. It continues to stack
> the tracks on the panel as per default. (So I have left it out, its not
> useful to see this). I know that it works, because I have seen it working
> in the wormbase UTRs.
>
> Here is some code:
> #   if (scalar @threePrimeUTR >0)
> #    {
> #      $panel->add_track(generic=>\@threePrimeUTR,
> #			-bgcolor      => 'lightblue',
> #			-fgcolor      => 'black',
> #		#	-bump      =>  +1,
> #			-spacing => 0,
> #			-utr_color    => '#D0D0D0', ##whats this about?, chnging makes no dif?
> #			-font2color   => 'blue',
> #			-height       => 10,
> #			-description  => 1,
> #			-label        => '3 prime UTR'
> #     }
>
> I have also tried to set spacing to 0 on the tracks surrounding the UTRs,
> but to no avail.
>
> Also, on a slightly differant vein, I cant seem to get the
> Bio::Graphics::Panel start end constructors to work either. All of which is
> making me increasingly suspicious of my perl skills. It just makes no
> differance if I provide these arguments or not. The segment or sequence obj
> always over-rides the start stop args. Not a massive problem, but it has
> confused me.
>
> More code:
>
> my $panel = Bio::Graphics::Panel->new( -segment   => $segment,
> 					   -width     => 600,
> 					   -key_color => '#ffffcc',
> 					   -start =>$panelStart,
> 					   -end =>$panelEnd,
> 			#		   -start => 4110000,
> 					 );
>
> Any help is of course appreciated.

-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)