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

[Philip MacMenamin]

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. 

-- 

Philip.