[Bioperl-l] Connecting Bio::DB::GFF::Features on a Bio::Graphics::Panel

Philip MacMenamin pm66 at nyu.edu
Mon Sep 8 14:47:26 EDT 2003


Apologies for previous question. I realised the solution to the problem just 
after I sent the question. Very simple, very silly of me. Always the way, 
stare at it for ages, then show some one else the code, and the answer 
instantly becomes painfully obvious. 

Use a Bio::Graphics::Feature object, and just tell it the segments in the 
constructor at the start. Works fine. No aggregator, no 
Bio::DB::GFF::Features, all very simple and above board. 

$joinedFeatureRef = Bio::Graphics::Feature->new(-segments =>[ 
[$KKstart,$KKstop],[($KKstopStop-1),$KKstopStop]]);

and

if ( scalar @KKs > 0 )
{
   $panel->add_track(group =>$joinedFeatureRef,
		    -bgcolor   =>  'blue',
		    -height     =>  4,
		    -fgcolor   =>  'darkgreen',
		    -key       => 'SuchAndSuch',
		    -connect   => 1,
		    -connector => 'dashed',
		    -bump      =>  +1,
		    -connect_color => 'lightpurple',
		   );
}

All the best. 
Philip.


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