[Bioperl-l] RE: Passing extra arguments to method references in Bio::Graphics::Panel::add_track

[Lincoln Stein]

	$start = 23;
	add_track(...
		-label => sub { gene_description($start, at _) }
		...
	);

In other words, pass an anonymous subroutine in which the $start variable 
(which has *ALREADY* been assigned) is passed to gene_description in front of 
the other variables.  If $start is going to change dynamically, you will have 
to use a global or something similar, because once $start is incorporated 
into the anonymous subroutine, it is stuck there.

Lincoln


On Monday 09 May 2005 11:30 am, michael watson (IAH-C) wrote:
> Hi
>
> Sorry, a bit hasty on the trigger....
>
> I am on bioperl-1.5.
>
> I'm using the following code to create some rather tasty images:
>
> $panel->add_track(transcript2  => \@includeCDS,
> 		  -bgcolor    =>  'blue',
> 		  -fgcolor    =>  'black',
> 		  -key        => 'CDS',
> 		  -bump       =>  0,
> 		  -height     =>  10,
> 		  -label      => \&gene_description,
> 		  -description=> \&gene_label,
> 		 );
>
> This is fairly standard, and @includeCDS is a bunch of feature objects.
>
> What I want to do is pass extra arguments to &gene_description, and then
> within &gene_description check to see if the feature start is greater
> than a certain value (the extra argument).  If it is, then I want to
> return an empty string, if it isn't I want to return the gene
> description.  Something like:
>
> -label      => \&gene_description($start)
>
> But when I tried that it didn't work ;-(.
>
> So is it possible to pass extra arguments to those functions I am
> referencing above?
>
> Many thanks
>
> Mick
>
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-- 
Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724