[Bioperl-l] Boxes and features...

[William Boileau]

Hi,

I tried to remove the box_subparts option (the hit is what I need, not
each HSP), but it doesn't seem to work.I still have the error "MSG: asking for tag value that does not exist name"
I didn't try to add the tag to each oh the HSPs, but now I hesitate...
How can I do that ? for the moment I add each HSP to the feature, but how
can i add tags to an HSP ?
Thanks for your answers ! (and I know I owe you much :) )

William

> Hi William,
>
> Sorry I didn't notice this before.  The problem is that you are using
> the  -box_subparts option when you add the track.  This is telling the
> track to  return the SUBFEATURES when you call boxes() rather than the
> top level  features.  So what you're getting from boxes() is the HSP
> subcomponents,  which don't happen to have tags.
>
> You can either:
>
> 	1) remove -box_subparts (or set it to 0)
> 	2) add the tags to each of the HSPs
>
> It depends on whether you want clicks to be directed at each HSP or at
> the hit  as a whole.
>
> Lincoln
>
>> >> my $track = $panel->add_track(-glyph        => 'graded_segments',
>> >> 			      -label        => 1,
>> >> 			      -connector    => 'dashed',
>> >> 			      -bgcolor      => 'blue',
>> >> 			      -font2color   => 'red',
>> >> 			      -sort_order   => 'high_score',
>> >> 			      -box_subparts => 1,
>> >> 			      -description  => sub {
>> >> 				my $feature = shift;
>> >> 				return unless $feature->has_tag('desription');
>
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor
> Laboratory lstein at cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
>
>
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