Fwd: Re: [Bioperl-l] Boxes and features...

[William Boileau]

Ok, now it works, I've found my error !
when adding the tag in the feature, I was calling the name method on the
hit ($hit->name)...But I mistyped, and in the code it was written $hit_name...
All things were clear after... I was just about going crazy when I realized.
So, I am sorry for all the inconvience, and next time, I'll try to look at
my code more precisely...Thanks for all the answers you brought me !

William Boileau


> For some reason, bioperl-l thinks the headers on this message are
> suspicious.   So I will forward as an enclosure.
>
> Lincoln
>
> ----------  Forwarded Message  ----------
>
> Subject: Re: [Bioperl-l] Boxes and features...
> Date: Fri, 7 Mar 2003 13:09:56 -0500
> From: Lincoln Stein <lstein at cshl.org>
> To: "William Boileau" <boileau at essi.fr>, <bioperl-l at bioperl.org>
>
> Hi,
>
> Most likely you are trying to fetch a tag from the arrow feature that
> you use as the scale at the top of the picture.  You should first check
> that the tag exists before you attempt to call it, or you can use the
> primary_tag to distinguish between different feature types.  The
> enclosed examples show you what to do.
>
> Lincoln
>
> On Thursday 06 March 2003 09:27 am, William Boileau wrote:
>> 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
>> > =======================================================================>
>> > >
>> >
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at bioperl.org
>> > http://bioperl.org/mailman/listinfo/bioperl-l
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at bioperl.org
>> http://bioperl.org/mailman/listinfo/bioperl-l
>
> --
> =======================================================================Lincoln> D. Stein                           Cold Spring Harbor Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, NY
> ======================================================================------------------------------------------------------->
>
> --
> =======================================================================Lincoln> D. Stein                           Cold Spring Harbor Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, NY
> =======================================================================