[Bioperl-l] Again, boxes in heterogenious segments

[Marco Aurelio Valtas Cunha]

Hi all,

  I'm replying myself because I'm really in trouble here. We have to decide if 
is possible to use Bio::Graphics or not to continue the project, or we have to 
develop another way to render the graphics we want. So if somebody has a thought 
  it will help a lot.

Marco.

Marco Aurelio Valtas Cunha wrote:
> Hi all,
> 
> I'm trapped trying to call $graphics->boxes on a heterogeneous_segments 
> track, how this is supose to work?  How to get the coordenates of 
> sub_SeqFeaures?
> Just to add, I'm trying to make a box with some snps in it, instead of 
> arrows bellow the box.
> The code is similar to this:
> 
> --snip
> 
> $gene = Bio::SeqFeature::Generic->new(-primary_tag=> 'region', -start=> 
> 0, -end=> 200, -source=>'region');
> 
> foreach(@my_snps){
> 
> my($snp_name,$coord) = @{$_};
> 
> $snp = 
> Bio::SeqFeature::Generic->new(-primary_tag=>"$snp_name",-start=>$coord, 
> -end=>$coord, -source=>'snp');
> 
> $gene->add_sub_SeqFeature($snp);
> }
> 
> $graphics = Bio::Graphics::Panel->new(-segment=> $gene, -width=> '200');
> $graphics->add_track( heterogeneous_segments  => $gene,
>                                         -fgcolor         => \&snp_color,
>                                         -exon_color      =>'blue',
>                                         -intron_color    =>'red',
>                                         -heigth          => 15,
>                                     );
> # Now calling boxes!!
> my @boxes = $graphics->boxes;
> 
> # This always print the gene coords...
> print "$_->[0]->primary_tag.$_->[1].$_->[2].$_->[3].$_->[4]\n" 
> foreach(@boxes);
> 
> exit(0);
> --snip
> 
> Marco.
> 

-- 
Marco A Valtas Cunha     http://scarecrow.fmrp.usp.br/~mavcunha/
Lab de Bioinformatica    http://bit.fmrp.usp.br
Hemocentro de Rib Preto  http://ctc.fmrp.usp.br
Fax: 55 16 3963-9309     Tel: 55 16 3963-9300 R:9603