[Bioperl-l] About graphic rendering

[Lincoln Stein]

Which glyph are you using to display these features? You may wish to set the
bump property to zero so that the features don't spread out vertically; this
happens automatically with some of the glyphs such as
"heterogeneous_segment"

Lincoln

On Wed, Dec 3, 2008 at 1:21 PM, Paolo Pavan <paolo.pavan at tecnoparco.org>wrote:

> Hi everybody,
> I've a question about a Bio::Graphics rendering. I would like to display a
> blast HSP on a track but I would like to draw the "tails" of my mapping
> sequence that don't match the subject. So I instantiate these 3 object that
> represent all the three segments I want to display:
>
> my $feature = Bio::SeqFeature::Generic->new(
>                                    -display_name
> =>$sequence_to_map->display_id,
>                                    -start        =>$hsp->sbjct->start,
>                                    -end        =>$hsp->sbjct->end,
>                                    );
> my $feature_pre = Bio::SeqFeature::Generic->new(
>                                    -start        =>($hsp->sbjct->start -
> $hsp->query->start),
>                                    -end        =>$hsp->sbjct->start-1
>                                    );
> my $feature_post = Bio::SeqFeature::Generic->new(
>                                     -start        => $hsp->sbjct->end+1,
>                                     -end        => $hsp->sbjct->end +
> $sequence_to_map->length - $hsp->query->end
>                                    );
>
> now I have to add these features to my $track in a manner that the
> $feature_pre and $feature_post paint or color in a different way than
> $feature but align horizontally.
> I tried with:
>
> $feature->add_sub_SeqFeature($feature_pre, 'EXPAND');
> $feature->add_sub_SeqFeature($feature_post, 'EXPAND');
>
> $track->add_feature($feature);
>
> This does not work, because the features spread vertically, and more I
> cannot change the glyph because seems to be a track property, not a feature
> one.
>  Any idea?
>
> Thank you for your help,
> Paolo
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-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
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Cold Spring Harbor Laboratory
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Assistant: Sandra Michelsen <michelse at cshl.edu>