[Bioperl-l] About graphic rendering

[Paolo Pavan]

Hi Lincoln, thank you for your answer.
It actually seems that I don't have a glyph called "heterogeneous_segment",
maybe is it a BioPerl version problem? I have 1.5.2 installed.
( MSG: The requested glyph class, ``heterogeneous_segment'' is not
available: Can't locate Bio/Graphics/Glyph/heterogeneous_segment.pm in @INC
... )

However, I could even use a generic glyph if I can change the color of the
external features. I tried to use a bump = 0 but this cause to collapse more
segments I would like to add.
This is the graphic initialization part of the code:

        my $axis = Bio::SeqFeature::Generic-> new(
                             -start => 0,
                             -end => $database_seq->length
                                  );

        my $panel = Bio::Graphics::Panel->new (
                            -length => $database_seq->length,
                            -width     => $graphic_length,
                            -pad_left => 10,
                            -pad_right => 10
                            );

        $panel->add_track(            $axis,
                            -glyph    =>'arrow',
                            -tick    =>2,
                            -fgcolor=>'black',
                            -double    =>1
                            );
        my $track = $panel->add_track(
                            -glyph     => 'generic',
                            -label     => 1,
                            -bgcolor =>'blue',
                            #-bump =>1
                            );

Maybe isn't clear the idea of the final picture I would like to obtain?

Thank you again.

2008/12/4 Lincoln Stein <lincoln.stein at gmail.com>

> 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
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
> --
> Lincoln D. Stein
>
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>
>
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724 USA
> (516) 367-8380
> Assistant: Sandra Michelsen <michelse at cshl.edu>
>