[Bioperl-l] Bio::Graphics Description layout question

[Roels, Steven]

Nathan

>-----Original Message-----
>From: Agrin, Nathan [mailto:Nathan.Agrin at umassmed.edu]
>Sent: Friday, July 16, 2004 10:19 AM
>To: Roels, Steven; bioperl-l at bioperl.org
>Subject: RE: [Bioperl-l] Bio::Graphics Description layout question
>
>Thanks for the help,
>
>Using the -key_style=>'right' seems to work on some tests I ran, but as
>soon as I feed -key the function " sub { $des =
>$feature->each_tag_value('description'), "$description"; } " it stops
>working.  I can feed the -key something like sub { return "test" } and
>it works fine.  I've been really frustrated trying to deal with this
and
>any help is appreciated.
>

You need to handle to passed-in feature:

sub { ($des) = $_[0]->get_tag_values('description'); }

or 

sub { my $feature = shift;
      ($des) = $feature->get_tag_values('description'); }

this assumes your features always have that tag - otherwise you need to
test for it:

sub { my $feature = shift;
	( $feature->has_tag('description') ) ? 
      ($feature->get_tag_values('description'))[0] : "no_desc"; }


warning - didn't test the above, so pardon any typos :)

Hope that helps.


>
>
>-----Original Message-----
>From: Roels, Steven [mailto:Steven.Roels at mpi.com]
>Sent: Thursday, July 15, 2004 6:57 PM
>To: Agrin, Nathan; bioperl-l at bioperl.org
>Subject: RE: [Bioperl-l] Bio::Graphics Description layout question
>
>
>Nathan,
>
>I believe you need:
>
>-key_style=>'right'
>
>as an option to
>
>Bio::Graphics::Panel->new()
>
>But then you need to have:
>
>-pad_right=>$padright
>
>as well, such that $padright is big enough to fit the keys
>
>See the poddoc for Bio::Graphics::Panel...
>
>-Steve
>
>>-----Original Message-----
>>From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
>>bounces at portal.open-bio.org] On Behalf Of Agrin, Nathan
>>Sent: Thursday, July 15, 2004 1:13 PM
>>To: bioperl-l at bioperl.org
>>Subject: [Bioperl-l] Bio::Graphics Description layout question
>>
>>Is there anyway to get the bioperl graphics package to draw the
>>descriptions for the tracks to the right of the tracks?  I've seen
>>something like this done with a browser developed by JGI.  Here is the
>>link to an example:
>>
>>http://genome.jgi-psf.org/cgi-bin/dispGeneModel?db=chlre2
>><http://genome.jgi-psf.org/cgi-bin/dispGeneModel?db=chlre2&id=157911>
>>&id=157911
>>
>>Thanks,
>>Nate
>
>
>
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