[Bioperl-l] [Bio::Graphics::Panel] code reference cannot pass to -link, why?

[Xianjun Dong]

Hi,

I have a problem while using the -link in Bio::Graphics (version 1.96):

As the POD of Bio::Graphics described 
(http://search.cpan.org/~lds/Bio-Graphics-1.96/lib/Bio/Graphics/Panel.pm#Creating_Imagemaps), 


link format like:

  -link => 'http://www.google.com/search?q=$description'


works well in my code, but the format like

  -link => sub {
         my ($feature,$panel) = @_;
         my $type = $feature->primary_tag;
         my $name = $feature->display_name;
         if ($primary_tag eq 'clone') {
            return "http://www.google.com/search?q=$name";
         } else {
            return "http://www.yahoo.com/search?p=$name";
         }


does not output image map as expected.

Here I attached a simple code as example for anyone who is willing to 
test for me:

        #!/usr/bin/perl
        use strict;
        use Bio::Graphics;
        use Bio::Graphics::Feature;
        my $ftr= 'Bio::Graphics::Feature';
         
        # processed_transcript
        my $trans1 =
        $ftr->new(-start=>50,-end=>10,-display_name=>'ZK154.1',-type=>'UTR');
        my $trans2 =
        $ftr->new(-start=>100,-end=>50,-display_name=>'ZK154.2',-type=>'CDS');
        my $trans3 =
        $ftr->new(-start=>350,-end=>225,-display_name=>'ZK154.3',-type=>'CDS',
        -source=>'a');
        my $trans4 =
        $ftr->new(-start=>700,-end=>650,-display_name=>'ZK154.4',-type=>'UTR');
        my @trans = ($trans1,$trans2,$trans3,$trans4);

        my $panel= Bio::Graphics::Panel->new(-start =>0,-length=>1050);

        $panel->add_track(\@trans,
                  -glyph   => 'transcript2',
                         
                          # This works well!
                          #-link =>
        'http://www.google.com/search?q=$name', 
                         
                          # while, the following code does not work as
        expected.
                          -link => sub {
                                      my ($feature,$panel) = @_;
                                      my $type = $feature->primary_tag;
                                      my $name = $feature->display_name;
                                      if ($type eq 'CDS') {
                                         return
        "http://www.google.com/search?q=$name";
                                      } else {
                                         return
        "http://www.yahoo.com/search?p=$name";
                                      }
                                 }
                          );
        my $map = $panel->create_web_map("mapname");
        print $map;
        $panel->finished();

In my test (Bioperl 1.6.0), its output is:

        <map name="mapname" id="mapname">
        <area shape="rect" coords="11,0,58,7"
        href="http://www.yahoo.com/search?p="  />
        <area shape="rect" coords="57,10,115,17"
        href="http://www.yahoo.com/search?p="  />
        <area shape="rect" coords="257,0,401,7"
        href="http://www.yahoo.com/search?p="  />
        <area shape="rect" coords="743,0,801,7"
        href="http://www.yahoo.com/search?p="  />
        </map>


It seems $feature->primary_tag returns 'track' (I don't know where this 
come from...), but not the type of features.  Anyone has clue for this 
problem?

Thanks

-- 
==========================================
Xianjun Dong
PhD student, Lenhard group
Computational Biology Unit
Bergen Center for Computational Science
University of Bergen
Hoyteknologisenteret, Thormohlensgate 55
N-5008 Bergen, Norway
E-mail: xianjun.dong at bccs.uib.no
Tel.: +47 555 84022
Fax : +47 555 84295
==========================================