GBrowse/AJAXhandlerScript

Proposal to convert gbrowse_details to an AJAX request handler

A temporary page to describe a low-impact change to existing code to provide a built-in ajax handler for Gbrowse

Examples

• A balloon hover with contents generated using an AJAX call to gbrowse_details and the params callback shown below

• A sticky balloon with contents generated from gbrowse-details (via an <iframe> element) and the default callback shown below.

Changes to gbrowse_details

• A new CGI parameter to invoke the AJAX-handling behavior

my $rmt   = param('remote');

• A response is triggered after the feature(s) are defined but before PrintTop is called.

 if (defined $rmt) {
   print header,start_html;
   print remote_content($rmt,$features[0]);
   print end_html;
   exit 0;
 }

• The remote_content subroutine will get the text or coderef. It will return the text or execute the callback with user-defined arguments

 # do something for popup balloons
 sub remote_content {
   my $key = shift; # the key for the text or code-ref in the gbrowse config file
   my $feat = shift;
   my $contents = $CONFIG->config->code_setting('TOOLTIPS',$key) or die "$key is empty";
   my $coderef = (ref $contents||'') eq 'CODE';
   return $contents unless $coderef;
   # paranoia?
   die "Error: $key is not a CODE-REF" if ref $contents && !$coderef;
   # args are user-defined
   my %args = (feature => $feat) if $feat;
   for my $arg (param()) {
     my @vals = param($arg);
     my $val  = @vals > 1 ? \@vals : $vals[0];
     $args{$arg} = $val;
   }
   return $contents->(\%args);
 }

Changes To Configuration File

• A new section [TOOLTIPS] that has all the named text sections or callbacks you need to access through gbrowse_details
  • NOTE: This section must be placed at the end of the [GENERAL] section.

• The [ORF] configuration stanza used to generate the images above. The relevant section is highlighted

Changes to Bio::Graphics::Browser

• Minimal changes to balloons code. Width option introduced to allow custom width constraints. Setting the iframe width should hopefully make the contents stay inside the balloon boundaries.