This is the new server for GMOD.org. Please let us know if you notice anything weird while it's getting broken in.

GBrowse/AJAXhandlerScript

From GMOD
Jump to: navigation, search

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

Sample1b.png


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

Sample2b.png

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||&#39;&#39;) 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.

Callbacks


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

Orf stanza

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.

Browsercode