[Gmod-ajax] Embeding jbrowse in a web site

[Mariette <jma...@to...>]

Hi everyone,
I'm trying to add jbrowse to our website, which is basicly a detection 
and annotation
platform for non coding RNA. When RNAs are detected, I'd like to show 
them up using
jbrowse, but I got some trouble adding it to our web page !
So I added all the javascript and css to our page and then placed the 
following code (
which is the one provided in the index.html) to the javascript section :
  
var queryParams = dojo.queryToObject(window.location.search.slice(1));
    var bookmarkCallback = function(brwsr) {
        return window.location.protocol
               + "//" + window.location.host
               + window.location.pathname
               + "?loc=" + brwsr.visibleRegion()
               + "&tracks=" + brwsr.visibleTracks();
    }

    var t = new Browser({
                            containerID: "GenomeBrowser",
                            refSeqs: refSeqs,
                            trackData: trackInfo,
                            defaultTracks: "DNA,gene,mRNA,noncodingRNA",
                            location: queryParams.loc,
                            tracks: queryParams.tracks,
                            bookmark: bookmarkCallback
                        });

then I added the div to my page content (still just like it is in the 
index.html page of jbrowse) :
<div id="GenomeBrowser" style="height: 100%; width: 100%; padding: 0; 
border: 0;"></div>

I can see my page changing but I'm far from having the result I can get 
when using it localy !!
So I was wondering if using it the ?loc and &tracks are important, we 
give to our page some
arguments and it may be a problem ?

Also, there was something wrong in the Utils.js file, I had to change 
the following function from :
function $(element) {
   ...
}

to
function (element) {
   ...
}

It may be a problem has well !
Thanks for giving me some info if I'm doing something wrong or not,

Jerome