Re: [Gmod-ajax] Feature Mark Up

[Steve T. <st...@mo...>]

Hi,

Been away for a few days but I have committed the code now. To get the required mark up you will have to run generate-tiles.pl which will generate html files containing the image map data in the same 
dir as the .png files. Currently, all the mouse over events are also stored in the html too. Yuk. This is a pretty low tech way of doing things and not very desirable in the long run esp. when we 
start populating it with real data... I tried to set mouseovers the on the fly using Ajax.Updater/onSuccess but had some problems that were related to caching (I think). I am sure Andrew would be able 
to fix this extremely quickly.

I have added a new var called htmlFiles in ViewerComponent.js. Setting this to 1 causes the browser to update the divs by pulling in the html, setting it to 0 means it uses the old style of specifying 
the path of the local image src.  htmlFiles default is 1 so if you do a cvs update and haven't run generate-tiles.pl remember to change it to 0.

> Actually, what I wrote before isn't quite correct; while the gbrowse cgi
> doesn't server up raw information, other cgis in the gbrowse
> distribution can.  You can get both DAS1 and biomoby, though I don't
> know that much the details of what the streams look like (DAS2 is XML, I
> don't think DAS1 is).  It is possible that javascript client-side code
> is already written for these services, I just don't know about it.
> 

Gbrowse Moby certainly looks like it could be a viable solution. In theory it seems to have in its favour that it should be straightforward to GET the data via a URL...

Cheers,

Steve


> Scott
> 
> 
> On Thu, 2006-11-16 at 09:54 -0800, Ian Holmes wrote:
> 
>>Chris Mungall mentioned something a while back about some sort of  
>>universal markup language he & Seth had specced out for GO. He also  
>>suggested some kind of protocol for publishing feature annotations in  
>>a sort of universal ontology framework.
>>
>>Chris, are you on this list? it'd be good to get these & related  
>>ideas in more concrete form...
>>
>>As well as rich pop-up info, we need to develop client-server  
>>protocols for (i) search and (ii) annotation upload.
>>
>>
>>On Nov 16, 2006, at 8:46 AM, Scott Cain wrote:
>>
>>
>>>On Wed, 2006-11-15 at 20:47 +0000, Stephen Taylor wrote:
>>>
>>>>Hi Andrew,
>>>>
>>>>>Next comes the figuring out how to populate the pop up menu with
>>>>>relevant info...
>>>>>
>>>>>
>>>>
>>>>Yep. This is more tricky... I think we should try and use as many
>>>>'official' GBrowse calls as possible to ensure future  
>>>>compatibility. I
>>>>wonder if Lincoln or Scott (if they are reading this) could offer any
>>>>advice?
>>>>
>>>
>>>The GBrowse cgi doesn't expose much in terms of fundamentals that one
>>>could use for populating popup menus with data.  Currently, people who
>>>use popups with gbrowse create all of the data up front and encode  
>>>it in
>>>javascript elements in the imagemap.  I suppose that works fine from a
>>>cgi point of view, but is not as appropriate for an ajax  
>>>application (is
>>>it?).  So if we want to make it work in an 'ajaxy' way, we'll need
>>>either to expand the api of the gbrowse cgi, or create another cgi for
>>>serving up xml for requests like that.
>>>
>>>If you want to see an example of how people are currently generating
>>>popups, you can look at this example:
>>>
>>>http://www.plasmodb.org/cgi-bin/gbrowse/plasmodb/? 
>>>start=101357;stop=121356;ref=MAL12;width=800;version=100;label=Annotat 
>>>edGenes-SyntenySpansVivaxMC- 
>>>SyntenyGenesVivaxMC;id=9cf36ae32368b7ec3e3c516c08c358d4
>>>
>>>which is done with this conf file:
>>>
>>>http://gmod.cvs.sourceforge.net/gmod/Generic-Genome-Browser/contrib/ 
>>>SynView/gbrowse.conf/plasmodb.conf? 
>>>revision=1.1.2.1&view=markup&pathrev=gbrowse-session
>>>
>>>Scott
>>>
>>>-- 
>>>---------------------------------------------------------------------- 
>>>--
>>>Scott Cain, Ph. D.                                          
>>>ca...@cs...
>>>GMOD Coordinator (http://www.gmod.org/)                      
>>>216-392-3087
>>>Cold Spring Harbor Laboratory
>>>----------------------------------------------------------------------