[Jalview-discuss] question about using DAS service and JalviewLite

[Sai Tong]

Hi Jim, Andrew

thanks for your responses.  These ideas are very cool. 

In order for the DASTY server side DAS proxy system to be used by 
JalviewLite, does it necessarily mean that a proxy (the retrieval 
module) would need to be installed in people's own web server ? 

 If a JQuery/JalViewLite plugin is to be made successfully, does it mean 
that web developers can just give a bunch of (i.e.) uniprot ids as 
parameters to JalviewLite and JalviewLite would take care the rest of 
the communication and data retrieval steps with the DAS servers? 

Will something like the following  JS library for DAS be part of this 
proposed plugin?
http://code.google.com/p/jsdas/

Currently, I've written some server-side codes on my server to retrieve 
uniprot sequences  (based on selected uniprot ids) in a jsp file and 
then submit these sequences for alignment in JalviewLite by using this:

<param name="sequence1" value="yyyy TSPVV">
<param name="sequence2" value="zzzz TSPVV">

and as for getting sequence feature annotations, I'm writing server-side 
codes to retrieve gff file from uniprot (one by one for each sequences 
in the alignment)

http://www.uniprot.org/uniprot/Q65GN7.gff

and then I'd concatenate the contents from all of the gff files in order 
to make 1 single file to be applied into JalviewLite's alignment:

<param name="Features" value="file.gff">

(just a side question, can multiple Feature parameters be applied to 
sequence alignment in JalviewLite ? Haven't try this yet...)

I'm interested to help to extend the DAS-connection of JalviewLite.  But 
I am not sure if I'd qualify for doing this as a "Google Summer of Code" 
project.

-Sai

Andrew Waterhouse wrote:
> Hello Sai,
>
> The reason JalviewLite cannot search and retrieve uniprot sequences 
> directly is due to the security of web browsers, ie a page cannot run 
> scripts that access files that come from a different server without 
> the users permission.
>
> When you start up the Jaliew standalone version, you agreed to allow 
> the program to access other web servers, so the program connects to 
> many DAS servers around the world.
>
> The applet in Jalview 2 was designed to be dropped into any web page 
> anywhere for easy use by researchers. In order to access other 
> servers, such as Uniprot, then an amount of coding is required, and 
> this would reduce the portability of the applet.
>
> I would suggest a jQuery JalivewLite plugin would be very useful for 
> javascript web developers, for sequence/feature retrieval from DAS 
> servers. However, this would still require the coder to do some server 
> side coding (a proxy server would be the easiest solution)
>
>
> Would this be a good project for "Google Summer of Code" Jim?
>
>
> Andrew Waterhouse
>
>
>
>
> Jim Procter wrote:
>> On 10/03/2010 04:45, Sai Tong wrote:
>>  
>>> So from what I understand, there is no way one can pass-on uniprot id
>>> directly into JalviewLite (applet version of Jalview) to  search 
>>> uniport
>>> and retrieve protein sequence and sequence feature annotations, similar
>>> to what one can do using the standalone version of  Jalview. Is that
>>> correct ?
>>>        
>> It is.
>>  
>>>    in order to add feature annotations to JalviewLite , one needs to
>>> first create a gff file containing the feature annotation and then use
>>> the following:
>>>
>>>   <param name="Features" value="file.gff">
>>>
>>> in order to make the features annotated and visualizable inside
>>> JalviewLite .  What other ways that one can add feature annotations via
>>> the use of JalviewLite applet.
>>>        
>> Sequence features can be imported using the Jalview feature file or 
>> GFF files - and the ordering and colouring of the features are 
>> controlled using the feature colourscheme definitions (see the 
>> jalview feature file format 
>> http://www.jalview.org/help/html/features/featuresFormat.html ).
>>
>> The 2.4 version of JalviewLite has no specific features for database 
>> querying - this is because its designed as a web app user interface 
>> component, so its restricted to the browser's sandbox (and cannot 
>> query arbitrary URLs). However, its relatively straightforward to set 
>> up a server-side service that the applet could use to retrieve a gff 
>> or Jalview features file containing alignment annotation.
>>
>> All you need to do is put the URL of the service in the value field 
>> of the 'Features' parameter. You can also upload and control the 
>> display of features via javascript - check out the example and API 
>> for details (http://www.jalview.org/examples/formComplete.html - 
>> scroll to the bottom of the page).
>>
>> One development path for JalviewLite is to introduce some components 
>> that people can use on their servers to more tightly integrate the 
>> applet with their own web services. For instance, the DASTY server 
>> side DAS proxy system could be used by JalviewLite, with only a few 
>> modifications. Let me know if your interested in this.
>>
>> Thanks for the email, and please get in contact if your interested in 
>> extending what JalviewLite can do for your application!
>>
>> Jim.
>>
>> -------------------------------------------------------------------
>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>
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