Hi Barry.
I am interested to contact anyone who has implemented using JALVIEW with a local DAS server that serves features so that
I can ask for assistance on how to implement this. While I have managed to get a simple DAS server following the tutorials
up and running, I have not figured out the glue needed to configure jalview to send it a request or specifically what
I need to do on DAS side to support JALVIEWs requests. I have read the documentation on JALVIEW and DAS and
still have a lack of understanding.
Has anyone contacted you yet ? If not, I can probably call you via skype if you'd like to discuss what problems you are having. If your das source is working correctly, it really should be simple to add the URL for the source to Jalview's DAS source settings using the 'Add source' dialog box. Here's an example:
My DAS server has a web address like this:
http://das.intranet.university.edu/nameofserver
That means that I can get an XML document (or list) of features for a sequence with an accession number of XYZ123 by opening the following URL:
http://das.intranet.university.edu/nameofserver/../features?segment=XYZ123
In the above URL, the contents of the '..' depends on which DAS server you have set up. Many servers (proserver, dazzle, mydas) can serve a number of das sources, so you need to add in the source name like so:
http://das.intranet.university.edu/nameofserver/mydassource/features?segment=XYZ123
Assuming you've got all that working with the server, you should be able to load an alignment including your sequences - e.g. :
>XYZ123/1-10
ASDASDASDA
>XYY122/5-9
-----DASD-
Then, open the feature settings dialog box from the alignment window, select the 'DAS settings' tab, and click on the 'Add source' button.
In the dialog box that opens up, add the URL for your source like so:
http://das.intranet.university.edu/nameofserver/../
And also, give your source a nickname - its important that this is unique - since Jalview will tag every feature provided by your source with this nickname.
Finally hit 'OK'. If you look at the list of DAS sources, you should see your source listed, and it should also be enabled for feature retrieval (if it isn't, then toggle the checkbox to make sure it is). Then, simply press the 'Fetch Features' button to retrieve features for your sequences.
Jim.
···
On 19/11/2010 12:15, Kesner, Barry Alan wrote:
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J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
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