[Jalview-discuss] groovy scripting on jalview startup

[Jim Procter]

Hey David .. thanks for the email.

On 03/08/2011 00:09, David M. Goodstein wrote:
> I was wondering if anyone had developed a template for a groovy 
> start-up script that, after initial loading of an sequence set, can 
> fire off one of the web services (e.g., Muscle).
nope :(  but that is mostly because there are not many people working 
with groovy in Jalview as yet.

Looking at the code, this probably isn't immediately straightforward to 
do, since the web service clients in jalview desktop are designed to be 
run on an already displayed alignment. That being said, I do have an 
interactive testing script that loads a file into a new alignment window 
which could be adapted to launch a web service job and close the window 
once the job has completed.

Since the adaptation of the script might be made easier if I modify some 
of Jalview's java code, I've opened a bug to collect all the git commits 
together: http://issues.jalview.org/browse/JAL-894

What timescale were you thinking of for being about to do this ?
Jim.