[Jalview-discuss] Automate overview window

[Jim Procter]

Hello Albert, thanks for the interesting question! :)
> A quick question about Overview window. I am using the latest full
> version of Jalview (not the applet) to quickly inspect a list of a few
> hundred alignments. I would like to know if it's possible to automate
> the process of doing a snapshot of the Overview window.
There's no command line option to do what you ask, but it should be 
possible to automate this - firstly using a jalview properties file with 
a line containing 'SHOW_OVERVIEW=true' (which you'd pass in via the 
'props' argument) and a bit of groovy script (passed in using the 
-groovy option) that would maximise the overview window.

Before I go further, though, I'm slightly curious as to why you want a 
snapshot of the overview window. Presumably you want to generate an 
overview of the set of alignments, but I wonder if you might not get the 
same effect by using Jalview's existing PNG output command line option 
and then rescaling the images to get a set of standard size thumbnails ? 
You could even do the second step by embedding the images in an html 
page where you specify the width and height as a standard size.

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.