[Jalview-discuss] Automate overview window

[Albert Vilella]

Hi Jalviewers,

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. Here is what I
do now:

for file in `ls *clustalw`; do java
-Djava.ext.dirs=/home/avilella/9_opl/jalview/Jalview/lib -cp
/home/avilella/9_opl/jalview/Jalview/jalview.jar jalview.bin.Jalview
-open $file; done

Then I manually click on View->Overview Window, maximize the window,
and take a screenshot of it. Then close jalview, and the next
alignment opens up.

Is there a option to automatically open the overview window when I
call it from the command line? Something like:

-open $file -overview_window

Looking forward to hearing from you,

Cheers,

Albert.