[Jalview-discuss] Automate overview window
avilella at gmail.com
Tue Jan 19 09:56:55 GMT 2010
Ah, yes! The PNG output is exactly what I need. I wasn't aware of it.
So say I have a directory with the files, what's the commandline to
call jalview and generate the PNGs of the overviews?
The next question it's going to be, how do I generate the PNG overview
with the associated tree at the left-hand side of the image?
On Mon, Jan 11, 2010 at 3:14 PM, Jim Procter
<jprocter at compbio.dundee.ac.uk> wrote:
> 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.
> 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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