[Jalview-discuss] Automate overview window

[Albert Vilella]

Hi Jim,

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?

Cheers,

Albert.

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.
>
> 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.
>
>