Export overview window

Hi everyone,

I was wondering if it was possible to export the overview window directly to PNG to create full genome alignement figures ?

Albert has raised a similar question (see below) in 2010 and I don’t really understand the answer about using the console to do the export….

Thanks a lot for your help.


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?



><i> Hello Albert, thanks for the interesting question! :)
</i>>> >><i> A quick question about Overview window. I am using the latest full
</i>>><i> version of Jalview (not the applet) to quickly inspect a list of a few
</i>>><i> hundred alignments. I would like to know if it's possible to automate
</i>>><i> the process of doing a snapshot of the Overview window.
</i>> ><i> There's no command line option to do what you ask, but it should be possible
</i>><i> to automate this - firstly using a jalview properties file with a line
</i>><i> containing 'SHOW_OVERVIEW=true' (which you'd pass in via the 'props'
</i>><i> argument) and a bit of groovy script (passed in using the -groovy option)
</i>><i> that would maximise the overview window.
</i>> ><i> Before I go further, though, I'm slightly curious as to why you want a
</i>><i> snapshot of the overview window. Presumably you want to generate an overview
</i>><i> of the set of alignments, but I wonder if you might not get the same effect
</i>><i> by using Jalview's existing PNG output command line option and then
</i>><i> rescaling the images to get a set of standard size thumbnails ? You could
</i>><i> even do the second step by embedding the images in an html page where you
</i>><i> specify the width and height as a standard size.
</i>> ><i> Jim.
</i>> ><i> --
</i>><i> -------------------------------------------------------------------
</i>><i> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
</i>><i> Phone/Fax:+44(0)1382 388734/345764  [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk/)
</i>><i> The University of Dundee is a Scottish Registered Charity, No. SC015096.
</i>> >

On Mon, Jan 11, 2010 at 3:14 PM, Jim Procter <jprocter at compbio.dundee.ac.uk> wrote:

Hi Thomas

I was wondering if it was possible to export the overview window directly to PNG to create full genome alignement figures ?

Well done for digging out Albert’s question. We actually kind of faded out on that conversation - he found a workflow that worked at the time, and I drafted a new feature request about making it easier for people in the future.

What kind of export would you like ? A simple ‘write as PNG’ is certainly feasible, but the way the overview window works is that it takes samples the alignment according to the number of pixels in the image being rendered (e.g. if you make the overview window bigger, more detail is rendered in the overview figure). That means you might want to set the width and height too.



On 26/01/2015 15:37, Thomas Rensch wrote: