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