***UNCHECKED*** Finished in Dundee

Well, that was terrific fun!

We have a preliminary port to JavaScript that is pretty much only missing GUI components (menus, pop-up forms and dialogs, scrollbars). No promises on when I will get to that. It runs locally, but there is something odd about the way it runs remotely, and http://chemapps.stolaf.edu/jalview/buildSite.xml does not work. Jim, it does not recognize http://chemapps.stolaf.edu/jalview/site/ file as a FASTA file:

Resource ‘uniref50.fa’ was located by classloader.
Protocol identified as ‘ClassLoader’
File identified as ‘BLC’

So something is wrong there. I have no more time to work on this in Dundee, so I will have to take a look at that as I have the opportunity.

Jim, last night I did a few optimizations and removed the most egregious issues with method overloading. Still plenty to do there.

The good news is that it does actually work, and pretty smoothly – at least locally. Attached is a working copy (for me, tested in FF only).

The bad news is that the core download for Google Closure Compiler processed Jalview classes is 2.7 MB. That’s on top of the 1.1 MB core SwingJS load. I’m sure that can be trimmed down – that includes all the files listed in http://chemapps.stolaf.edu/jalview/buildSite.xml and hopefully not all those are actually needed. But it is pretty large.

Zhou Renjian and Udo – I found some more bugs in the J2S system, mainly in the j2slib runtime, not the compiler. I have those all listed in a document I will share with you.

Zhou Renjian, note that I am using a substantially modified “j2slib.js” – see http://chemapps.stolaf.edu/jalview/site/js/j2sSwingJS.js lots of notes in there. It’s pretty heavily diverged from what we started with.

Jim, this should have the latest, although I did not actually run it from that project, just copied my Eclipse 4.2 project files into it. Please give it a go. Note that it is master, not debug

Username for ‘https://source.jalview.org’: hansonr
Password for ‘https://hansonr@source.jalview.org’:
Counting objects: 293, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (129/129), done.
Writing objects: 100% (140/140), 23.13 MiB | 564.00 KiB/s, done.
Total 140 (delta 99), reused 0 (delta 0)
To https://source.jalview.org/git/jalviewjs.git
5b669b6…e34e405 master → master

Jalview_site.zip (4.19 MB)


Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department of Chemistry
St. Olaf College
Northfield, MN

If nature does not answer first what we want,
it is better to take what answer we get.

– Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Hi Bob,

Thanks for all the details and for spending time with us to see if it was possible to translate Jalview to JavaScript in a manageable way.

I’m stunned by how much progress you made in the short visit here and absolutely delighted to see Jalview working in Javascript and pretty responsive too! You have given the Jalview project a really solid base to build on. If over coming months we can get this to the point of being part of the standard production build for Jalview, the 100s of 000s of webpages that currently embed the Jalview applet will have a powerful option!

Again, thanks for taking the time to visit us and work on this challenging project!

All the best,



On 25/07/2015 08:52, Robert Hanson wrote:

Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology   
College of Life Sciences | University of Dundee, Scotland, UK | [g.j.barton@dundee.ac.uk](mailto:g.j.barton@dundee.ac.uk) 
Tel: +44 1382 385860 | [www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk) | twitter: @gjbarton

The University of Dundee is registered Scottish charity: No.SC015096