Hello, Geoffrey.
We are working on a couple of different approaches for allowing Jalview to run within the browser. One is to cross-compile Jalview as a pure javascript component: You might have seen some posts on our jalview development list - including this image showing a jalview applet view rendered purely in Javascript:
http://www.jalview.org/pipermail/jalview-dev/attachments/20150725/40d17b69/attachment-0001.png
JalviewJS is far from complete and we will be working with Robert Hanson (who also developed JmolJS and Jmol) over the next few months to improve its performance and capabilities.
The other approach is to provide support for data exchange with in-page alignment visualisation components. There are a number available, and we are working on a JSON data interchange standard that will allow in-page visualisations to be used in concert with the Desktop application. For very large alignments, native Java still provides far superior performance, particularly when working with phylogenies and 3D structure data.
Oh - there’s one other thing… whilst NPAPI might be eliminatated from Chrome there has been talk of the creation of a new jRE plugin based on chrome’s native plugin system… I doubt the Jalview team will be involved in that but we’re certainly interested in the results… if any!
Let us know if you’re interested in following up on any of the above…
Jim Procter.
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On 07/08/2015 15:47, Geoff Kemball-Cook wrote: