The version, build date and originating commit ID are given in swingjs/j2s/.build_properties.
Clone this repository somewhere, and when you want to provide a JalviewJS component on a page, you just need to reference the SwingJS bootstrap script for JalviewJS, and include a call to start JalviewJS in one of the following ways:
You probably want to have the ‘sysoutdiv’ hidden or omitted, of course.
By default, the jalview.bin.Jalview entrypoint for JalviewJS will look at the first argument passed on the URL and process it as a standard Jalview command line.
SwingJS calls the main method of the class specified by the ‘main’ key. If an ‘args’ key is defined then this will be parsed as command line arguments in the same way, except URL-encoding of spaces to separate each argument is not necessary.
args:"-open examples/uniref50.fa -tree examples/ferredoxin.nw -annotations examples/plantfdx.annotations"
For JalviewJS alpha, embedded mode is still a work in progress. The principle is that when JalviewJS is started up in embedded mode, the Jalview Desktop is hidden, and any windows opened are shown in specially tagged <div> elements.
JalviewJS is still experimental, and we are working to improve its functionality and also the way in which JalviewJS is built.
Either clone Jalview’s git repository and check out the version you need, or download the corresponding Jalview source distribution. Instructions for setting up the SwingJS/Java2Script toolchain and building JalviewJS are given in documentation accompanying Jalview’s source.
The Jalview build system will ultimately generate a tarball ‘jalviewjs-site.tar.gz” that can be deployed on a local or remote web server.
This repository contains a subset of the full jalviewjs-site.tar.gz tarball:
Until the process is fully automated, this git repository is manually updated by:
cd jalview-js # change to repository working directory rm -Rf swingjs # delete existing jalviewjs files tar -zxf jalviewjs-site.tar.gz # unpack the latest JalviewJS distribution git add -u # add any updated files in swingjs, or examples directory git add swingjs # add any new files in swingjs git commit # make sure you state which version the release includes
It is probably also a good idea to verify the links above for JalviewJS.html and JalviewJS_embedded.html still work. If they don’t, then patch them and add and commit those changes.