starting Jalview via webstart from your own website

Hi again Marcelo.

I've cc'ed this to the discussion list, just for the record.

Marcelo bertalan wrote:

Thank you for your reply.

no problem.

I have been using Javaws for artemis without any problem, but I still
have problems with Jalview.

oh - ok...

I was wondering if is possible to use jalview.jnlp and ask to open my

yes. that's the preferred (and only reliable) way of doing that.

    <application-desc main-class="jalview.bin.Jalview"/>

that looks ok - but you need the -open parameter before the alignment
filename. The example file will only be opened if there were no valid
input files given on the command line *and* the user preferences
indicate that the example should be opened on startup by default. My
guess is that you haven't specified the argument correctly.

There's a jalview jnlp generator servlet here:

Try this URL:;%20R,K,H=FF5555;%20D,E=5555FF

wget on this url returns a jnlp with the following args:
<application-desc main-class="jalview.bin.Jalview">
<argument>C=yellow; R,K,H=FF5555; D,E=5555FF</argument>

Can I open Jalview from your server opening files from my server (like I
do with artemis) or should I put Jalview in my server opening my files ?

If you want, you could just use the
service directly - by embedding the URL in pages served by your own
site. We try to make sure the servlet is available continuously and it
will always refer to the latest Jalview webstart install. As far as
privacy goes we do occasionally analyse the logs there, but won't touch
the data otherwise, since for us its nice to know that Jalview is being
used on other people's sites. If your concerned about that, then feel
free to host a jnlp or jnlp generator of your own!

you should also check out the development URL for jalview - we are
hoping to release version 2.4 sometime this year (actually sooner rather
than later, but ... oh well). The development build is refreshed here: - here you can
see the most up to date versions of the applet, application and source.
I wouldn't recommend using the webstart build there for your website,
though - since it is an automated build from CVS - and not guaranteed to
be stable.

best of luck - and please send us a URL for your site so we can make a
link to it on the Jalview links page !



J. B. Procter (ENFIN/VAMSAS) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764
The University of Dundee is a Scottish Registered Charity, No. SC015096.