(no subject)

Dear all,

is it possible to use Jalview in a web browser without an http server ?
I’d like to use something like file:///somewhere/xxxx.html
containing

It works well through an http server but I get
Jalview can’t open file “myfile.tfa”

Any idea ?
Thanks
Raymond

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Raymond Ripp raymond.ripp@igbmc.fr
Laboratoire de Bioinformatique et Génomique Intégratives
Département de Biologie et Génomique Structurales
Institut de Génétique et de Biologie Moléculaire et Cellulaire
IGBMC 1 rue Laurent Fries 67404 Illkirch-Strasbourg France
tel (33) 3 88 65 33 05 fax (33) 3 88 65 32 76

Hi Raymond.

is it possible to use Jalview in a web browser without an http server ?
I’d like to use something like file:///somewhere/xxxx.html
containing

It works well through an http server but I get
Jalview can’t open file “myfile.tfa”

If you get this message, it means that JalviewLite has started up, but it couldn’t access one of your input files. Check that you can open each file that Jalview is trying to load using the same base URL ‘file:///somewhere/’+

Any idea ?

I suggest you enable the Java console (see the ‘advanced’ settings in your java prefences), and check to see if there are any warnings popping up. Set the ‘debug’ parameter to ‘true’ to make JalviewLite emit more detailed information about what URLs it’s trying to retrieve.

Hope that helps…
Jim.

(sorry to answer directly to you but I don’t know how to answer to the list … and I forgot also the subject)

no worries :slight_smile: (the email you are using may may not be subscribed to jalview-discuss, by the way - you need to send to the list with an email that is registered here http://www.jalview.org/mailman/listinfo/jalview-discuss ).

I didn’t find the Java console on my Linux Firefox and and tried on Windows and … it works well !!!
(It’s the same xxxx.html as on Linux)
The applet, xxxx.html and myfile.tfa are in the same directory !!!

On Linux I tried all possible solutions with myfile.tfa, /somewhere/myfile.tfa, and also http://…/myfile.tfa but got always “can’t open …” , and I saw them using file:///somewhere/myfile.tfa or http://…/myfile.tfa

I’ll try to install the Java Console on my Linux Firefox or Chrome browser, and I’ll tell you what happens.

I think this is almost certainly a java applet security issue. It’s been a while since I did much work with local files and the applet on a linux box, so I can’t tell you off-hand what magic you need to invoke to make this work, but I think I did manage to get around this problem in the past (but it’s over 5 years since linux was my main dev environment for jalview :slight_smile: ).

If you aren’t worried about HTML layout, however, then the appletviewer will probably do everything you need.

Otherwise, try and experiment with java applet security policy files: http://java.sun.com/developer/technicalArticles/Security/applets/

best of luck!
Jim.

ps. you should be able to enable the java console when java starts up in the browser via the java console’s ‘Advanced tab’. Open it via the ControlPanel binary in your JRE directory’s bin directory (http://www.java.com/en/download/help/enable_console_linux.xml ).

[Apologies for cross-posting]

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==============================
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