Firefox 3.6 on Mac OSX fails to run JalviewLite

Hello,
My applet doesn't run in Firefox on OSX for some reason. My code
appears below. There are no error messages, only "The application
failed to run".
I hope someone has seen this before and knows the solution. I'm
guessing I have a <param> missing.
It runs on other platforms and in Safari on OSX. Even the demos run in
Firefox on OSX http://www.jalview.org/examples/applets.html

My Jalview applet page: http://nbase.biology.gatech.edu/tools/align/lcbs.cgi
---code---
   <applet width=100 height=40 code="jalview.bin.JalviewLite"
archive="/tools/snp/jalviewApplet.jar">
       <param name="file" value="/tools/snp/SNPtool/current/LCB0.aln">
       <param name="defaultColour" value="Clustal">
   </applet>
---code---

Thanks,
Jay Humphrey

Hi Jay.

Hello,
My applet doesn't run in Firefox on OSX for some reason. My code
appears below. There are no error messages, only "The application
failed to run".
I hope someone has seen this before and knows the solution. I'm
guessing I have a<param> missing.
It runs on other platforms and in Safari on OSX. Even the demos run in
Firefox on OSX http://www.jalview.org/examples/applets.html

My Jalview applet page: http://nbase.biology.gatech.edu/tools/align/lcbs.cgi

I had to allow Java to run on that page - and then it worked fine, although it did take a while to grab the data. Admittedly, I'm on FF4, but I can't imagine there's any problem with your code. Its simply a browser permissions issue.

I'm not sure what's the best way of informing the user that they have to allow Java to run for a site.. browsers do give some indication, but its often a very discrete box or icon somewhere that the user has to click on (in the FF4 case - the dialog box was camoflaged and blended in to the page's own layout!). Some sites have an alert box pop up if you haven't allowed Java for the site.

Does anyone have any javascript that will pop up a 'you must allow Java' alert box for Jay ? I've tried using sun^H^H^HOracle's own javascript library (www.java.com/js/deploy.js) which does some checks like this, but it doesn't behave well on Chrome, so I can't recommend it.

Jim.

···

On 06/05/2011 13:24, Jay Humphrey wrote:

Hi Rebecca

Hi,

I’ve tried to send this to the mailing list but it keeps bouncing back - I’ve registered and am receiving other people’s questions so not sure what’s wrong. The message I get back is:

----- The following addresses had permanent fatal errors -----
jalview-discuss-bounces@compbio.dundee.ac.uk
(reason: 550 jalview-discuss-bounces@compbio.dundee.ac.uk: Recipient address rejected: User unknown in local recipient table)

Yep. - we’re having some config issues with our mail server - if you send emails to jalview-discuss@jalview.org then they should get through, but the alternate email address (containing lists.compbio.dundee.ac.uk) is broken at the moment.

The question I’m trying to ask is:

Our IT team has recently upgraded my 64-bit linux computer to Fedora 14. Now when I open an alignment in Jalview and try to scroll to the right, the image becomes distorted and impossible to read. Is this a known problem and are there any fixes?

It’s not something I’ve heard about before, though I can imagine what might be going wrong, since there have been problems in the past with the latest linux window managers not being properly supported by the latest version of Java. I’ve lodged a bug here:
http://issues.jalview.org/browse/JAL-830

If you’d like to register and log in to the bug tracker, you should be able to add a screenshot of the problem as an attachment.

Jim.