problem with fasta files


Begin forwarded message:

From: Judith Cohn <>
Date: June 10, 2009 1:24:15 PM MDT
To: James Procter <>
Subject: Re: [Jalview-discuss] problem with fasta files

Thanks. Just for fun, I recompiled the source code and indeed it works (at least when calling Jalview from the classes directory I generated - I have not made a jar file yet).


On Jun 10, 2009, at 10:18 AM, James Procter wrote:

Hello Judith.

It sounds like the 2.4 release has caused you a number of problems,which

is a shame. I’m not sure what’s going on with your Dock icon - all I can

suggest there is removing and re-pinning the icon. However, as to your

other problem:

Judith Cohn wrote:

p.s. I have a similar problem with a clean install of the latest version

of Java 2.4 on Linux. It works similar to my colleague’s copy on Mac

with Tiger. I can load fasta files from muscle manually using menu

option but cannot open them with my script.

The issue is a known one - there seems to be a problem with the jars

generated by InstallAnywhere under the new (well - 6 months old now)

automated build system. I had originally thought it to only really be an

issue on the OSX InstallAnywhere distribution, so its a worry that

you’ve also noticed it on Linux. On windows, the LaunchAnywhere .exe

file passes command line arguments correctly, so the problem isn’t so

serious. However, the workaround for command-line launching on OSX was

to either download the jars for the webstart release

( and use those, or build the jalview

jars using the source distribution.

I’m hoping to put up a bugfix release (2.4.0b2) on in

the next few weeks. This will use the latest version of InstallAnywhere

to create the local installation distribution, and will - I hope - fix

this particular problem. I’ll let you know directly if this really the

case so you can test on your Mac.

until the next email…

Jim Procter.

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.