Hi Timothy.
I've cced this reply to the discuss list to see if anyone else has any
ideas here.
Timothy Hughes wrote:
I have some problems starting Jalview from the command line on Mac.
Java version: 1.5.0_13
i386 Mac OS X 10.5.4
Jalview Version: 2.4
Thanks for trying the new version out - there are still teething
problems with the release, but I'm nearly there 
Jalview works fine if I start it via the dock or spotlight.
Ok.
But if I try to start it from the command line which is very handy in
some cases (especially when one wants to open a specific file) then I
get the following bug:% declare JALVIEW="/Applications/Jalview/";
% java -Djava.ext.dirs=${JALVIEW}lib -cp ${JALVIEW}jalview.jar -Xms500M
-Xmx750M jalview.bin.Jalview -open alignment.fa
Java version: 1.5.0_13
i386 Mac OS X 10.5.4
Jalview Version: 2.4
# INFO: Setting default net timeout to 30 seconds.
Opening file: alignment.fa
Exception in thread "Thread-7" java.lang.VerifyError: (class:
jalview/datamodel/Sequence, method: parseId signature: ()V) Incompatible
object argument for function call
at jalview.io.AlignFile.parseId(AlignFile.java:229)
at jalview.io.FastaFile.parse(FastaFile.java:124)
at jalview.io.AlignFile.<init>(AlignFile.java:72)
at jalview.io.FastaFile.<init>(FastaFile.java:59)
at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:157)
at jalview.io.FileLoader.run(FileLoader.java:272)
at java.lang.Thread.run(Thread.java:613)
error
I can verify this on our own Mac, which is an earlier OSX (10.4).
From what I can tell, it is something to do with the default Java
environment that is being launched from the command line. The
InstallAnywhere launcher seems to be doing something additional, and its
going to take a little time to track down.
However, I have verified that if you build Jalview from the source
distribution then it launches correctly from the command line. I am
currently in the process of updating the website to reflect the new
release, so for the moment, get it from
http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/release/jalview-source.tar.gz
Jim.