InstallAnywhere distribution cannot launch from command line in OSX

Reported by Timothy Hughes (tim.hughes at mbi.uib.no) to help@jalview.org

Hi,

First, thanks for creating such a nice piece of software!.

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

I had the same problem with the 2.3 version. It would be great if you could fix this.

Jalview works fine if I start it via the dock or spotlight.

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

****** ADDITIONAL INFORMATION ******


verified bug on OS X 10.4

Verified that source distribution can be built and launch from same Java environment so something must be 'different' with the Jars distributed with the InstallAnywhere install that is corrected for when using the LAX launcher through spotlight/dock/FileChooser.