Ah. ok.
I was going to suggest you make sure that you are running the ‘buildindices’ target before launching Jalview - this will copy the various additional resources (jalview/resources, jalview/help, jalview/schemas) into the build directory. That’s usually far quicker than rebuilding the Jar each time.
Glad that this is all sorted out!
Jim.
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J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a Scottish Registered Charity, No. SC015096.
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J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764 [http://www.compbio.dundee.ac.uk](http://www.compbio.dundee.ac.uk)
The University of Dundee is a Scottish Registered Charity, No. SC015096.