Thanks for all the sudgestions. I got this working in the end. The bug appeared in JBoss as well as various tomcats. It was fixed by doing a totaly clean rebuild of biojava-live followed by a totaly clean rebuild of biojava-ensembl. I blame the pixies. The only thing I can think is that some files may have had debugging (-g) information, and others may not have. Weird.

Matthew

Thomas Down wrote:
On Tue, Jan 21, 2003 at 01:27:48PM +0000, Matthew Pocock wrote:

Hi,

I'm having some problems with biojava in a web service I wrote. I'm using biojava.jar and bj-ensembl.jar along with my own jsp and servlets. It used to work (before xmas), but now I get an exception: "NoSuchFieldError: naturalOrder". This is a field in Location (in biojava.jar), and the calling code is EnsemblTranscript (in bj-ensembl.jar). I can build both jars from scratch using ant, so javac thinks the field exists. I can javap the Location interface (using the biojava.jar in the deployed .war) and naturalOrder appears, so it realy should be available.

I've just experienced this very same probelm, also using
biojava-ensembl, from a simple command-line script, so there's
definitely no container-specific classloading issues.  I was
able to fix it by doing a clean build of biojava-ensembl.

Any chance of version skew in your case?

   Thomas.
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