I want to export more than standard information in the base-file sent to my
plug-in. That is more "sections" describing the samples, hybs, arrays and
their relationships.  My first plan was to extend BioAssaySetExporter and
Base1PluginExecuter, and then override the methods where the information is
written to file (stdin.txt) adding my extra stuff. This approach failed when
I encountered lots of private methods in Base1PluginExecuter and
BioAssaySetExporter, making them less useful for extension since I have to
override all the private parts I need even if I don't need to alter them.
Why are those methods private and not public? Is there a better way to solve
my problem?

A more cumbersome approach is to copy both files (and others if needed),
rename them, do my modifications and it will work. This is what I have done
for years with BASE1, giving me an extra cut and paste job each time base1
was updated and I had to re-update my custom files. I hope BASE2 can do this
in a more neat way.

Best Regards

Vegard Nygaard
Software Engineer
Department of Tumor Biology (Montebello)
Rikshospitalet-Radiumhospitalet Medical Center 0310 Oslo
Bioinformatics user support (NMC)
Phone 0047 22935590

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