[Biojava-dev] exceptions

[Matthew Pocock]

Ok - nucked NestedException & friends. Checked in all
my changes. Also, updated demos to work with these API
changes.

I've fixed a couple of glitches in compiling demos on
the main trunk. A couple of things aren't easy to fix:

ssaha\CreateDNAFastaHashTableCompact.java was using
SeqIOTools to guess sequence format from a File. This
funcitonality is no longer in SeqIOTools - it is
needed. I don't care if 10% of the time the guess is
wrong or blows chunks. I just want it to work 90% of
the time.

demos\ssbind\SubHitBuilder.java is using an old
constructor on line # 91 - this needs changing to fit
the new constructor's signature.

Also, in build.xml, the junit tasks seem to have
dissapeared. Was that an accident that happened while
merging the 1.4 trees in?

Matthew

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