[Biojava-dev] The great deprecation clean up

[Schreiber, Mark]

Hi -

After the recent change in the way BioError and BioRuntimeException are
constructed observant biojavaites would have noticed that there were
several hundred deprecation warnings during a compile of the source
code. In a fit of insanity never to be repeated I have cleaned all of
these up. 

On the upside I got to look at parts of BioJava that haven't seen the
light of day for a long time, bits I never new where there (if only I'd
known about NucleotideTools a month ago!!) and bits that should never be
seen by either man or beast!

On the downside your next checkout from CVS might be a little heavy
weight (anyone like to guess how many classes can throw a BioError or
BioRuntimeException??).

There are now a respectable 21 deprecation warnings for BioJava-live, I
leave these as an exercise for the interested reader :)

- Mark
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