[Biojava-dev] Cleanups for 1.4

[Matthew Pocock]

 --- Thomas Down <thomas at derkholm.net> wrote: 
> Once upon a time, Matthew Pocock wrote:
> > Great!
> > 
> > So the next step is to merge the src-1.4 and src
> > trees, yes?
> 
> Right, this is done now.  All the main source code
> is
> in back in the src/ directory (and likewise tests
> and demos).  Make sure you do a:

Great.
 
> The only remaining bit of pre-1.4-ism that I can
> think of is
> the biojava-specific implementation of nested
> throwables.

I'm happy to be responsible for this. The options are:

  1) leave well alone

  2) add 1.4-style constructors to all these
throwables, deprecate our constructors (args the other
way round) and chain onto the 1.4 throwable
functionality

  3) drop Nested* from the tree, and inherit
exceptions as needed

I personaly favour option 2, since we will still have
things like BioException that need fixing.

If nobody complains by tomorrow afternoon, I will go
with 2.

Matthew

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