[Biojava-l] Re: HMM's and Distributions

[Matthew Pocock]

Perhaps we should tag API as stable in the javadoc once we believe that it
shouldn't change?

Thomas Down wrote:

> On Wed, Jan 17, 2001 at 02:54:40PM +1300, Mark Schreiber wrote:
> >
> > It does raise a point though. At what point will the biojava API become
> > stable. ie shouldn't we deprecate outdated methods from now on rather than
> > removing them entirely??  It would seem to be breaking one of the
> > fundamentals of OO design.
>
> Part of the problem here is that different parts of BioJava have
> distinct lifecycles.  There's `core' stuff which is pretty stable --
> certainly things like the Alphabet, SymbolList, and Sequence
> interfaces really /ought/ to be stable, and we should probably
> go the deprecation route if we ever do need to remove old methods.
> Hopefully sequence input is reaching this point now, after the
> refactoring of the last few months.
>
> The dynamic programming toolkit is still in rather more of a
> state of flux, and has changed architecture quite a bit since
> it was originally written.  It certainly /will/ stabilize, but I'd
> guess it's up to Matthew (who's done almost all the architecture
> work in this package) to say when.
>
> That said, I hope there won't be too many more upheavals -- the
> current API (while very different from what was released in 1.0)
> has been fairly stable for a while now.
>
> Matthew?
>
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