[Biojava-l] Refactoring the .seq package

[Matthew Pocock]

Hi.

Adding in the mutability api seems to have gone quite smoothly. Nearly
all of my programs worked without recompiling, and when comiling I had
to add in checks for some ChangeVetoExceptions here and there. It is now
all seralization safe. Cool.

The next thing is the gene features model. Thomas & I have added an
org.biojava.bio.seq.genomic package that will contain the interfaces for
genome-related stuff. It will probably also get package docs that
explain how to use them. The simple implementation is a different issue.
The seq package contains quite a few private or pacakge classes that
provide the vanilla implementation. This should all be used silently by
SimpleSequenceFactory. Some of these classes will need to become public
due to the the joys of the Java security model. Our solution is to add a
seq.impl package that would contain the vanilla implementation. This
makes the seq package purely the API for what you should provide when
implementing sequences. The only gotcha that I can see is that
SimpleSequence will move to impl, so if you instantiate these directly
(shame on you for not using the sequence factory), then you will need to
add an import for the impl package and re-compile.

Have fun.

Matthew