[Biojava-dev] BioJava 3 current status

[George Waldon]

On Mon, Sep 27, 2010 at 1:40 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

>In an ideal world we would have a clear separation of biojava 3 and
>biojava 1.  However the way things are at the present there is some
>mix and  there is still legacy code in SVN. e.g. the module "core" is
>essentially a lot of biojava1.7. It is up to the module maintainers to
>upgrade their code. We will need to take a decision soon if we want to
>drop all legacy code from SVN and only support biojava3 based code
>from that point on. ( need to do a dependency analysis how many
>modules are still depending on the old core).

I see a few (rather lonely) BioException in the biojava3-ws module and a "biojava1-core" dependency in org.biojava3.core.sequence.transcription.DefaultRNAProteinTranscription in the sequence-core module. I also see that many of the classes of the sequence-core module are duplicated in the biojava3-core module. Is-there a meaning for this duplication?

George