[Biojava-dev] Biojava.util package?

[Peter Cock]

On Wed, Mar 28, 2012 at 8:04 PM, Hannes Brandstätter-Müller
<biojava at hannes.oib.com> wrote:
> Hi,
>
> I browsed around in the sister projects Biopython and Bioperl a bit,
> and noticed that many of the user interaction with the code goes
> through classes like SeqIO, SearchIO, AlignIO...

Technically in Biopython at least those are module names rather
than classes. However one of the key points is all the file formats
produce objects of the same class (or perhaps subclasses of that),
i.e. common class for annotated sequences, a common class for
multiple sequence alignments etc. BioPerl has something along
the same lines with defined interfaces.

We're hoping to have a GSoC student working on SearchIO for
Biopython this summer - which will be similar to the module of
that name in BioPerl for sequence searches / pairwise alignments.

Regards,

Peter C.