[Biojava-dev] Suggestions for the BioJava project

[Len Trigg]

Andreas Dräger wrote:
> I am and currently working with BioSQL and BioJava. Trying to insert
> the NCBI taxon hierachy and also different kinds of biosequences into
> the database I got to know that there are still some open problems in
> BioJava. Since I wrote some classes anyway, I would like to contribute
> them to the community.

Good stuff.  The work that I did with the TaxonSQL classes was based
on the fairly simple requirements of the project I was working on,
which is why you found the current implementation a bit limited. (I
don't have projects involving BioJava at the moment, so haven't been
doing much other than following the mailing list.)


> I modified the functions to put and retrieve taxa into the database so
> that they consider that the names Map could sometimes point to a Set of
> names instead of  normal name Strings.
> In addition I considered the other information that can be inserted in
> the database like genetic code and so on.

Excellent improvements.


> However, there are some methods in TaxonSQL.java that are defined to be
> private. If they were protected, an extension of this class could call them.
> But because they're private, I had to copy and paste them.

That class isn't really designed for extension, since it's plugged
directly into calls from BioSQLSequenceAnnotation and BioSQLSequenceDB
(you presumably had to change these to point to your MySQLTaxon) and
there's no need for multiple implementations.  I'd say that your
changes should instead be folded directly as improvements to TaxonSQL
itself so that everyone gets the improvements out of the box.


Cheers,
Len.