[Biojava-dev] [patch] BioJava -> BioSQL taxon

[Len Trigg]

Hi guys,

I've added/ported code to BioSQLSequenceDB that adds write support
between Taxon and the taxon tables in BioSQL. There was some code in
there commented out, but it looked like it belonged to an older
version of the BioSQL schema. Could someone knowledgable take a look
at the patch and see if I've done things the right way.

Notes:
1) If you have some particular style guide, you can get emacs to adopt
it with a comment at the top of the file, e.g: I put a
  /* -*- c-basic-offset: 4-*- */
to tell emacs to use 2 char indentation offsets (I'm not sure what you
recommend, I've seen both 4 and 2 used through the code). Just an idea.

2) The commented out code looked for a sequence annotation with key
OrganismParser.PROPERTY_ORGANISM, and within that it required key
EbiFormat.PROPERTY_NCBI_TAXON to point to the ncbi id. The patch keeps
that convention. To populate the taxon_name table if a new taxon entry
needs to be created, the patch expects another key
EbiFormat.PROPERTY_TAXON_NAMES to point to a name_class, name map. (If
it is not present, no names will be assigned)

3) I haven't yet looked at adding support in the other direction
(i.e.: creating Taxon objects when reading a sequence from the
database).


Cheers,
Len.


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