[Biojava-dev] OrganismParser and Taxon io

[Len Trigg]

Hi guys,

I added BioSQL support for persisting any Taxon information that was
annotated to a sequence with the key OrganismParser.PROPERTY_ORGANISM,
and now I'm looking at how to get the different sequence file formats
to produce the appropriate output. I have come up against a bit of
confusion.

Taking Embl-like output first, I was going to ensure that when a Taxon
object associated with this key was encountered, two lines are output:
an OS line containing information from the Taxon object; and an OC
line containing information from the Taxon.getParent() up to the root.

I didn't want to break compatibility with any existing taxonomy io, so
I looked through the code for OrganismParser (which is never actually
called, AFAIKT). It seems to be capable of parsing an OC line of an
Embl-like file into a Taxon object and adds this as an annotation with
the OrganismParser.PROPERTY_ORGANISM key. But since the OC line seems
to only contain the lineage, not the the species itself, wouldn't
OrganismParser also need to incorporate the OS line? Does anybody
actually use OrganismParser?

Cheers,
Len.