[Biojava-dev] BioSQL implementation

[Simon Foote]

Hi Thomas & Mathew,

I've been following the development of the BioSQL schema and I noticed 
in an email from Hilmar last week on the BioSQL list that a release was 
imminent.

Thus, I've been modifying the biojava code to get it working with the 
latest schema within MySQL.  The main changes have been the following:

1) Ontology_term table to term table with applicable id name changes.

2) Seqfeature_location table to location table with applicable id name 
changes

3) Seqfeature_relationship table --> parent and child changes to object 
and subject

4) Changes to generate unique rank numbers within several tables as the 
schema has unique indexes on several of them. (bioentry_qualifier_value, 
seqfeature, etc) - some were already there but commented, others I added 
& commented the code

5) Also, changed the thrown exceptions to conform to the non-deprecated 
constructors.

6) A bunch of little things that I have commented in the code

7) The only part I haven't touched is the Assembly parts as I couldn't 
figure out how they are incorporated with the latest schema.

I've been testing the various methods (addSequence, removeSequence, 
getSequence, etc) with a bacterial genome from genbank and I think I 
have everything working correctly.

I've attached the modified files for your perusal and addition to CVS as 
I don't have access anymore.

Regards,
Simon Foote
-- 
Bioinformatics Specialist
Institute for Biological Sciences
National Research Council of Canada
[T] 613-990-0561  [F] 613-952-9092
simon.foote at nrc-cnrc.gc.ca
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