[Biojava-dev] flatfile indexing woes

[Keith James]

I want to create SequenceDBs from the whole of EMBL and the whole of
SWALL. I've been looking at at the OBDA biojava indexing
implementations which came out of the hackathon.

I could do with some help getting this working. If I run
demos/indexing/CreateSPIndex on the current version of swall it
completes with no errors. However, I get the following index

config.dat:
index   flat/1
primary_namespace       ID
secondary_namespaces    AC

id_AC.index:
21

key_ID.dat:
46

and that's it. I imagine this is not correct.

I've just spent 6 hours with a printout of the OBDA spec documenting
the code, so I'm passing on this for now. There seems to be two (or
more?) indexing frameworks and we also have two IndexStore interfaces,
each with different methods.

I saw a mention of a SleepyCat implementation. Does this exist for
biojava?

Keith

-- 

- Keith James <kdj@sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -