[Biojava-l] extra seqDB things to add

[Gerald Loeffler]

Matthew Pocock wrote:
> FileIndexerSequenceDB
> - indexes a list of files
> - uses a normal seq.io object to specify the format
> - creates a file bla.index with the indexing info
> - possibly auto-manages updates using file dates/times

could use Berkeley DB (which has a Java API) for indexing so as not to
reinvent the wheel...

On the other hand i'm not sure whether it's wise to introduce yet
another indexing mechanism - we already have NCBI-BLAST, WU-BLAST, SRS
which all index the (huge) sequence databases in incompatible ways.
Wouldn't it be better to write a SRSSequenceDB which would be a
SequenceDB that
	o either knows how to decipher the SRS index files and create Sequence
objects from that
	o or (alternatively) knows how to load a sequence file (in e.g. EMBL
format) from the command-line (getz) or web-version of SRS and construct
a Sequence object based on that,
	o or (alternatively) knows how to load a sequence file (in GenBank
format) from Entrez and construct a Sequence object based on that.

	cheers,
	gerald

> 
> Any thoughts?
> 
> Matthew
> 
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