[Biojava-l] extra seqDB things to add

[Gerald Loeffler]

Matthew Pocock wrote:
> The indexer is realy amied at the relatively common case where you have 3
> fasta-files with your interesting sequences spread among them (exons between 150,
> 230 nt long from sachDB), and need random access to them. The files are not
> integrated to SRS, as only you think that they are interesting, and SRS is scary.
> It then allows you to do a getSequence(id), and efficiently pull out the
> apropriate chunk of the file. Next week, you blow these files away, and forget all
> about them (you now are interested in introns containing repeat elements from
> mouse).

okay - this makes sense. But then i'd make the indexing process
(probably) completely transparent, i.e. i'd index on-the-fly when e.g.
constructing the IndexedSequenceDB from a FASTA-file. The index-files
could be kept in an "invisible" directory and the user would never ever
have to index manually...

and yes, SRS is scary!

> 
> Am I trying to create a solution for which there is no problem?

you have to ask a biologist about that (-:

	gerald
> 
> Matthew

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