[Biojava-l] extra seqDB things to add

[Ewan Birney]

On Thu, 13 Jul 2000, Gerald Loeffler wrote:

> 
> 
> 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...

I'd go the Berkeley DB stuff *and* the SRS/BLast indexing (this is 
what we do in bioperl. Sort of.) 

Berk DB - good for a clean room environment who does not want to install
SRS (anyone who has installed SRS will know what I mean)

SRS - good when you have SRS around.

Talk t the SRS folks as well - they are planning to implement - I
think/hope - the biocorba interfaces. Then you will get that "for free".


> 
> 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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> 
> -- 
>    Gerald.Loeffler@vienna.at _________________ Software Architect
>    http://www.imp.univie.ac.at ____ http://www.daemonstration.com
>    OOA&D, Java, J2EE, JSP, Servlets, JavaBeans, ODBMS, RDBMS, XML
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> 

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