[Biojava-l] extra seqDB things to add

[Triplett, Terry]

<I'll interject a slight tangent here for information purposes if nothing
else ...>

I played around a bit with the Berkeley DB stuff recently.  Not hard to use
at all once it is set up and has many nice features (not the least one being
that it works).  However, installation can be tricky and borders on
non-trivial.  Granted, I was mucking about with rpm building and maintaining
compatibility with preexisting DB files created with Perl, but I still had
second thoughts about deploying it due to installation and portablity
issues.   

A Java-based small database is preferable over JNI-based solutions, I think.
I'm still trying to find one - there isn't much available.  One of the only
resources I found for lightweight databases using Java is here:
http://aurora.rg.iupui.edu/~schadow/dbm-java 

Of the JNI-based solutions, Berkeley DB is by far the best.

The W3C JDBM is the only 100% Java solution mentioned and appears to be a
port of GDBM code to java.  The informal tests showed that I could't read
JDBM databases using PERL GDBM and vice-versa which kept me from making use
of it.  I mention it in case anyone else finds it of interest.


> -----Original Message-----
> From: Ewan Birney [mailto:birney@ebi.ac.uk]
> Sent: Thursday, July 13, 2000 12:37 PM
> To: Gerald Loeffler
> Cc: Matthew Pocock; Biojava-l@biojava.org
> Subject: Re: [Biojava-l] extra seqDB things to add
> 
> 
> 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
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l@biojava.org
> > http://biojava.org/mailman/listinfo/biojava-l
> > 
> 
> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>. 
> -----------------------------------------------------------------
> 
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