[Biojava-l] extra seqDB things to add [off-topic]

[Triplett, Terry]

> > <I'll interject a slight tangent here for information 
> purposes if nothing
> > else ...>
> > 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.
> 
> Terry, have you looked at JDataStore from Inprise?

Actually no, Simon.  A quick glance shows that it's beyond what I wanted at
the time, so I would have ignored it.  I just wanted to read simple index
files containing byte offsets to records in huge flatfiles using Java.  In
this particular case, the index was generated by a perl script using
Berkeley DB and made available to the java client via NFS.  The Berkeley DB
java interface did the trick in that case, but at the time I was struck by
the absence of an equivalent in Java since DB files are such a useful thing.

I guess that niche is being filled by small databases like JDataStore, which
are fine if you are sticking to a pure Java environment.  In a heterogenous
environment it would be nicer to have something more portable, so that one
could create a single indexed sequence database that could be read by
bio-[java|perl|python].

Incidentally, the Cloudscape database that is included in the Sun j2sdkee
(Java 2 SDK Enterprise Edition) seems to fit the same niche, and appears to
be free to use.  I haven't used it yet so don't know if it is a full version
or cripple/demoware.  If its presence can be relied upon, it might be worth
using in biojava.

 
> Simon
> --
> Simon M. Brocklehurst, Ph.D.
> Head of Bioinformatics & Advanced IS