[Biojava-l] Re: Biojava-l digest, Vol 1 #90 - 1 msg

Aaron Kitzmiller AKitzmiller@genetics.com
Thu, 29 Jun 2000 13:23:21 -0400

Couple of things regarding this thread...

1. I ring in on the side that is against frequent changes to interfaces.  We still haven't made the switch to SymbolList from ResidueList, mainly because the switch came right in the middle of time-delimited project.    

2. Our experience with home-grown persistence wrappers has been very good.  Our Broker classes combine the functionality of SequenceFactory and SequenceDB into a single persistence manager that encapsulates the persistence method (SQL in our case) which often has impact on both query and construction.  As I mentioned some weeks ago, we're in the process of evaluating a number of third-party alternatives for storing sequence data and have seen data bases that use almost every imaginable API (PL/SQL, OODB-like RMI, and EJBs).  

"Where's the code?" you might ask.  As I mentioned, we're a little bit stretched at this point, but after a few name changes and other tweaks, I can at least send out the interfaces for review if anyone is interested.  As for an end-of-July time-frame, I suspect we would be too late.

Aaron K.

Aaron Kitzmiller
Manager Systems Development -Cambridge
Bioinformatics Department
35 Cambridge Park Dr.
Cambridge, MA 02140
Phone: (617) 665-6831
Fax: (617) 665-8870
Email: akitzmiller@genetics.com 

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Today's Topics:

  1. Gearing up for a 'stable' 1.0 release (Matthew Pocock)


Message: 1
Date: Thu, 29 Jun 2000 17:03:48 +0100
From: Matthew Pocock <mrp@sanger.ac.uk>
Organization: The Sanger Center
To: "biojava-l@biojava.org" <biojava-l@biojava.org>
Subject: [Biojava-l] Gearing up for a 'stable' 1.0 release

Dear all,

I guess enough people use this code now that interface stability has
become a serious issue. I believe (possibly mistakenly) that the core
sequence modules are reasonably feature-complete. Sorry if the latest
changes (ambiguity symbols & database names) break things. When I rolled
all of my code over, it turned out to be mainly simple search&replace
things to fix the incompatibilites.

So - the point to this is - I propose that we gear up to a 1.0 release
over the next month (before the end of july). Any missing features
should be mentioned now, and added over the next fortnight. From then
on, it will be bug-fixes only. As far as I can see, the missing bits

blast parsing (ok - so I know it is comming)
mutability of the underlying sequences / seq dbs
possible hooks for custom sequence persistance
more sequence formats

What do you all think? Am I being realistic? What do you think is
missing? What needs to be set in stone before 1.0?



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