[Biojava-l] features pre 1.0

[Jason Stajich]

Updateable sequence database interface. I can't remember where this fits in
with the hierarchy so no full name.  I would like to see this capability
added to Biocorba as well so need a java implementation.
Would be essentially a sequence database that allow retrieving of sequences,
updates to those sequences, and then a commit back to the db.  Additions and
removals would be supported as well.  I *might* be able to work on it - I am
finishing up the bioperl implementation of updateable seqdbs.

-Jason
----- Original Message -----
From: "Matthew Pocock" <mrp@sanger.ac.uk>
To: <biojava-l@biojava.org>
Sent: Friday, July 07, 2000 7:21 AM
Subject: [Biojava-l] features pre 1.0


> Dear all,
>
> This is the last call for 1.0 features. What would you like to see in
> BioJava?
>
> I have changed:
>
> o AlphabetManager now has only static methods & the instance() method is
> depricated
> o propper support for ambiguous symbols (like n, x)
>
> So far we have the possibility of:
>
> o sensible ways of retrieving databases by name
> o blast parsing
> o blast object model
>
> I would like to add:
>
> o prety printing of alignments / dp results
> o alignment io framework - possibly with no implementations
>   - should eventualy handle things like msa as well as simple-stupid
> formats
> o a ParseException that stoores:
>   - uri (file name, url etc.)
>   - line number
>   - char offset
>   - string of current line
>   - message (inherited from Exception)
>
> Wishlist (I don't have time, but mabey you do):
>
> o structure databases support - pdb, dssp, msa etc.
> o well known alphabet of secondary structure elements
> o proper URI support & naming-and-directory service support
> o HMMs could expose transition scores as probabilities, not log
> probabilities
> o world peace
>
> Thomas is overhauling the GFF parsing code as we speak, so that may work
> better.
>
> If you don't say that you want it, we can't put it in...
>
> Matthew
>
> --
> Joon: You're out of your tree
> Sam:  It wasn't my tree
>                                                  (Benny & Joon)
>
>
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