[Biojava-dev] 3.0.1 release...

[Andy Yates]

Hi Sylvain,

Maybe rather than checking if it's a ProteinSequence instance (or DNA) could you check the Sequence's compounds or the CompoundSet backing the Sequence? Only because then it would be feasible to accept an instance of BasicSequence<DNACompound> (or something similar) which would be a valid set of amino acids or nucleotides without the need to wrap it in a specific class. 

Also there seems to have been a lot of files added into the biojava-live/biojava3-ws/target directory which should have been in the ignore files. Done that one loads of times myself. Damn these languages which require compile phases :)

Cheers :)

Andy 

On 2 Feb 2011, at 19:13, Sylvain Foisy Ph. D. wrote:

> Hi Andreas,
> 
> Ok, here goes... I committed some more code that fixes the bugs that were reported to me. I also added some very basic sanity checks to match sequence to program; for example, you can't use blastn on a ProteinSequence. I also added a page on the wiki that provide a simple recipe that is working for me.
> 
> A call to users: pleaser use and abuse this code. Only by your feedbacks can I work at improving this :-)
> 
> A+
> 
> Sylvain
> 
> On 2011-01-31, at 12:54 PM, Andreas Prlic wrote:
> 
>> sure, no problem, let us know when the fixes are ready.. This will fit
>> nicely to our new  "release early, release often" policy ;-)
>> 
>> Andreas
>> 
>> On Mon, Jan 31, 2011 at 9:51 AM, Sylvain Foisy Ph. D.
>> <sylvain.foisy at diploide.net> wrote:
>>> Hi Andreas,
>>> 
>>> Could you wait a bit on this, like late this week or early next week? I am working on some major fixes for the QBlast code and I need to confirm that the fixes work and that I perform some more tests...
>>> 
>>> Best regards
>>> 
>>> Sylvain
>>> 
>>> 
> 
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-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/