[Biophp-dev] CVS and memberlist

Serge Gregorio biophp-dev@bioinformatics.org
Tue, 29 Apr 2003 03:25:39 +0800

Oh okay.  I'll use the SF repository to post my experimental
code then (the equivalent perhaps of Sean's point-and-laugh?)
and to further my knowledge of CVS, and the BioPHP CVS for 
major releases so there won't be any confusion.  =)

>If we all agree that we are basically working on the same thing, we
>should have a single cvs repository.  I don't care where it is, >Serge and Sean should decide on this soon, or we will have a major >headache.

>I suggest to merge the 'sean' and 'genephp' directories as soon as
>possible, and have it all located on 1 and only one server.

Well, I did make that suggestion in my email re: IO class.

The main rationale behind the IO class is to simplify things
for the user. And one way is to reduce the number of classes
we have. Biology is complicated enough (would require a good
number of classes) that I wouldn't want to "punish" the user
further by adding more task-related classes.  

Having said that, may I clarify that the IO clas is still a 
rough proposal, which shouldn't be grounds for a "religious 
schism" or delineation as mentioned by Sean.

In designing BioPHP, I heartily recommend taking a look at the 
other BioXXX languages out there.  I'm not suggesting we copy
them wholesale, but we can LEARN from them.

For instance, BioPerl uses the SeqIO class to read data.  In
my 1.0 release, its counterpart was the SeqDB.  However, I 
acknowledge its limitations as pointed out by Nico (that it
was tie up to an assumption that the user wanted a flatfile
database system).  And thus was born the IO class.  



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