[Biophp-dev] Is a May 2003 release possible?

[Serge Gregorio]

Hi guys!

Just came back from a trip out of town.  Will try to catch
up with the discussion...

>> Can we pass the data to the parsers by reference?  That can 

Wow... when you start talking about passing by reference, then
it only means you've gone a long way already...  =)

Btw, would it be possible to make a release before the end 
of May?  I've been working on release 1.1 since April 1st,
and am ready to go public with it May 15 (which was my origi-
nal plan back then when the only Sean I knew was Sean Penn.)

But if Sean can make his eFetch/eUtils work around that time
(May 15 - 21) and Nico can write a few more parsers (PIR or
mmCIF perhaps?), maybe it would be better to release all of
our work a week later (May 25 - 30).

By the way, I'm working a variety of stuff, from the Enzyme
class to some esoteric sequence alignment code.  That's why
I used the term "miscellaneous code" in the action plan.

What do you think?  =)
 
Regards,

Serge 

--

On Wed, 7 May 2003 23:52:04   
 S Clark wrote:
>On Wednesday 07 May 2003 10:31 pm, nicos@itsa.ucsf.edu wrote:
>> I added the pdraw parser (there is a test file specific for this parser).
>> Although I started with Sean's fasta parser, it changed quite a bit.  I
>> guess I am simply more comfortable with this approach, and I think it
>> will be easy to adapt the Genbank and Swissprot parsers using this
>> approach.
>
>What?  You deviated from my Sacred Style?  Blasphemy! :-)
>
>Looks just fine to me, really.  Cool - I think we're onto an
>overall winner for the general parsing system structure.
>
>> Some questions/suggestions:
>> - Can we rename the parser include file to delete the '_class' again?
>> Those names get so long....
>
>I've got no problem with that - appending "_class" is just a convention
>I picked up on my own to distinguish files containing classes from those
>containing e.g. random functions or regular scripts, but really I think
>the existing .inc.php serves the same general purpose.  I say go for it.
>
>One minor change we might think about doing soon is changing the class names 
>slightly - the PEAR standards say that class names should always start with a
>capital letter.  Not that we necessarily have to stick to that, but it might
>be worth doing while there are relatively few classes to deal with.
>
>> - Can we pass the data to the parsers by reference?  That can save quiute
>> a bit of copying (need to remove that unset command in the parse
>> constructor)
>
>Hmmm, don't see why not.  That'd reduce peak memory usage a bit further, 
>and slightly improve readability while it's at it.  Works for me.
>
>> - Do we need to thinnk about closing files? 
>
>Also a good idea, I think.
>
>I'll go back and implement get-by-reference and "close the file handle if
>there is one when you hit the last record" in the Fasta and Clustal parsers
>and commit them tomorrow morning.


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