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. Need a new email address that people can remember Check out the new EudoraMail at http://www.eudoramail.com