[Biophp-dev] My brain hurts.

[Serge Gregorio]

Hello again.
 
>I am now a little unsure what you accomplished.  You replaced the >seq object by an 'intermediate' array that is basically an object >without functions (but otherwise exactly the same as what the seq >object intends to be), and you replaced the approach of keeping >track of positions by tracking the index (pointer) to the data, by >buffering the data in an array (causing much more data being moved >in memory than otherwise would be needed).  I don't think progress >has been made in dealing with streams.  Am I missing something?

Well, as I've said before, these two features (parser capable of returning arrays, and a buffer array of pointers to data) are ok
from a development point of view, but from an application point
of view, it's a nice-to-have feature, not essential.

I can't be more specific (in my comments) than that at the moment.
I have yet to setup WinCVS to work with the CVS here.  I'm also
into the Amateur Gene Finder thingie... which reminds me, Sean,
any word if Bioinformatics.org allows installation of custom
Perl/BioPerl scripts?  

My other comment is that an array of pointers to data is okay,
if it's not too large.  However, beyond a certain size (e.g. >
1000 pointers), they consume too much memory and are not reco-
mmended for use in web scripts, where you'll have to pass this
buffer array around from page to page via GET, POST, or SESSION
variables.

Regards,

Serge


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