[Biophp-dev] parser news

S Clark biophp-dev@bioinformatics.org
Mon, 2 Jun 2003 10:20:36 -0600

On Sunday 01 June 2003 02:30 pm, nicos@itsa.ucsf.edu wrote:
> Just finished reworking the parser class.  Methods move_Next() is now
> called next() and method move_Previous() is called prev().  I propose to
> use these names in all methods that 'walk' through records.

Sounds fair to me - I take it that you'd favor the "single interface" 
style for interface methods, also?

> I still have to rename the parser class.  Also,I do want to shorten the
> names of the individual parser files (from
> parsers/parse_genbank_class.inc.php to parsers/genbank.inc.php).

Sounds good - I'll refrain from messing with things in the parser section
for a little while.  The extra-long names I started using there are
partly leftover from my own convention of using "_class.php" instead of
".inc.php" and at the same time not wanting to "override" the convention
everyone else was using (and still not wanting to "clobber" the already
existing .inc.php files.).  

Good work on the parsing code - I think it's gotten to be really easy to

> How is the rest of the code coming about?  Is there now a single cvs
> repository that we all use?

The NCBI-URL blast interface is slow going - there is a great deal going on
out here right now and I can't seem to get more than a few minutes at a time
to work on things.  (My employer is busy going out of business, and I'm
down to being a "consultant" instead of a full-time employee.  I am still
amazed at how I have ended up having MORE things to do in this situation than
when I was officially employed full-time...)

My wife and I will be "on the road" for about a week starting on Wednesday, 
but I intend to spend some time working on aspects of BioPHP-type work that
can be tested without an internet connection.  (Is there an
already-established "simple procedure" for doing a quick evaluation
of the "quality" of a pre-calculated alignment between two sequences?)

I'm HOPING that today or tomorrow I can get a few hours uninterrupted to get
the NCBI stuff finally split up and working before I leave.

So far as I know, the bioinformatics.org cvs is the only one that's set up
currently, isn't it?

More later.