[Biophp-dev] Fasta filetype parser updated

[biophp-dev@bioinformatics.org]

Only had a quick glance, but the methods:
isFromFile()
setSource()
findNextLabel()
readtoLabel()
might be needed (unchanged) in many other parsers.  Should we have a
parser class that can be extended by the specific parsers, or is that
getting too ugly?  

I'll try to get started on the Genbank parsers soon.  That will extend
the array returned by the parsers dramatically,so we should have a
careful look at that array once the Genbank parser is done.  Also, I'll
probably take the approach to have the findNextInfile in that parser read 
a whole record into an array,and do the actual parsing only in the array.

Sean, do you want to have a go at the clustalw parser too?


Nico


On Tue, 6 May 2003 15:44:11 -0600 S Clark wrote:

> Okay, got it committed.  It seems to work okay with the test script.  I've
> gone back to line-by-line parsing as Nico originally had it, so memory
> usage should be more rational.
> 
> It still needs some cosmetic fixes and minor tweaks to bring it in line
> with PEAR coding standards (working on that now) but it should be
> fully functional in the way we discussed now.  Let me know what you
> think...
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