[Biophp-dev] Fasta filetype parser updated

[biophp-dev@bioinformatics.org]

> I was thinking about that - it might be a good idea overall.  A lot 
> of the parsers will end up doing very similar things, so I imagine
> there'll
> be a fair amount of code re-use that we can do.

Shall we wait untill we have a few more and then see how much redundancy
there is?  I somehow dislike creating yet another object, chain will get
so long, and harder to understand...


> Heh...just committed it - I BELIEVE both clustalw and clustalx use
> the same file structure (at least, as far as the way the parser

I thought that clustalx is simply the X-windows interface to clustalw.
Fileformats should be identical.


> can tell).  There should now be an updated parse.inc.php (with clustal
> auto-detect), the filetype parser for clustal, and an updated test.php
> which also tests clustal.  Oh, and a lamin.aln file to test with...
> 
> Let me know if you spot any problems.

I added seqlength to both the clustal and fasta parsers.  Also, it is (a
little bit) better to quote with single quotes if you do not need
variable interpolation, that way php does not have to invoke it's parser.
The clustal parser output has a whole lot of dashes in the sequences.
Can you have a look at those? (reg expressions are not my strong point as 
you might have noticed)

Cool!