[Biophp-dev] CVS overhaul

[Nico Stuurman]

I put some effort this weekend in PEARifying parts of biophp.  As a 
consequence, a couple of classes have undergone substantial 
rearrangements.  The most important is the Seq class.  All the 
nucleotide specific stuff has been moved to the NucSeq class (extending 
class Seq), and the protein specific things were moved into the 
ProteinSeq class (also extending class Seq).  Thanks for suggesting 
this very logical organization Can!

Functions/methods have been - when possible - moved into files in the 
directory functions/ and are only included when needed.

An important change occurred in the method $NucSeq->translate().  The 
variable $readframe used to be 0,1, or 2.  It has been renamed to 
$frame and can be 1,2,3,-1,-2,-3 (which is the convention in biology).

I included the function hydropathy from Can in 
functions/protein.inc.php.  I was confused by the two last variables, 
which - I later realized - are only used to return values.  I guess I 
would prefer to return an array holding the results as one or two 
arrays.

To make it easier for people not familiar with cvs, I put the current 
code for download at:
http://valelab.ucsf.edu:/~nico/biophpcvs.tgz
Also, the documentation generated by phpdocumentor is available at:
http://valelab.ucsf.edu:/~nico/biophpdoc/
Don't forget to click on the 'biophp' link on the right, which contains 
the part I worked on.

If it is OK with everyone, I'll try to go through all classes and do 
something similar with them.  We can then also move this outoff 
directory 'genephp' up to the root level 'biophp'.

Best,


Nico