[Biophp-dev] The humunguous IO class etc

[Nico Stuurman]

I have to let this sink in a bit before I make up my mind, but  - in 
general - I do not think it is a good idea to try to do everything with 
a single class/function.  Better to chop is up in small manageable 
pieces that can be reused elsewhere.


> I've also attached a code snippet from GenePHP 2.0's IO
> class, in which the "parser class" you were mentioning
> earlier are its methods.  The general idea here is that
>

That will break the code  (it is a class, not a function).  It could be 
a subclass though.


> people only use ONE AND ONLY ONE class to read/write
> data from WHATEVER SOURCE (console, variable, file, SQL
> DB, etc.) to WHATEVER DESTINATION.


I would keep the read and write routines separate.  What use is it to 
have to pass a 'r' or 'w' as an argument, if you could just name the 
function/class accordingly?  Or, I'd prefer:
IOseq_read($whatever) // this is a better name than 'parse'
and
IOseq_write ($whatever) returns //
over:
IOseq($whatever,'w') and IOseq($whatever,'r')
The reason is that the objects returned when doing writing or reading 
are going to be quite different (an IO_seq_read and IO_seq_write object 
will not share much in functionality).

If they need to be merged it could be:
IOseq->read($whatever)
and
IOseq->write($whatever)


Best,

Nico