[BioRuby] Bioruby design

[Tomoaki NISHIYAMA]

Hi,

 > As people tend not to think of Paml as a toolbox I would prefer

 > to have one object names Paml. With behind it the codeml 'engine'

 > and reporter. This would work for me (also note Paml does

 > not return a report, but rather a result):


I don't agree in this point.  PHYLIP is clearly a package or  
collection of
programs, and so is considered Molphy, PAML, ...

 > result = Paml.new(:program => 'codeml')
And if you make a single object, it is not to obvious to divide based  
on the program,
since aaml is now done by codeml but should be considered clearly  
different
function.

>>>  include Bio
>>>  report = Codeml.new
>>>
>>
>> I think it is enough to write "include Bio::PAML" instead of (or in
>> addition to) "include Bio".
>>
>
> Not really. It brings in another source of errors for users if they
> have to think about that context every time. We will get all
> variants, like Bio::Kegg, Bio::Sequence etc.


These are short enought, since we have to write something like
"PAML ver XXX (Yang, XX) was used for XX" and "KEGG (Kanehisa, XXX)"...
in the manuscript of the paper if we use that module.
Stating their use explicitly in the first lines of the
program is considered good.

On the other hand, I don't like "include Bio::Sequence", since it is  
a function
of bioruby in itself.
-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan