[Biococoa-dev] more ramblings

Alexander Griekspoor mek at mekentosj.com
Fri Dec 3 20:44:19 EST 2004

Op 4-dec-04 om 2:13 heeft Koen van der Drift het volgende geschreven:

> On Dec 3, 2004, at 8:06 PM, Alexander Griekspoor wrote:
>> Well, a complement doesn't make sense for a protein does it?
> No, it doesn't. That's why I made it such that if you pass it to a 
> protein, the result will just be an empty sequence. This is actually a 
> good example of  what I mean by putting the convenience methods only 
> in BCSequence.

I know, but again at some point it doesn't make any sense anymore, than 
we can just as well get rid of the subclasses if that's where you are 
pointing at (again ;-). Either we go in your direction and throw 
everything in one class, or we do it nicely with subclasses. The fact 
that your complement tool object returns nil if you hand it a protein 
sequence is very elegant and nice (if that is what you want per se), 
but I don't see any reason why we are obliged to add the method call in 
BCSequence instead of only in the DNA/RNA subclasses. Again, it doesn't 
make any sense to add the possibility to call complement on a protein 
sequence, unless there is only one bcsequence class. And if I'm 
outnumbered in this opinion, than I even rather switch to the 
one-BCSequence approach, as now we're ending up in some strange hybrid. 
John, I think it's your call...

                     ** Alexander Griekspoor **
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                     Tel:  + 31 20 - 512 2023
                     Fax:  + 31 20 - 512 2029
                     AIM: mekentosj at mac.com
                     E-mail: a.griekspoor at nki.nl
                 Web: http://www.mekentosj.com

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