[Biococoa-dev] more ramblings

[John Timmer]

>>> 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...

Well, if it's my call, I'm pretty sure you know where I stand.  It just
seems like silliness to me to allow the following:
Have a method associated with the data it can't possibly act on
Have a method to be called on sequences that it has no relevance to
Make it easier to have developers accidentally make stupid mistakes.

As Alex said, failing with an empty sequence is a relatively elegant way of
handling the situation.  But  there's absolutely no need for the situation
to be handled - placing the method into the appropriate subclass (in this
case the currently non-existent BCSequenceNucleotide, parent of DNA and RNA)
is just clearer, safer, and more sensible.  I just don't see a big benefit -
the one claimed was preventing duplication of code, but adding the
appropriate subclass eliminates the duplication.

So my vote is definitely against putting these in BCSequence.  Until there's
some decision that the subclasses have to be eliminated, we should use them
appropriately.

JT

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