[Biococoa-dev] Subclass organization

[Charles PARNOT]

At 14:54 -0500 2/24/05, John Timmer wrote:
> >> I see that Koen (probably long ago) put the ambiguous amino acids in place.
>>> That means that all subclasses of BCSymbol now have ambiguity.  That, in
>>> turn, means that the method "isSingleBase" can be moved to the BCSymbol
>>> class, and renamed to reflect its more broad applicability.  I could either
>>> do "isSimpleSymbol" or "isCompoundSymbol" accordingly.  Any preferences or
>>> alternate suggestions?
>>
>> isCompoundSymbol: maybe more technical but also more precise than 'simple', so
>> I like it better.
>
>In a related issue, I see that BCSymbol now has the representedSymbol
>methods, which is good, but contains the complement method, which seems bad,
>since it returns nil.  Is there any advantage to having it there, instead of
>moving it down to a Nucleotide class?
>
>Again, I'm very nervous about providing a method that returns nil (and thus
>increases the chances of terminal bugs) to the amino acids, which have no
>reason to ever support this.
>
>JT
>

I have not had time to go down to that level of details, yet, but it could be better that the BCSymbol superclass responds to the message (even if not in the header). It could return 'self' instead, though. I agree that would be safer.

charles

-- 
Help science go fast forward:
http://cmgm.stanford.edu/~cparnot/xgrid-stanford/

Charles Parnot
charles.parnot at stanford.edu

Room  B157 in Beckman Center
279, Campus Drive
Stanford University
Stanford, CA 94305 (USA)

Tel +1 650 725 7754
Fax +1 650 725 8021