[Biococoa-dev] Subclass organization

John Timmer jtimmer at bellatlantic.net
Thu Feb 24 14:54:58 EST 2005

>> 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.


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