[Biococoa-dev] Subclass organization

Charles PARNOT charles.parnot at stanford.edu
Wed Feb 23 00:44:05 EST 2005

At 10:44 PM -0500 2/22/05, John Timmer wrote:
>The reasoning is that, over time, we're going to add a lot of methods that
>will operate on some subset of sequences.  Some of these will operate on a
>specific type of sequence (ie - restriction enzymes, splice site
>recognition), some will more generically work on nucleotide sequences (ie -
>translation or complement).   As the framework expands, things will probably
>be easier if we can put the more generic ones in a single class, even if
>they're only convenience methods.
>Looking things over, I'm not sure I see the need for further parallelism,
>but I could be mising something.  The exception might be if we wanted to do
>symbol-specific attributes (phosphorylation, or something similar), instead
>of having attributes with a length of 1.  I'd expect that this would be
>necessary, but I'd be happy to hear otherwise.

I agree that we probably don't want to parallel the sequence class structure in the symbol subclasses. But where do we need a BCSymbolNucleotide?

The phosphorylation et al. idea is a good point and something to keep in mind, yes!


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