[Biococoa-dev] Subclass organization

John Timmer jtimmer at bellatlantic.net
Tue Feb 22 22:44:17 EST 2005

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.


>> Quick question:  in order to set things up to provide method calls
>> appropriate for sequence types, I was going to put in a
>> BCSequenceNucleotide.  I've since realized that to make any sense out
>> of the
>> method signatures, I'm going to need to make a BCSymbolNucleotide.  Any
>> objections to this?  In the end, it looks like it's going to be an
>> abstract
>> class with most of the possible methods there.
> John,
> I am not sure if I understand why we need a BCSequenceNucleotide (and
> BCSymbolNucleotide) class. There are only a few methods in both
> subclasses, so right now I don't see the need for an additional layer
> that takes care of those methods. Maybe you can refresh my memory?
> thanks,
> - Koen.
> PS, what probably needs some more thoughts is to create a similar
> structure for the BCSymbol classes that we have just introduced for the
> BCSequence classes.
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