[Biococoa-dev] Weighted sequence score

[John Timmer]

I'm looking into implementing the weighted sequence score that I mentioned
earlier.  Two questions about the design of this that I'd appreciate input
on.

The first is rather simple:  The easiest way to set up the scoring is to
have an array of dictionaries.  Given a symbol and a position, you grab the
dictionary at that position, and get an NSNumber out of it based on the
symbol, or nil, which gets converted to the user's defined default.  Very
easy to code, but it does not seem that efficient - lots of object messaging
and looking things up.  Does anyone have an alternate suggestion on how to
structure this?

The second thing is that this problem is clearly "embarrassingly parallel",
meaning that it's a great candidate for threading.  I though it might be a
good example case on how to properly and safely set up threads, so that we
can use it as an example as we expand the framework.

To keep the complexity out of the way of users, I was hoping to define a
public class definition in the header that provided a civilized interface to
the actual processing, plus offered either simulated synchronous execution
or asynchronous execution with a callback.  The actual objects that would
perform the threaded processing would be defined in a private interface in
the .m file.  Does this sound like a good idea?  Any alternate suggestions?

Looking forward to your input -

John

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