[Biococoa-dev] More on BCSymbolSets

Charles PARNOT charles.parnot at stanford.edu
Thu Mar 3 01:25:51 EST 2005

>ps you guys are going *way* too fast with all those emails. I only have a limited time each day to read them, understand them and possibly reply to them. Sorry if I don't address all issues :(

We slowed down ;-)

I am particularly interested in getting that symbolSet thing settled (for some reason, I am focused on the sequence classes for now!). So let's try to make decisions by answering these questions (I seem to answer some of these without leaving room for discussion, but please you know me now, I tend to be very -too?- affirmative about things):

* do we want symbol sets?
I am in favor of them, Koen is, it looks like John is too. As long as somebody is ready to write code, I don't think we can stop them! So this has to be yes...

* what do we want symbolSet for?
Koen and I both had 'filtering' in mind, it seems John had it in mind too a long time ago. If we use symbol sets in teh sequence classes, they have to do something and that something would be filtering then. There are problems raised by John. We will have to tackle them and if we can't, then we will just give up the symbol sets (or maybe we could go to the point where any remaining problems would be unlikely to appear in reasonable use of the framework).

* Do we let the user define the symbol set at creation by providing a 'symbolSet' argument in some of the initializers? The other option is to decide the symbol set ourselves.
My opinion is we should give the user the possibility to use the symbol set she wants, but also provide a default symbol set when she just wants to create a sequence and not bother.
Another option is to let that option open for later and internally use symbol sets for now, and see how it is doing (performance, usability,...), and then add more possibility for the user later.

About sequenceTypes:

* Should we extend the number of sequence types to take into account the different symbol sets?
Proposed by Koen. John and I agree this would be redundant with symbol sets, and an enum would not catch all the possibilities that we may end up having. The whole idea of symbol sets is to indeed extend the sequence type.

* Will all instances of one given sequence classalways have the same sequenceType? e.g. all instances of BCDNASequence will be of type 'BCDNASequence'. It seems to be the case at present. Given the answer to the previous question, I don't see a case where we would want to have a different sequence type. It seems symbol set will provide for more refined typing. So the answer to the question seems to be yes.

There are probably more basic questions that I am missing. After answering the design questions, we can move to the details of the implementations.


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Charles Parnot
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