[Biococoa-dev] More on BCSymbolSets

[Koen van der Drift]

On Feb 27, 2005, at 10:26 PM, John Timmer wrote:

> I think the idea of using a symbol set to limit the possible options 
> for
> initializing a sequence is a good one, provided we make the process 
> very
> streamlined.  The class itself looks to be good in that regard.

Not only in the init methods. They can be used all throughout the 
framework.


>
> I've got a couple of ideas on the implementation.  One idea that 
> suggests
> itself is to have a BCSequencType variable for the symbol set - that 
> way the
> sequence being initialized could pick up its sequence type from the 
> set it
> gets passed during initialization.

Then we might have to extend the different BCSequenceTypes to include 
strict, ambiguous, etc.


>
> The other thing I'd do is take the methods like "baseForSymbol" and
> "aaForSymbol" and formalize them to be a single selector, like
> "symbolForCharacter".  That way, you could call the same selector on 
> any
> class.  This would allow you to make code that looked something like 
> this
> (given passedString and passedSet as the arguments):
> TheClass = [passedSet anyObject];
> TheChar = [passedString characterAtIndex: loopCounter];
> TheSymbol = [theClass symbolForCharacter: theChar];
> If ( [passedSet containsObject: theSymbol] )
>     // add it to our sequence

This is indeed similar to what I have in mind, yes.

> If we're making symbol sets this central to sequence creation, though, 
> I'd
> make a lot of combinations, rather than the two we have for each type. 
>  We
> don't want any of the commonly used sets more than a single call away.

Sets can always be combined, using formUnionWithSymbolSet and 
formIntersectionWithSymbolSet.


> Basically, I'd do strict, ambiguous, those with gap, those with 
> undefined,
> those with both, etc.  We may also want to make the standard ones
> singletons.

Sounds good.

- Koen.