[Biococoa-dev] functional groups

[Koen van der Drift]

Hi,

I am thinking about adding a class that will take care of functional 
groups on sequences, eg methyl, phosphate, etc. My first thought was to 
make it a subclass of BCSymbol. However, it will then also inherit the 
representedBy code, etc. That is not so useful for functional groups 
(or maybe they are?). So, what I plan to do is to make a new, abstract 
root class for symbols, maybe called BCRoot. Then BCSymbol and 
BCFunctionalGroup wll inherit from BCRoot. The BCRoot class will have a 
lot of the code of BCSymbol, eg for name, mass, etc. However, some 
things will be in BCSymbol, eg initializeSymbolRelationships. The 
functional groups can be attached to the sequence, using the 
not-yet-existing BCFeature class. The BCFunctionalGroup can also have 
an ivar pointing to the symbol it is attached to.

What do you guys think? For proteins functional groups are very 
important, and the probably need their own class. What about DNA/RNA? 
Are functional groups important, eg when digesting?


Also, when looking at the code of BCSymbol, I noticed that we use the 
initializer initWithSymbol:(unichar)aChar. Maybe we can change this to 
initWithChar, or even add that method? When using the word 'symbol' I 
would expect a BCSymbol, not a char. I remember we discussed this 
earlier, but I forgot why we eventually decided to use initWithSymbol 
instead of initWithChar.


cheers,

- Koen.