[Biococoa-dev] functional groups
Koen van der Drift
kvddrift at earthlink.net
Sat Mar 5 17:12:28 EST 2005
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.
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