[Biococoa-dev] Base design

[John Timmer]

Okay, about to start coding.  Before I take the plunge, I'm thinking of the
following setup:

BCSequenceDNABase -
An abstract superclass, allows for easy testing of a sequence for DNA
content.
Would also include all the .h's for the individual bases, so including this
header would get you all bases (though I may have to think about how to
avoid circular importing - is this a problem?).
If you tried to initialize this class, it would generate an "N" base.
It would have class methods for changing strings to sequences and vice
versa.

Each base would implement the following methods:

(NSString *) name; // Adenine, Purine, etc.
(NSString *) symbol; // A, T, etc.
(BOOL) representsSingleNucleotide; // YES if G, NO if W, etc.
(BCSequenceDNABase  *)complement;  // obvious
(NSArray  *)matches;  // an array of all base objects represented by this


What have I forgotten?

JT

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