[Biococoa-dev] Base design

John Timmer jtimmer at bellatlantic.net
Wed Aug 11 12:07:47 EDT 2004

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
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

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?


This mind intentionally left blank

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