[Biococoa-dev] Translation

John Timmer jtimmer at bellatlantic.net
Sat Feb 26 14:32:32 EST 2005

Okay, for translation, I think we're going to need three instance variables
and their setter/getter methods;

- (int) readingFrame;
- (void) setReadingFrame: (int)theFrame;

- (BCGeneticCodeName) codeName;
- (void)setCodeName: (BCGeneticCodeName)aName;

- (BCAbstractSequence *) sequence;
- (void) setSequence: (BCAbstractSequence *)theSequence;

Again, I'll check the sequence type prior to translating and return
[sequence copy] if it's not DNA or RNA.

One thing I'm thinking of doing:  changing the genetic code so that it
doesn't specify sequence type.  Since we're going to be testing the sequence
type, there really isn't a reason to specify whether to use DNA or RNA for
the translation.  In fact, not specifying them should allow us to avoid the
possibility of a code/sequence mismatch error.  So, instead of looking up
"BCUniversalGeneticCodeDNA", we would have a method like:
geneticCode: BCUniversalGeneticCode forSequenceType: BCDNASequenceType

Does this sound reasonable?  Have I missed something?


This mind intentionally left blank

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