[Biococoa-dev] Symbols, codons and functional groups

[Alexander Griekspoor]

> I thought of that too at some point.
> And my idea was: codons could simply be symbols, to benefit from the 
> BCSymbol/BCSequence/BCSymbolSet design. At this point, symbols are one 
> char, but a subclass could add  an ivar.

If I'm correct, this is exactly the BioJava approach where Codons are 
symbols as well...
For instance, what they call Alphabets is what we call SymbolSets.
It might be handy to let us further study their approach a bit more to 
see the pros/cons.
Some quotes from the cookbook:

> CrossProductAlphabets are used to represent groups of Symbols as a 
> single Symbol. This is very useful for treating things like codons as 
> single Symbols.

> CrossProductAlphabets result from the multiplication of other 
> Alphabets. CrossProductAlphabets are used to wrap up 2 or more Symbols 
> into a single "cross product" Symbol. For example using a 3 way cross 
> of the DNA alphabet you could wrap a codon as a Symbol. You could then 
> count those codon Symbols in a Count or you could used them in a 
> Distribution.

http://www.biojava.org/docs/bj_in_anger/index.htm

Again, I have absolutely no problem to adapt for a large part their 
setup/basic ideas. I've noticed with the advocacy of the symbolsets and 
recent discussions on features etc that we're seeing a nice example of 
convergent evolution ;-)
Cheers,
Alex


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                     ** Alexander Griekspoor **
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              The Netherlands Cancer Institute
              Department of Tumorbiology (H4)
         Plesmanlaan 121, 1066 CX, Amsterdam
                    Tel:  + 31 20 - 512 2023
                    Fax:  + 31 20 - 512 2029
                    AIM: mekentosj at mac.com
                    E-mail: a.griekspoor at nki.nl
                Web: http://www.mekentosj.com

       Microsoft is not the answer,
       Microsoft is the question,
       NO is the answer

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