RNA alphabet

[Julien Yann Dutheil]

Hi all (but most particularly Sylvain :D)

I have found that the method DNA::getAlias(int) did not work anymore with gaps, that is, getAlias(-1) returned an empty vector, while it returns -1 in proteins for instance (and that is the behavior we want... this was the cause of the bug in the parsimony class, see the help forum).

I made a small modification to account for that, but maybe there is a better way to do so using the binary codes that Sylvain introduced, so maybe you may want to double-check the code I modified...

Also, I realized that all the modifications carried on by Sylvain using the "binary codes" were only present in DNA and not in RNA. I cannot see any reason for that, so I duplicated all the code in DNA to the RNA class. Sylvain, is there a problem in doing so? Could that code go in a common class instead of being duplicated in both DNA and RNA, or am I missing/forgetting something?

Cheers,

Julien.

[Sylvain Gaillard]

Hi Julien,
I'll take a look at that asap ... but time is a precious thing that I
miss currently ;-)
Sylvain

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[Sylvain Gaillard]

I've taken the time to look at your modifications. That's OK for me.
Duplication of code in DNA and RNA is not a problem as these classes are
independent, they just inherit form the NucleicAlphabet class and
provide two distinct classes used in different context. I don't think
that the code had to be shared just for ease of coding as they are two
distinct classes that happen to have the same implementation because of
their similarities in term of biochemistry.
Best,
Sylvain

[Julien Yann Dutheil]

Ok Sylvain, thanks a lot.

We leave it as is (at least for now).

Cheers,

J.

--
Julien Y. Dutheil, Ph-D
0 (+49) 6421 178 530

§ Max Planck Institute for Terrestrial Microbiology
Department of Organismic Interactions
Marburg -- GERMANY

§ Intitute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE