[Biococoa-dev] BCNucleotideRNA

[Alexander Griekspoor]

I'm afraid a few of these things are indeed attributable to all changes 
made in John's vacation. It's a pity there's not a single good log of 
changes from what I did, but that was impossible given the fact I had 
to do a complete new import to get the new folder hierarchy.. I guess 
we just all three have to check on regular basis what should still be 
changed...

>> - Is it necessary to duplicate all the code from BCNucleotideDNA,
>> except for the uridine instead of thymidine?

uridine  (uri·dine) ([umacr]r¢[ibreve]-d[emacr]n)  a pyrimidine 
nucleoside, uracil linked by its N1 nitrogen to the C1 carbon of 
ribose. It is a component of ribonucleic acid, and its nucleotides 
participate in the biosynthesis of polysaccharides and some 
polysaccharide-containing compounds. Symbol U.

So is it uridine or uracil ? I think uracil as we're talking about the 
complete nucleotide right, not only the base...
That would be my daily portion of nitpicking ;-)

>> Why not have a class
>> BCNucleotide that takes care of everything, and just have two
>> subclasses with the small differences?
> That was my long-term intention.  I just wanted to get things working
> quickly so that I could get translation and codons handled.  Once I was
> happy with how they worked, I figured I could go back and sort out a 
> better
> class structure.  Even so, all the base methods have to be separate 
> for DNA
> and RNA, as they need to return something different so that == works as
> expected, so the classes won't shrink as much as I'd have hoped.

That's fair. The only thing we have to keep thinking of if in that case 
there isn't a better alternative of doing things such that we can put 
more stuff in the superclass, like we did earlier for the string 
searching methods. But I'm not in the position to judge over that, I 
leave that up to you guys...

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

                             iRNAi, do you?
              http://www.mekentosj.com/irnai

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**************************************************************
                         ** Alexander Griekspoor **
**************************************************************
                  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

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