[Biococoa-dev] About BCSequence (again ;-)

Alexander Griekspoor mek at mekentosj.com
Mon Jul 4 05:12:46 EDT 2005

See, that's what I mean, the diagram doesn't make sense to me  
already! What's the difference between bcsequence and  
bcsequencenucleotide. The implementation is even harder to get. Let's  
not throw everything away, but I would like to see how practically  
the one-for-all bcsequence would work. In addition, I have the  
feeling (but might be terribly wrong) that annotations are way  
simpler to implement if there's only one kind of sequence object.
If I understand it right, a BCSequence object than becomes "typed" on  
the basis of the BCSequenceSet it has been assigned right? Koen or  
Charles, could you do a proposal on what the BC world would look like  
if we choose this model of the general BCSequence object. Could you  
perhaps speculate/describe:

1 how you create such objects
2 what role sequence sets play in this
3 how one would be able to get its "type"
4 how you would do a simple reverse and what would be returned (for  
DNA and Protein)
5 how you would do a translation from DNA to Protein
6 how annotations would fit it?

Pfeww, all our problems solved ;-) Just kidding, but if we can agree  
that these problems can be tackled nicely with a single BCSequence  
object in a way logical to ourselves and new users, IMHO I think we  
have our design...

On 4-jul-2005, at 7:27, Charles Parnot wrote:

> I mostly agree with all the discussions and ideas.
> Of course, there is one point I want to make clear again: the  
> BCSequence thing! And I will jump right to it!!!
> I made a diagram to illustrate my points:
> <Picture 1.png>
> Sorry, I renamed BCSequenceAbstract into BCSequenceRoot, because I  
> just thought of that name and it sounds better...
> First, there is no such thing as a class cluster in the current  
> implementation. As Phil points out, all the subclasses are exposed.  
> The BCSequence indeed uses a trick similar to class cluster, it is  
> a placeholder class. The implementation is thus the confusing part.  
> It is not very elaborate, though, and once you get past the point  
> where the alloc-ed object can still change class at init, you have  
> it all ;-)
> Second, the basic idea of having BCSequence along the other objects  
> is to provide two different types of classes: typed and not typed.  
> Historically, the group was divided about 50/50 between the two  
> options. I was on the side of having a one-for-all class that can  
> be blindly sent any message and do something. I know Koen is also  
> in favor of a unique sequence object that include all the possible  
> types. In the end, we decided to keep both typed sequences and the  
> one-for-all BCSequence. With a diagram like above, it is fairly  
> easy to show the use of the different objects, no?
> Finally, I just want to add that BCSequence does not require  
> additional code and will probably not even need rewriting when we  
> change the internals of the sequence classes, and should not  
> require much in the future. In fact, I volunteer to maintain that  
> code if we keep it! Not writing any code is something I can easily  
> promise ;-)
> cheers all!
> charles
> --
> Xgrid-at-Stanford
> Help science move fast forward:
> http://cmgm.stanford.edu/~cparnot/xgrid-stanford
> Charles Parnot
> charles.parnot at gmail.com
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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

                             iRNAi, do you?


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