[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...
Cheers,
Alex
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
>
>
>
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>
*********************************************************
** 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?
http://www.mekentosj.com/irnai
*********************************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.bioinformatics.org/pipermail/biococoa-dev/attachments/20050704/c96df8a0/attachment.html>
More information about the Biococoa-dev
mailing list