[Biococoa-dev] more ramblings

John Timmer jtimmer at bellatlantic.net
Thu Nov 18 15:53:38 EST 2004

> To a certain point yes, at least I agree with the latter part. I'm strongly in
> favor of the wrapper classes, I use them a lot myself and think they nicely
> separate the model from the "controller". Also, with convenience methods one
> can still keep things "hybrid" I think.
> In principle, I don't believe in untyped sequences, but of course the biojava
> way shows one possibility to indeed have a general BCSequence that is typed by
> the attached BCSymbolSet (Alphabet) you attach to it. I'm not sure as I can't
> overlook many consequences and problems that this strategy has. Most
> important, I think that the current solution works nicely, though more methods
> could be transferred to wrapper classes. Finally, the annotation stuff and
> alike are indeed very general, but hey that's why they belong in the
> BCSequence super class right!

Yeah, the more I look at BioJava¹s actual code, the less excited I become
about using their progress as a model.  Have you ever tried to trace through
their process for translation?  I never got to the point where I could see
anything actually related to an amino acid.  It calls through so many
methods before it attempts to do anything that it must take about a half an
hour to accomplish anything

BioJava rant aside ­ I¹m  comfortable with the idea mentioned somewhere in
Alex¹s message of shifting the actual code for some of the sequence
manipulation/calculation into wrapper classes, but providing call throughs
to the methods in the sequence classes.  Another alternative would be to
have these methods attached as categories on BCSequences.  With either of
these, you would get Koen¹s code separation and I¹d be happy about the more
direct connection of methods to data.

Anyway, to stir up more controversy around here, I had always envisioned
something along the following structure:

Sequence bundle
(groups related sequences)
Sequence wrapper
(holds features, notes, etc.)

The reason being that I see features as being abstractions, not inherent to
any type of sequence.  They¹re mostly a bit of information and a range it¹s
relevant to.  There are some exceptions to this ­ for example, a
phosphorylation site changes the MW of a protein ­ but they are largely
exceptions.  These exceptions are going to be difficult to handle regardless
­ how to tell if a site is or isn¹t glycosylated is going to be very context
dependent.  The majority of features (ORFs, kinase domains, restriction
sites, etc.) don¹t require that sort of heavy lifting.

Just something else to think about....



This mind intentionally left blank

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