[Biococoa-dev] more ramblings
Koen van der Drift
kvddrift at earthlink.net
Fri Dec 3 15:30:37 EST 2004
On Dec 3, 2004, at 12:03 PM, Alexander Griekspoor wrote:
>> I like the BCAnnotatedSequence name. Although it kinda leaves out the
> True, but in some way also in that case I like to think as the
> sequence being annotated...
Yes, that is true.
>> BTW, I'm still confused about what is the difference between a
>> feature and an annotation. I think we should define very well what we
>> want to store in either one. And if the BCFeature and BCAnnotation
>> aren't objects, what do you intend them to be?
> Oh sorry, in the previous email you wrote:
>> -> has-a BCSequence, BCFeatures, etc
>> -> has-a dictionary of features (d'oh)
> ..so I thought you wanted to create a BCFeatureS class, which would
> have a dictionary of features (BCFeature?).
I don;t know - I thought that was similar to what John proposed last
week. I really have no idea what the structure should be. It was just
an example to get the discussion going.
> But I guess you meant the same thing as I do: A BCSequenceWrapper
> (object) has a dictionary containing multiple BCFeature objects.
Yes. Although we probably will use BCAnnotatedSequence which is a
BCSequence, instead of has-a (see my other email).
> As for the distinction between features and annotations: it's pretty
> simple, features are linked to certain symbol ranges (phoshorylation
> at 12, helix from 15-18), annotations are like metadata, author =
> koen, link to article = ... , creation date.. etc
Yes, that makes sense.
> I think that both should be tagged by string identifiers (like
> BCFeatureTypeAlphaHelix and BCAnnotationTypeAuthor), and we can
> predefine a complete set of them to be sure that things like author,
> date etc are standard items. The main advantage is that a developer
> can add it's own tags to for instance save a marked region in a
> sequence: (AGFeatureTypeMyMarkedRegion). We will make sure that these
> get written in and out of files for him, so he doesn't have to invent
> his own filetype.
> Note that it should be no problem to add multiple instances of
> BCFeatures with same tag (like authors).
Sounds like a good plan. Not that this will not work with a dictionary,
because it can have only one of each key. BTW, I'm pretty sure that
there is a xml scheme out there that tries to unify these things for
various dataformats. We could consider adapting such a thing (if it
>> Should we also make a special class BCAnnotatedSequenceReader that
>> takes care of extracting as much as info as possible from a file? Or
>> should we do everything with BCSequenceReader.?
> Good question, I don't know, there should definitely be the option to
> either read in the features and annotations or not. It can go into one
> class, but it's perhaps nicer to have to classes. Then again, it would
> require a lot of code duplication which we don't want. We could make
> the one a subclass of the other, the annotated one takes off where the
> super class stops. No idea...
Food for thought.
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