[Biococoa-dev] more ramblings

[Alexander Griekspoor]

>
>>  Wait, would it be an idea to make it:
>
>> BCAnnotatedSequenceBundle - a bundle of BCAnnotatedSequences (in an 
>> array)
>>
>> BCAnnotatedSequence - contains a dictionary of BCFeatures (so no 
>> BCFeatures object, because that has no advantage over a dictionary), 
>> a BCSequence, a dictionary of BCAnnotation
>
> I like the BCAnnotatedSequence name. Although it kinda leaves out the 
> features.
True, but in some way also in that case I like to think as the sequence 
being annotated...
>
> 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:

>
> BCSequenceWrapper
>       |
>       -> has-a BCSequence, BCFeatures, etc
>
>
> BCFeatures
>       |
>       -> 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?).
But I guess you meant the same thing as I do: A BCSequenceWrapper 
(object) has a dictionary containing multiple BCFeature objects.

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

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).

>
> 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...

>>> Actually, I think that is a good point. But we have to be aware of 
>>> the fact that a developer can have all compiler warnings turned off.
>> Then it's a stupid developer IMHO....
>
> Yep - and we all know there's plenty of them ;-)
Very true (I tend to be one sometimes), but they tend to turn the 
warnings back on when things don't work ;-)
Cheers,
Alex

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                     ** Alexander Griekspoor **
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               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
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                  E-mail: a.griekspoor at nki.nl
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