[Biococoa-dev] BCSequenceRecord

Alexander Griekspoor mek at mekentosj.com
Sat Jul 9 14:08:37 EDT 2005

The discussion feature vs annotations is another one to tackle, I  
think an annotation is independent of position, a feature is. Author,  
creation date, species etc would be an annotation, phosphorylation,  
alpha-helix, etc would be a feature. But there are many things in the  
gray area. Again, I'm with charles, it doesn't make sense to separate  
annotations/features from sequences because we would end up with more  
lightweight sequences, we don't. In the end we have to keep both  
around, in one or two objects doesn't make a difference in ram (in  
fact, it's probably more because of overlap). In addition, it makes  
syncing much more difficult. If you are not interested in the  
annotations, don't touch them, we use pointers anyway so passing  
around of sequences with or without annotations doesn't make a  
difference. Finally, the particular problem you mention (large  
datafiles) has nothing to do with this problem, in your case simply  
ask the importer to not handle the metadata and only import the  
sequence (an option we definitely have to build in into the seqIO  
classes). Plus, BCSequence should have methods to ask a (sub)version  
of the sequence with or WITHOUT annotations. Charles gave an example  

On 9-jul-2005, at 14:02, Koen van der Drift wrote:

> On Jul 9, 2005, at 2:40 AM, Charles Parnot wrote:
>> But, still, your initial argument seems to be that BCSequence  
>> should remain a light object, hence no annotations. However, an  
>> additional ivar for the annotations will not make it heavier if it  
>> is set to nil.
> What I want to avoid is that when a large datafile is read (eg pdb  
> or swissprot) not all the metadata is stuffed in to the  
> annotations, making the sequence object heavy.  However, sequence  
> specific information such as C=C bonds, PTM, probably should be in  
> the sequence object. Or would they then be called features?
> cheers,
> - Koen.
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                     ** Alexander Griekspoor **
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