[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
already...
Alex
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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E-mail: a.griekspoor at nki.nl
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