[Biococoa-dev] BCSequenceRecord

Koen van der Drift kvddrift at earthlink.net
Sat Jul 9 15:16:37 EDT 2005

On Jul 9, 2005, at 2:36 PM, Alexander Griekspoor wrote:

> I'm not sure, the question is how heavy the annotations will be, I 
> think not too much. The question why I'm kind of reluctant is the idea 
> for instance that NSAttributedString would be separated into an 
> NSString and an NSStringAttributes object, somehow this doesn't make 
> sense to make. It will also be more problematic to keep things in sync 
> after editing, and would certainly require all kinds of notification 
> and delegates "hacks" to make it work. In the end I don't think we 
> even need light weight sequences so much. After all, we're passing 
> around pointers to objects, so imagine a bcalignment, it will get the 
> pointers to the sequences, it will use the ivar to the raw data to get 
> access to the char arrays, and do it stuff. Whether or not the 
> bcsequence object contains the annotations or not doesn't make a 
> millisecond or kb or ram difference!! This is one of the nicest things 
> of the char array setup in fact. I don't like the idea of a separate 
> record for the annotations too much. The question in the end comes to 
> whether we see the sequence as the center of our universe, also 
> containing annotations, or whether we see the metadata as the most 
> important part, with one of its attributes being the sequence data in 
> the form of a bcsequence object. I don't get the overall picture. If 
> you really want to do the separation, it would make even more sense to 
> me to make BCSequence the metadata/annotations object and have a 
> separate BCSequenceData object...
> Alex

Hi Alex,

I think you convinced me :)

Let's start implementing the char array and BCSequence structure first. 
  Are we merging BCSeqeunce and BCAbstractSequence so that we just will 
have a regular subclass - superclass structure?  For the ivars I 
suggest to make them immutable:

const char *sequence
NSArray *symbolArray

And what will be the role of the BCParser class? It's still not very 
clear to me how this will fit into the BCFOundation picture.


- Koen.

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