[Biococoa-dev] BCSequence class cluster? [Was Re: Introducing myself]

Koen van der Drift koenvanderdrift at gmail.com
Sat Feb 28 13:38:53 EST 2009

On Feb 28, 2009, at 12:51 PM, Scott Christley wrote:
> * I'm not very enamored with the BCSequenceArray class.  I'm not  
> sure how it is any better than just using a standard NSArray, I  
> tried looking in the archives for discussion but didn't really find  
> anything.  However my guess is that BCSequenceArray would somehow  
> provide additional sequence specific functionality?  Personally, I  
> don't really want to treat BCSequence objects in any special way.  I  
> think its best if users can include into standard collections  
> (NSArray, NSDictionary, NSSet) instead of having to use specialized  
> collections.  Thoughts?

I think I added it to be a replacement for NSArray. I cannot really  
think what any additional functionality could have been, if I remember  
I'll post it here.

> * Craig makes a good point about being able to do -sequenceWithId:  
> to lookup a sequence.  One issue to be aware of is that the id's in  
> the FASTA files are not necessarily unique.  In fact, the definition  
> of the sequences often lie outside of the fasta file.  Now if you  
> download from  NCBI then you have a good chance of getting unique  
> id's, but take UCSC's goldenPath for example.  If you download the  
> human genome from there, the id just says chr1, chr2, etc.  Mix and  
> match with another organism and you can quickly forget which chr  
> goes with whom.
> So from this perspective, we need to be careful not to rely upon the  
> id's being unique.  Typically id's are unique within a file, but  
> this would really have to be a contract that the user enforces, it  
> is not part of the FASTA format.

This is why we added the BCAnnotation and BCFeature classes. Most data  
formats have different labels for name, sequence, authors, etc. I  
think the idea was to make our own definitions (BSSequenceName,  
BCSequenceAuthor, etc), and let BCSequenceReader take care of putting  
the right annotation and or feature in combination wth the actual  

- Koen.

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