[Biococoa-dev] BCSequenceRecord

Alexander Griekspoor mek at mekentosj.com
Sat Jul 9 14:36:15 EDT 2005

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...

On 8-jul-2005, at 2:26, Koen van der Drift wrote:

> On Jul 6, 2005, at 6:30 PM, Charles Parnot wrote:
>>> One of the things I also read about on the biopython mailinglist  
>>> is that we could keep the BCSequenceXXX classes very light, and  
>>> create a new class BCSequenceRecord, that is used to store all  
>>> info from a datafile. In that case, the BCSequence is just one of  
>>> the key/value pairs.
>>> cheers,
>>> - Koen.
>> Sorry, Koen, but I have no idea what you are talking about here!
> What I am suggesting is that we keep the BCSequence class just for  
> managing the sequence, such as creating, inserting, etc, and thus  
> keep it very lightweight. To store any annotations and features we  
> create a new class BCSequenceRecord. This is what will be created  
> in the IO classes, and it will have a BCSequence object in one of  
> its key-value pairs. So we remove NSMutableDictionary *annotations  
> from BCAbstractSequence and move it to BCSequenceRecord.
> The advantage is that when you are just dealing with sequences, you  
> want it to be as small as possible, and don't have the additional  
> luggage of all the annotations.
> Does that make more sense?
> - Koen.
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                     ** Alexander Griekspoor **
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
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                   AIM: mekentosj at mac.com
                   E-mail: a.griekspoor at nki.nl
               Web: http://www.mekentosj.com

                             iRNAi, do you?


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