[Biococoa-dev] Sequence Structure

Alexander Griekspoor mek at mekentosj.com
Wed Jul 13 10:09:06 EDT 2005

On 13-jul-2005, at 15:50, Koen van der Drift wrote:

> On Jul 13, 2005, at 9:44 AM, Alexander Griekspoor wrote:
>> I thought that the idea was to have the NSData be the char array,  
>> so no separate const char*, that IS the NSData object already.
>> So to go over the list
>>> BCSequence
>>>     const char *sequence;
>>  -> is NSData so this one goes away, if you want access to the  
>> data, you would do: [sequenceData bytes]; which gives you the pointer
> Good point. Any preference for the ivar name? I would prefer  
> sequenceData over sequence for the NSData member.
Yes, I like sequenceData, or just data would be fine as well. In fact  
the shorter the better, the fact that you ask a sequence object for  
its data suggests you will get sequencedata right ? ;-)

>>> NSData *sequenceData;
>>>     NSArray *symbolArray;
>>  -> this one only if we decide to cache it, otherwise, this would  
>> be a method only. So what was the consensus again on this?
> Did we have one ;-)   Still undecided, I guess.
My concern is that the caching will potentially increase the size of  
the object enormously. If we build in the caching in the accessor,  
even an internal call could invoke caching without the user knowing.  
This can be pretty dangerous in terms of killing performance and ram  
requirements. I would propose to have methods to control caching  
actively, including a method to clear the cache... What do you guys  

                     ** Alexander Griekspoor **
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                   AIM: mekentosj at mac.com
                   E-mail: a.griekspoor at nki.nl
               Web: http://www.mekentosj.com

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