[Biococoa-dev] BCNucleotideRNA

[Alexander Griekspoor]

>> Yes, it is. Still, that doesn't exclude that ours is not elegant as 
>> well ;-) Seriously, we have discussed this way back and I pointed to 
>> the way BioJava does things. Indeed the alphabet stuff is quite nice, 
>> but overall I like the way we have done things just as much. In fact 
>> the way we use class methods to generate shared instances, instead of 
>> factory objects is something more elegant in my opinion.
>
> I agree for the way we create the symbols. But for creating sequences, 
> I still think it would be beneficial if we pass a string (or other 
> BCSequence) plus the required BCSymbolSet either to BCSequence, or to 
> an external class that will return a BCSequence. We don't have to 
> replace the current code, this can be just an additional way to do 
> things.

Sure we can add this possibility, let see how the BCSymbolSet turns out 
and then discuss how to add that exactly...


>>>> Looking up methods in an ObjC superclass is significantly slower
>>>> than having them in the object being used.
>>>
>>> I didn't know that. Is this only for ObjC, or also for other OO 
>>> languages, such as C++ and Java?
>>
>> I was curious as well, and did some searching on the web on the 
>> Objective-C runtime. I found this snippet:
>>
>> The method is looked up BY NAME, first in the class and then in each 
>> superclass in order. Once a successful lookup has occurred (or failed 
>> to occur) the associated function pointer (or pointer to the error 
>> function) is cached so that future invocations are fast (~ 2-3x a 
>> simple function call).
>>
>> So it seems you're right in principle, but given the fact that most 
>> methods we're talking about are only one superclass up, and that 
>> after the first time, the function pointer is cached, I can hardly 
>> imagine that you will see anything of this.
>
> The first lookup is during the init of the symbols, so any further 
> manipulations should be fast, if I understand you correctly?

I'm not sure whether the methods are looked up for the first time when 
called  or when the class is initialized. Anyway, I think it doesn't 
matter in either case..

Cheers,
Alex

*********************************************************
                     ** 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

               4Peaks - For Peaks, Four Peaks.
        2004 Winner of the Apple Design Awards
                Best Mac OS X Student Product
              http://www.mekentosj.com/4peaks

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*********************************************************
                     ** 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

                             iRNAi, do you?
              http://www.mekentosj.com/irnai

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