[Biococoa-dev] Sequence Structure

Philipp Seibel biococoa at bioworxx.com
Sun Jul 10 19:42:52 EDT 2005

Hi Koen,

Am 10.07.2005 um 22:17 schrieb Koen van der Drift:

> On Jul 9, 2005, at 8:20 AM, Philipp Seibel wrote:
>> Hey,
>> i looked arround for a solution of our sequence structure problem  
>> and found a very interesting design pattern called flyweight.
>> It is something similar we did with our BCSymbol structure. Here  
>> is my suggestion:
>> <BCSequenceStructure.jpg>
>> I think it's a very flexible structure. The handling with  
>> sequences, should to be done by tool-classes.
>> So far my suggestion, please comment :-)
> Hi Phil, interesting picture. What I don't see now are the  
> BCSequence subclasses and the BCAbstractSequence class. Are those  
> omitted for simplicity or really not present? Also I suggest to  
> deprectate the use of BCSequenceType. IMO it is redundant because  
> we already are using symbolsets and typed sequences.

I suggest to use one single class to represent a sequence ->  
BCSequence. (BCAbstractSequence and others are really not present :-)).
But it seems everybody except from me likes the oversized ( just my  
opinion ;-) ) inheritance model.

> I don't understand the BCSymbolAnnotation part of the picture. Is  
> this additional or replacing some of the current classes?

This is to replace BCSymbol and BCSymbolSet classes, following the  
Flyweight-Pattern. It's hard to explain, perhaps you look at the  
links i sent.

> cheers,
> - Koen.
> ps what program did you use to make the picture?

OmniGraffle 3.x



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