[Biococoa-dev] sequence wrappers

Koen van der Drift kvddrift at earthlink.net
Fri Dec 17 14:34:45 EST 2004

On Dec 16, 2004, at 1:46 AM, Alexander Griekspoor wrote:

>> Actually, it should have sequenceType and symbolSet. Just not the 
>> annotations and features. So basically it's the same as the current 
>> BCSequence. The current BCSequence will then be promoted to a 
>> BCAnnotatedSequence, but without the name change.
> Exactly, that would be the idea; it's more a renaming of the current 
> BCSequence while we shifted the BCAnnotatedSequence in between the 
> original BCSequence and the BCAnnotatedSequence. Again, the real 
> question is whether we want the BCAnnotatedSequence be higher or lower 
> in the hierarchy compared to BCSequence....
>> I also propose to rename sequenceArray to symbolArray.
> Yep

If nobody objects I will go ahead and make the following changes this 

* add a new class BCSymbolList, which is the same as the current 
BCSequence class

* remove all code from the current BCSequence class and make it a 
subclass of BCSymbolList

* replace sequenceArray with symbolArray

* replace the occurences of BCSequence throughout the code with 
BCSymbolList, if only a bare sequence is needed (eg for finding or MW 

After this is done we can start adding the code for features and 
annotations to BCSequence.

It will involve many edits, so I want to be sure that everybody agrees 
with the proposed changes.


- Koen.

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