[Biococoa-dev] sequence wrappers

[Alexander Griekspoor]

No objection your honor ;-)  Looking forward to the changes...
Alex

Op 17-dec-04 om 20:34 heeft Koen van der Drift het volgende geschreven:

>
> 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 
> weekend:
>
>
> * 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 
> calculating)
>
>
> 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.
>
>
> cheers,
>
> - Koen.
>
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>
>
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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

    The requirements said: Windows 2000 or better.
    So I got a Macintosh.

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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

MacOS X: The power of UNIX with the simplicity of the Mac

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