[Biococoa-dev] sequence wrappers

[Koen van der Drift]

On Dec 17, 2004, at 3:23 PM, Alexander Griekspoor wrote:

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

At your service.

The first three steps are now in cvs. So there will be some compiler 
warnings and broken code. I will do the rest later today or tomorrow.


- Koen.




> 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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>>
>>
> *********************************************************
>                      ** Alexander Griekspoor **
> *********************************************************
>                The Netherlands Cancer Institute
>                Department of Tumorbiology (H4)
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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
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