[Biococoa-dev] BCSequence

[Alexander Griekspoor]

>>> I think we should also discuss on how to make the original BioCocoa
>>> classes (I/O) compatible with the new classes. Do we maintain 
>>> backward
>>> compatibility, or do we start from scratch?
>>
>> I think that's a pretty easy choice, as we don't know of anyone using
>> BioCocoa at the moment, I think we should just start from scratch.
>> Cheers,
>> Alex
>
> Since the I/O classes also deal with metadata about the sequence 
> (especially
> NCBI), I'd always viewed them as being one object layer up from the 
> sequence
> containers that we've been working on.

They are one layer up, but they return strings at the moment. I guess 
that's very nice to keep around, but in addition I would like to see 
direct BCSequence class output in addition to prevent double parsing of 
the files. (first to create a string and a second time to convert the 
string to a BCSequence.). For that we need a sharedSeqIO controller or 
if we want to keep more or less the same setup as it is now, a BCReader 
and BCWriter controller/class.

> And I haven't had enough coffee yet this morning to consider 
> methylation....
Good morning!
Alex

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                     ** Alexander Griekspoor **
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               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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