[Biococoa-dev] BCSequenceRecord

[Alexander Griekspoor]

Yep, that's the way, just indicate whether you would like a bare  
sequence (faster) or a completely annotated bcsequence be returned  
from either methods like the one charles mentiones, or tools like a  
translator tool that returns a sequence...
Cheers,
Alex

On 9-jul-2005, at 6:25, Charles Parnot wrote:

>> What I am suggesting is that we keep the BCSequence class just for  
>> managing the sequence, such as creating, inserting, etc, and thus  
>> keep it very lightweight. To store any annotations and features we  
>> create a new class BCSequenceRecord. This is what will be created  
>> in the IO classes, and it will have a BCSequence object in one of  
>> its key-value pairs. So we remove NSMutableDictionary *annotations  
>> from BCAbstractSequence and move it to BCSequenceRecord.
>>
>> The advantage is that when you are just dealing with sequences,  
>> you want it to be as small as possible, and don't have the  
>> additional luggage of all the annotations.
>>
>> Does that make more sense?
>>
>> - Koen.
>>
>
> You are suggesting to add yet another hierarchy of classes, 6  
> total ??!?? ;-)
>
> Anyway, we already had that discussion and the bottom line was: the  
> annotations would be just one ivar = 4 bytes when nil, slightly  
> more when empty dictionary, which is anyway very small compared to  
> the sequence array of char.
>
> What we should provide are 'annotation-free' methods when spitting  
> out subsequences, alignements, etc... e.g. having a optional last  
> argument, e.g.:
>
> - (BCSequence *)subsequenceWithRange:(NSRange)aRange  
> keepAnnotations:(BOOL)flag
>
> charles
>
> --
> Xgrid-at-Stanford
> Help science move fast forward:
> http://cmgm.stanford.edu/~cparnot/xgrid-stanford
>
> Charles Parnot
> charles.parnot at gmail.com
>
>
>
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>

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                     ** Alexander Griekspoor **
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