[Biococoa-dev] more ramblings

Koen van der Drift kvddrift at earthlink.net
Wed Dec 1 20:20:28 EST 2004

On Dec 1, 2004, at 1:51 PM, Alexander Griekspoor wrote:

> I think we should choose here, at the moment we did for 
> BCSequenceType. Or, we adopt the whole BioJava approach with general 
> sequences, "typed" bases on the used BCSymbolSet. But I don't see a 
> real mix. In addition, we had many discussion about the BioJava 
> approach and I still see no clear advantage, even more there are some 
> real problems associated with it.

When using the BCSequenceType, we just use plain DNA, RNA, and protein. 
There is no info about the symbols that belong to it, eg is it  
'strict', 'ambiguous', etc. Using symbolsets, we actually define the 
possible symbols. And we could also differentiate easily between:

[BCSequenceDNA dnaSequenceWithString: string skippingNonBases: NO];


[BCSequenceDNA dnaSequenceWithString: string skippingNonBases: YES];

and even extend the possibilities.

- Koen.

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