[Biococoa-dev] About BCSequence (again ;-)

[Charles Parnot]

On Jul 4, 2005, at 2:12 AM, Alexander Griekspoor wrote:
> If I understand it right, a BCSequence object than becomes "typed"  
> on the basis of the BCSequenceSet it has been assigned right? Koen  
> or Charles, could you do a proposal on what the BC world would look  
> like if we choose this model of the general BCSequence object.  
> Could you perhaps speculate/describe:
>
> 1 how you create such objects
> 2 what role sequence sets play in this
> 3 how one would be able to get its "type"
> 4 how you would do a simple reverse and what would be returned (for  
> DNA and Protein)
> 5 how you would do a translation from DNA to Protein
> 6 how annotations would fit it?


Just as an exercise, I will briefly answer these questions:

1. The objects are created by the IO or by passing a string:
     - the type might be guessed
     - the type might be passed as argument, in which case the  
default BCSymbolSet is used (with all the ambiguous symbols)
     - a symbol set is passed as argument, which restrict the symbols  
that can be used

2. Symbol sets (I think that is what you meant?) are used to filter  
the sequence symbols. They are also used to translate from char to  
BCSymbol, as a char meaning is dependent on the symbol set, e.g. can  
be an alanine or an adenosine. The symbol set is the best object to  
ask. For performance, we might end up having a char/BCSymbol array as  
one of the ivar.

3. The type is set by an ivar. The BCSymbolSet also has a type and  
has to be the same. This is the current implementation.

4. To get the reverse, you take all the chars and put them backwards.  
Ah!
OK, I guess you meant 'complement'. If not DNA, return self.  
Otherwise, you get the array of symbols, and ask each symbol its  
complement, and then create the array of chars.

5. The current code is fine. I would however make BCCodon a subclass  
of BCSymbol for consistency.

6. Annotations are independent of sequence type.

OK, we are done, let's call it version 1.0 ;-)

charles


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Charles Parnot
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