[Biococoa-dev] More on BCSymbolSets

Koen van der Drift kvddrift at earthlink.net
Thu Mar 3 19:43:58 EST 2005

On Mar 3, 2005, at 1:25 AM, Charles PARNOT wrote:

> * Do we let the user define the symbol set at creation by providing a 
> 'symbolSet' argument in some of the initializers? The other option is 
> to decide the symbol set ourselves.
> My opinion is we should give the user the possibility to use the 
> symbol set she wants, but also provide a default symbol set when she 
> just wants to create a sequence and not bother.
> Another option is to let that option open for later and internally use 
> symbol sets for now, and see how it is doing (performance, 
> usability,...), and then add more possibility for the user later.

I think it would be a good idea if we allow the user to pass a 
symbolset, defining the type of sequence. In fact you not only make a 
filter for whatever string or array is supplied to create the sequence, 
but you also have immediately an identifier of the sequence.

> About sequenceTypes:
> * Should we extend the number of sequence types to take into account 
> the different symbol sets?
> Proposed by Koen.

I am not in favor of extending the number of sequence types, It was 
more a question based on the comments made by John. Actually, I would 
propose to not use the sequencetype at all, but only use symbolsets, 
since they also act as identifiers (see above).

> * Will all instances of one given sequence classalways have the same 
> sequenceType? e.g. all instances of BCDNASequence will be of type 
> 'BCDNASequence'.

Probably not. A BCSequenceDNA can have ambiguous symbols, but can also 
be strict. It can allow for gaps in an alignment, etc. By assigning it 
a sequence type, still doesn't tell anything about the possible 
symbols. Therefore a symbolset will be much more useful. Another thing 
that bugs me is that the sequence is BCSequenceDNA but the type is 
BCDNASequence. Very confusing :)


- Koen.

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