[Biococoa-dev] more ramblings

Alexander Griekspoor mek at mekentosj.com
Thu Dec 2 02:21:24 EST 2004

Very nice summary John, this indeed the state of the union ;-)

> Koen, who doesn't like the idea of sequence subclasses, wants to make 
> all
> methods accept all sequences, even if they can't make any sense out of 
> it -
> for example, a nucleotide sequence being sent to a hydrophobicity
> calculator.  Nonsense like this could be handled by throwing an 
> exception or
> something similar.

Again, this is the number one reason why I 'till now chose for typed 
subclasses, and still thinks it's a better option.
> Alex and I feel that it's better to help the developer recognize 
> potential
> errors by having type requirements for these methods, where possible.  
> The
> converse is that I can't see any possible benefit of allowing a 
> situation
> that can throw an exception when it can be prevented easily.  Koen may 
> be
> able to explain benefits I can't see, since he is advocating this.

He mentioned one, but it doesn't do it for me yet.
> One compromise would be to have the actual method implementation 
> (which is
> in a non-sequence class) accept any type of sequence, but place the
> convenience method that calls it in the specific sequence class(es) 
> that
> should be used with the method.  Again, I'd prefer otherwise, but if I 
> get
> outvoted on that, please allow me this concession.

It's better to choose, if we go for subclasses there's no advantage to 
do this, it even removes one as it lifts the type requirements!

                     ** Alexander Griekspoor **
               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?


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