[Biococoa-dev] the decorator pattern

Alexander Griekspoor mek at mekentosj.com
Sat Sep 11 16:01:01 EDT 2004

>>  I think you're right Koen, this is indeed better than further 
>> subclassing BCSequence. Certainly because it would mean you can 
>> nicely keep things separated for all kinds of manipulations through 
>> the addition of single wrapper objects instead of getting tons of 
>> different BCSequence subclasses.
> We already have some in BioCocoa: BCUtilDNATranslator, 
> BCUtilMassCalculator.

That wasn't so much the problem. What I meant was having not only the 
additional BCFragment class, but then in addition a BCFragmentDNA, -RNA 
and -Protein/Peptide class. That makes 4 already...

> Anyway, I am working now on the digest code, and want to make sure 
> that I get the design right.
> 1. BCUtilDigest is fed a BCSequence and enzyme information and does 
> the digest either by an external trigger or internally.
> 2. It returns an NSArray of BCFragment objects which are wrappers 
> conatining all info: the sequence, the original location, the enzyme.

Exactly the plan!
> Do we need a separate BCUtilDigestProtein, BCUtilDigestDNA?
Nope, not for a reason that I can think of at least.

> We have to make sure BTW, that we use the 1-based counting when 
> dealing with subsequences.
Good point.

                     ** 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

       Microsoft is not the answer,
       Microsoft is the question,
       NO is the answer


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