[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.
Alex
*********************************************************
** Alexander Griekspoor **
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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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