[Biococoa-dev] the decorator pattern

Alexander Griekspoor mek at mekentosj.com
Sat Sep 11 09:47:21 EDT 2004

>> The idea was to store not only the sequence, but also the enzymes 
>> that produced both ends and for example the original position in the 
>> uncut sequence. The solution we came up with was to have a BCFragment 
>> class that is a subclass of BCSequence which adds the needed 
>> variables to store the enzymes and position. And it would quickly 
>> mean three other classes, BCFragmentDNA/RNA/Protein. The 'decorator' 
>> pattern might indeed help, as we could make BCFragment normally 
>> descend of NSObject and act as a simple wrapper that stores a 
>> BCSequence (any type), the BCEnzymes which produce each end, and the 
>> position in the uncut sequence. The BCDigest class simply spits out 
>> BCFragments in this case.
> That's exactly what I had in mind. Are you going to work on this, 
> otherwise I can try something this weekend, if I can find some time.
Very nice! I'm currently working on the scanner, so go ahead if you 
like! Also, I made some rearrangements of groups in the project file, 
they do not (yet) represent a change in files so far, but I would like 
to do that as well. Can you guys let me know two things, first if I 
update the project file in the CVS, do you automatically get these 
changes if you use XCode as your SCM? John you had some experience with 
this wasn't it? The other thing is, could we agree on a timespan I get 
to do the changes. That would mean that you guys would have to check 
everything back in and not touch the CVS for a certain time. We should 
easily be able to pick a time where it's day here and still night at 
your places...
>> I'm not sure if the features/annotations would benefit from this 
>> approach, it somehow feels the wrong way around for those. There the 
>> BCSequence acts as a wrapper for a number of sequences, and these are 
>> also intrinsic parts of all BCSequence objects, guess therefore these 
>> belong just in the class itself. But if you can show otherwise, I'm 
>> looking forward to that....
> I don't know yet - but maybe we can use it for modifications? I will 
> need to think about this a little bit more.
>> Ps. perhaps I should really start reading the book to further mine 
>> new insights ;-)
> Maybe I should get my own copy as well, I only had it checked out from 
> the library a long time ago.
It certainly is a nice overview. I decided to take a gamble and order a 
second hand copy at amazon, instead of a brand new one. Well it turned 
out great as it certainly looks almost new!
Let me know about the CVS....

                         ** 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

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