[Biococoa-dev] BCSequence class cluster

Alexander Griekspoor mek at mekentosj.com
Sat Jan 8 07:45:50 EST 2005

Man, I'm running behind, this one goes really back, but I still had a 
few comments....

>> I'm still wondering a bit how we're going to implement these kind of 
>> methods, as we now have to start ALL methods with a test what the 
>> sequence type is.

As charles pointed out, I'm wrong here as all subclasses can/will 
handle things differently.
> You only need to put the test in the init of the BCTools subclasses. 
> No need to keep them in BCSequence, et al. Another  possible solution 
> could be to create a DNATools/ProteinTools class, which has 
> convenience methods to various manipulations only for that type of 
> sequence (this is the BioJava approach - I like the first one better, 
> though).

The comment I had was one I've expressed before that I would strongly 
argue against DNA/ProteinTools for every thinkable manipulation of your 
sequence objects. Although I have to admit I haven't practically used 
BioJava much, one thing that annoyed me in there examples was that for 
even the simplest manipulation of your sequences you have to 
instantiate and use tools. I think tools are the way to go for complex 
things, but for things like reverse and complement I don't wanna think 
of needing tools for that, so un-cocoa like..

>> To implement mutable objects in the class cluster could be a bit 
>> tricky, because there are two conflicting subclass organizations 
>> here: mutable/immutable and dna/rna/protein/codon. To get all the 
>> combinations, it seems that we need 8 subclasses!!
>> Oops, Koen won't like this, LOL ;-) On the other hand, look at the 
>> number of NSNumber subclasses...
> No, I don't like that :D, see my comment above. Another possibility 
> (also stolen from BioJava) is to make a BCToolsEdit class that takes 
> care of editing a immutable class.

Although practically a valid option, again, this sounds weird, I think 
we've clearly made a bad design decision the moment you start editing 
immutable classes ?!

                     ** 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

	Claiming that the Macintosh is inferior to Windows
	because most people use Windows, is like saying
	that all other restaurants serve food that is
	inferior to McDonalds


More information about the Biococoa-dev mailing list