[Biococoa-dev] peptides and proteins

Alexander Griekspoor mek at mekentosj.com
Fri Sep 10 05:18:09 EDT 2004

>>> Why not keep that data in the BCDigest class that did the actual 
>>> cutting? But I am open to more discussion, because below I suggested 
>>> a BCPeptide class :)
>> Exactly ;-) We both want the BCFragment subclass so it seems ;-)
> I guess so ;-) So, if I understand correctly, we have a general 
> BCDigest object that is fed a BCSequence. Then after the digest, the 
> BCDigest object spits out an array of BCFragments, containing all the 
> needed information. And the BCFragment class is a subclass of 
> BCSequence. But wait, then you lose the specific BCSequenceProtein and 
> BCSequenceDNA features. So maybe we should have a BCFragmentProtein 
> (or BCPeptide) and a BCFragmentDNA (or BCOligoNucleotide).

That was exactly the plan, but to keep things general I mentioned the 
BCFragment superclass in the examples. I prefer BCFragmentDNA/RNA for 
nucleotides as oligos are not necessarily made by enzyme cleavage, but 
I leave it up to you if you want to call
the protein version BCFragmentProtein or BCPeptide...

>>> This is already how I code my digest class. First create an array of 
>>> cutpositions using the NSScanner, then feed those numbers to the 
>>> actual digest, which returns the fragments.
>> Yep, exactly the plan. This brings up another thought I had, perhaps 
>> it would be nice to actually create an NSScanner equivalent for our 
>> BCSequences, I know the omni frameworks have constructed there own 
>> scanner as well, so we might look through their code for hints how to 
>> do it. The big advantage would be that we could in the 
>> implementations stay native in BCSequences instead of converting 
>> everything to strings all the time.
> Sounds fine - you've just assigned yourself some homework for the 
> weekend!
That's a deal! My girlfriend is out of town anyway this weekend, so 
I'll have a look at onmi's scanner ;-)

                     ** 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
                   E-mail: a.griekspoor at nki.nl
	        AIM: mekentosj at mac.com
               Web: http://www.mekentosj.com

                  EnzymeX - To cut or not to cut


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