[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 ;-)
Cheers,
Alex
*********************************************************
** 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
http://www.mekentosj.com/enzymex
*********************************************************
More information about the Biococoa-dev
mailing list