[Biococoa-dev] peptides and proteins
Koen van der Drift
kvddrift at earthlink.net
Thu Sep 9 20:36:44 EDT 2004
On Sep 9, 2004, at 7:19 AM, Alexander Griekspoor wrote:
> The way I did that in EnzymeX was to have a custom class EXMapCut
> (don't bother the stupid name) that stores the position and the
> enzyme, which I instantiated for each position an enzyme cuts. When
> you do this for each enzyme and store all of the cut objects in array,
> then the rest is simply to sort the array on position and itterate
> over the array and create the fragment objects accordingly. I could
> imagine that you could do this with a dictionary or set as well to
> prevent the need for a custom object.
>>> Something we have to watch out for is that the sequence object
>>> contained in the object is a mutable one, so potentially can be
>>> changed underneath us. Unless we do not store a pointer, but would
>>> copy it. This however might be expensive.
>> If we just store the sequenceString, which makes the use of an
>> NSScanner very easy, then we can store it as an NSString:
> I'm afraid this leads again to discussions we had before, but I'm not
> in favour of this approach for two reasons. First, you could just as
> well then copy the handed BCSequence and have your own copy that can't
> be edited. Second, we should use strings only within implementations
> and not as variables. Now if I want to ask the digest for its
> sequence, this has first to be created again from the sequencestring
> (losing all features for example)!
I think it is fine to use a BCSequence, I was under the impression that
you thought it would be expensive, which is why I suggested to use the
sequenceString. But using a BCSequence is more logical.
>> 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).
> The start and stop could just be a single NSRange variable. Hey, wait
> a minute, there we have our BCFragment class ;-) But again, this might
> be a good alternative. The real advantage of a BCFragment class that
> you could easily add logic for sorting for example, because how do you
> sort this dictionary on cutposition for example, or worse on enzymes?
You've convinced me here.
>> 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
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