[Biococoa-dev] Base test
Koen van der Drift
kvddrift at earthlink.net
Sun Aug 15 18:40:08 EDT 2004
On Aug 15, 2004, at 6:18 PM, Alexander Griekspoor wrote:
> - Koen, in your sequence class I saw you can init them with a string,
> great! But next you keep the string around and many methods depend on
> / work with the string. This leads to exactly the problems we
> discussed. Init with a string is logical of course, but then we should
> just let that go and completely depend on the sequence list containing
> John's bases. We shouldn't have to worry about keeping the string in
> sync here, the only string you can get back out is through the
> stringRepresentation; method which is generated at that particular
> moment back "translated" from the sequencelist. Of course I realize it
> is work in progress and perhaps to early.
I think the only other thing I do with the string are the 2 accessor
functions. Editing of the sequence is done for the NSMutableArray,
although this is still commented out until we agree on the naming of
> - I found the -position; method a bit confusing as to it's description
> vs what it does
It's used by my app to make a string that displays the start and end
position (1-based) of a subsequence. We can rename it.
> - What does the countedset do,
The counted set keeps track of the number of different aminoacids, see
the method countAminoAcids how to populate the set.
> and is that supported from Jaguar?
Not sure, the docs usually say if it is 10.3 and later, but there is no
such mention in the class description.
> The idea I would propose is that there is a shared translation util
> object that you could feed a dna sequence and get (in the requested
> frames) the translated sequences back as protein sequence objects.
> It's the app task to control/organize these.
Agree, good plan.
> Likewise, one could argue this for complements as well -> a shared dna
> utils object returns you the complement sequence if you hand it a
> sequence. Alternatively these translations could be added as features,
> but in all cases there's again the "how to keep things in sync upon
> editing" problem. I think we should keep things as separate and clean
> entities as much as possible.
> I guess before that however, many discussion will follow ;-)
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