[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.

Yes :)

> I guess before that however, many discussion will follow ;-)


- Koen.

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