[Biococoa-dev] Base test

Koen van der Drift kvddrift at earthlink.net
Sun Aug 15 19:45:08 EDT 2004

On Aug 15, 2004, at 7:10 PM, Alexander Griekspoor wrote:

> In that case the sequence and setSequence method definitely should be 
> made @private so they are only used internally. In general while 
> developing a framework we should take special care to nicely 
> "private-out" all internal methods to avoid people to get a bunch of 
> compiler warnings (the famous: "Also found bla bla method") when they 
> use our framework. Also, why the keep the string around? That only 
> takes up memory and leaves you most probably with one that is pretty 
> quickly out of sync with the array:

You're right, I'll remove that line and the two accessors.

>> 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.
> I thought so already, either we should rename it (if we decide to keep 
> the start/end position thing in) or remove it. If the positioning is 
> kept, why don't we include it in the general description? I think the 
> way it is now it's way to program specific, any developer might want 
> it in a different way, so leave it up to them as they can access the 
> integers anyway.

Agree. When I made the file today it was more a quick copy-paste from 
my Protein class. So stuff can be remved and added, no problem.

> Nice solution! The question if this is also something that we should 
> move to the BCProteinUtil shared object.

The same code can be used by all kinds of sequences, so it should be in 
the BCSequence class. Right now it says amino acid, but as soon as we 
decide on a name for the root-class, I'll change that to make it more 

>  If we go for a strict separation between model (data), controller, 
> and view (which I strongly am in favour of),

Me too! BioCocoa should focus on the model and maybe the controller 
part, I think.

>  we should move all these kind of methods outside of our data classes 
> (which the sequence clearly is). That way we don't have to update 
> these methods everytime we edit the sequence.

I disagree, the sequence takes care of it's own internal bookkeeping. 
But it doesn't have to be recalculated with each edit, only when 
another class want that info.

- Koen.

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