[Biococoa-dev] Should we choose?

Koen van der Drift kvddrift at earthlink.net
Tue Jan 11 20:37:29 EST 2005

On Jan 11, 2005, at 5:37 AM, Alexander Griekspoor wrote:

> Op 11-jan-05 om 11:21 heeft Peter Schols het volgende geschreven:
>> Hi Charles,
>> Thanks for your reassuring mail. Your description takes care of my 
>> major concerns about the schizophrenic nature of the framework and 
>> about the difficulties we could face explaining the interface to our 
>> users (developers).
>> It seems that BCSequenceGeneric would require very little effort to 
>> create and even less effort to maintain while offering users 
>> easy-access to the entire framework.
>> I also like your API documentation proposals.
>> It's my opinion too that - if everybody agrees with this structure - 
>> we can start implementing it.
> Hooray! Same here! Nicely done Charles, and yes indeed it make's me 
> very happy to see some implementations of all those ideas again, 
> although I'm still looking forward to long emails ;-)
> Cheers,
> Alex
> Ps. I'll take a look at the documentation proposals soon and see how 
> we can organize that a bit...

It seems like a good compromise to me, so let's move forward with this 
structure. I would like to add though that I think that is is important 
that we have a symbolset as one of the ivars of the sequence class. 
This has several advantages:

1. If the user by accident creates a DNA or protein sequence with a 
nonsense character (eg a number), then the framework will not create 
the sequence, and can inform the user that there was an error in the 

2. As soon as we have a valid sequence, there is no need to test for 
each BCSymbol if it is the right through every iteration, because we 
already know the sequence is created using the correct subclass of 
BCSymbol. This will also speed up things.

3. The symbol set can be used to test if the right sequence is passed 
to a method. As said in an earlier email, the cost of one test is 
minimal compared to a MW calculation, translation, etc.


- Koen (wants to buy a Mac mini and iPod Shuffle ;-)

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