[Biococoa-dev] Should we choose?

Charles PARNOT charles.parnot at stanford.edu
Wed Jan 12 01:05:37 EST 2005

>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 input.
>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 ;-)

Like I said, I think you guys have already set up a nice foundation! I see no reason to ditch the symbol set, and many to keep it!

Charles (get both)

Charles Parnot
charles.parnot at stanford.edu

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