[Biococoa-dev] Update

Charles PARNOT charles.parnot at stanford.edu
Fri Feb 25 19:32:40 EST 2005

At 19:23 -0500 2/25/05, John Timmer wrote:
>Okay, I'm ready to do a major update.  I've created BCNucleotides as symbols
>and BCSequenceNucleotides.  I've modified the corresponding BCSequence and
>Symbol subclasses for DNA and RNA.  I've modified BCSymbol to move
>complementation down to the subclass, while adding "isCompoundSymbol" to it.
>I added "containsCompoundSymbols" to BCAbstractSequence accordingly.
>I had to modify the Complement tool - if its sequence is a protein, it
>returns a copy of that protein (in keeping with Koen's idea of returning
>"self" when it can't return anything else).  If it's not, it uses
>BCNucleotides to create the complement.
>I can't guarantee everything's working properly, but the translation demo
>doesn't crash (though it produces a very short peptide, so it may not be
>working perfectly).
>Any objections before I commit this?  I may not be done with rationalizing
>things up from the subclasses, but I think the worst of it is now done.  I
>won't commit until I hear from Charles and Koen, who seem to be working the
>most on things right now.

Go ahead! It is a useful addition, and we will just work out te bugs.

While you and Koen are on, about me going ahead with the test framework? The main point is I will need to upgrade the cross-development level to 10.3 in the project settings, which means target that we want to be compiled for 10.2.8 deployment will have to be upgraded to 'native target', which means the project won't work with Project Builder, and everyone needs to use Xcode. This is probably already the case?

Koen, John, I know you are here?? The others?? Who is STILL using Project Builder?


Help science go fast forward:

Charles Parnot
charles.parnot at stanford.edu

Room  B157 in Beckman Center
279, Campus Drive
Stanford University
Stanford, CA 94305 (USA)

Tel +1 650 725 7754
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