[Biococoa-dev] BCSequence init methods

Charles PARNOT charles.parnot at stanford.edu
Fri Feb 4 01:35:47 EST 2005

>Hi Charles,
>Just noticed the new additions. However, BCAbstractSequence does not show up in my project. Make sure you also commit the project.pbxproj file in Xcode. To do this, click on the triangle next to 'SCM' in the left panel of the main window of Xcode. Then right click on project.pbxproj and select cmmit changes. Hopefully that will take care of it.

I had done that already, and redid it just now after doing some fake modifs to the project. Let's see if that works for you. Let me know!

>Again, I like the idea of shared code where possible, so this seems to me also a good idea. I don;t have an alternative for skippingUndefinedSymbols rijt now, but it says what it does, so why not leave it. This is also very related to my idea of finally implementing the BCSymbolSet, similar to alphabets in BioPerl and BioJava. I might have some time this weekend to finally implement this :-)

I thought BCSymbolSet was already done. I can't wait to see what else it can be used for...

>Not sure yet what to do in this situation. I would not do a translation or something else, because that would make the method unpredictable. I suggest to comment out both methods for the meantime. For transformation and translation we should use a class in the BCTools hierarchy.

Yes, exactly. Actually, we also have to come up with a name for transforming a type of sequence into another (translation being a particular case), like 'transformation' or something better (?)

>>I put at the end of the email what I would propose as init and factory methods for the different subclasses. There are not many changes from the current status, in fact. I put some comments to indicate which methods will really need to be implemented in the subclass (well, the code is already done, anyway). This little 'cleaning' would be nice before we add the annotations stuff, what do you think?
>I am not sure what you want to propose.

I am not proposing anything more than the 3 points raised above. I am not even proposing anything about annotations.

>>One more random thought: We probably don't need annotations in the init methods (or at least we can live without for a while). We would just need to set the ivar to nil at init and then alloc it at the first '-addAnnotation:'.
>Yep :)

Oups, just remembered the immutable/mutable issue :-)

Thanks for your input, I will do all of that... soon...


Charles Parnot
charles.parnot at stanford.edu

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