[Biococoa-dev] BCSequence

John Timmer jtimmer at bellatlantic.net
Tue Aug 24 21:47:51 EDT 2004

 > It's better if we make the method as follows:
>   - (float) molecularWeight (int) mode
That's a great idea.  The main reason I was putting in a new method was that
I added a separate weight for the ambiguous bases that's the average of
every base they represent, since that would be more accurate than returning
0 for estimating the weight.  I also wanted to avoid stomping on the figures
you put in, since I don't know enough about how they're typically used.  I
just wanted to use something different that didn't interfere with what you
were likely to do.

> Also we should always add water for any sequence (only one
> watermolecule is necessary for a whole sequence), so we might as well
> put it in the same method instead of delegating it to the subclasses.
> The masses in the plist are actually residue masses, so without H2O. I
> will make these changes tonight.
Yeah, I might want to handle providing options for whether there's a 5'
phosphate and such.  I'll have to think about that.  Even so, each of the
subclasses will probably need to override this method because of these sorts
of issues.

> You added the method length, but there is alreasy a method
> numberOfSymbols. However, because the naming of the first one is more
> logical, I will remove the numberOfSymbols method as well.
Just my carelessness there - didn't see yours.

> Otherwise, a great improvement! I started with a BCSequenceProtein
> class, but see that most of the sequence manipulation is already in
> BCSequence. Not sure right now what else should go in that class. As
> Alex already suggested, additional functionality (pI calculations,
> digests, etc) should be in helper classes, such as BCProteinTools.
I'll see if anything occurs to me, but I think we're getting close to moving
on to either the wrappers for the sequences that hold features and such or
some of the tools for translation and calculations.

My ISP and bioinformatics.org are not speaking to each other today, so I'm
done committing for today.   I'm going to work on a small program that links
to the framework and lets you do sequence transformations. To test whether
everything is working.



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