Koen van der Drift
kvddrift at earthlink.net
Tue Aug 24 22:38:48 EDT 2004
On Aug 24, 2004, at 9:47 PM, John Timmer wrote:
>> 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
> 0 for estimating the weight.
I think for the time being that will do. But I'll check some of the
literature to see how this is solved when people do MS on nucleotide
> 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
> subclasses will probably need to override this method because of these
> of issues.
We should think about a class that stores modifications on nucleotides,
amino acids, etc. I think we discussed this a few weeks ago
(modifications, I mean). This should be handled the same for all
BCSymbol classes. A phosphate or methyl group is the same for every
> I'll see if anything occurs to me, but I think we're getting close to
> on to either the wrappers for the sequences that hold features and
> such or
> some of the tools for translation and calculations.
I think we should also discuss on how to make the original BioCocoa
classes (I/O) compatible with the new classes. Do we maintain backward
compatibility, or do we start from scratch?
> My ISP and bioinformatics.org are not speaking to each other today, so
> done committing for today. I'm going to work on a small program that
> to the framework and lets you do sequence transformations. To test
> everything is working.
Sounds good - we can add it to the project in a folder 'demos'
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