[Biococoa-dev] Progress!

[John Timmer]

Just thought you guys would want to know, since we've been doing everything
in theory so far:

I have the test app done and working (including a linked BioCocoa build and
bundling the framework).
I needed two bug fixes:
1 related to the change to an "initWithSymbol" method from my original
"initWithName".
1 related to me using pyrimidine in the .plist and pyrimadine in the .m
file.

And that's it!  Reverse complementing the sequence worked, and it was even
pretty fast on an 11Kb transcript - pretty good, what with all the object
creation required (in fact, I just checked and NSDate says it takes 0.069829
of a second).

One question:  How does one handle sending a nib file via CVS?  I'm going to
add my test project, although bioinformatics.org has dropped off my ISP's
radar screen again (can't even ping the place).

Two comments:  
I don't have a strong opinion on how modifications are handled - I'll see
how it's done on amino acids, and handle it accordingly for DNA.

Molecular mass really isn't my thing, so I'll defer to Koen on how best to
name things.


Think that's it -  Cheers,

John