[Biococoa-dev] starting BCAlignment
biococoa at bioworxx.com
Thu Mar 10 03:46:23 EST 2005
Am 10.03.2005 um 00:31 schrieb John Timmer:
>>>> If all of this is correct, then I think I know enough to actually
>>>> help ;).
>>> you are completly right !!! :-)
> Good to know. So, coding efficiently, how do matrix lookups normally
> It's easy to see how a dictionary of dictionaries would work (ie - get
> dictionary with the key "Cys", look up value for "Tyr" in it), but I'd
> imagine they're normally implemented in much faster C code
There is no need for a dictionary, i would suggest to have a NSArray of
That would allow to access the substitution score with the indices of
the Symbols in a int* matrix.
It's perhaps not the fastest, but it works well and is a clean
So internally we have a int* matrix for the scores. Just look at the
small interface i just submittet.
> The reason I ask is that I'm expecting the lookup to work with char
> variables, but I'd imagine the code could be adapted to use pointers
> of a char. If it is, since all our individual bases/amino acids are
> instance pointers, it'd be very easy to get this to work, and I'd be
> to help you populate the matrix, as well as helping set up a .plist
> format to store it.
Yes, i also thought of storing the matrix in a .plist file. I also
think we should provide the most common matrices with our framework.
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