[Biococoa-dev] can't compile framework
jtimmer at bellatlantic.net
Tue Mar 8 16:13:18 EST 2005
> i just checked out the latest version and tried to compile the project, but it
> didn't work. Very strange problem:
> BioCocoa_Prefix.h:6:38: Foundation/Foundation.h: No such file or directory
> BioCocoa_Prefix.h:7:30: AppKit/AppKit.h: No such file or directory
> I think it has something to do with the new framework setting. I'm not very
> familiar with framework settings in cocoa, so perhaps anyone can help me.
> please :-)
I just did a clean checkout, and switched to the new Framework target, and
things worked without a hitch. Check that your target isn¹t the ³old
> I want to start with the BCAlignment stuff and there are many things to
> 1. what exactly do we want an BCAlignment to be ?
> A slim Datastructure for different Alignment algorithms
> Or a comfortable datastructure, which is perhaps not very useful for
> programs concentrating on performance
Both, obviously ;). From what I¹ve seen of many alignment programs, they¹re
pretty processor intensive. I¹d be willing to sacrifice using the full
sequence classes in order to up the performance.
> 2. We need a BCMatrix (protocol or class) for substitution matrices
Could you explain what you need this for? Be gentle I haven¹t taken a
math course in about 15 years, and I¹m a developmental biologist now.
> 3. A protocol for alignment generating algorithms
Well, as the person writing the code, what would you need in order to set
To ask you another question are there any values that would help you
perform alignments that we could put in the base symbol classes (nucleotide,
> I'd like to know what you think about it and what you want to do with
> alignments in your application
Two things, really contig generation from overlapping sequences, and
multiple alignments of related sequences so that I could generate a nice
looking view of the conservations. As to what I¹d think about it, I¹m very
This mind intentionally left blank
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