[Biococoa-dev] can't compile framework

John Timmer jtimmer at bellatlantic.net
Tue Mar 8 16:13:18 EST 2005

Philip -
> 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
format² one.
> I want to start with the BCAlignment stuff and there are many things to
> discuss: 
> 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
things up?

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,
amino acid)?

> 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




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