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<TITLE>Re: [Biococoa-dev] can't compile framework</TITLE>
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<FONT FACE="Verdana, Helvetica, Arial"><SPAN STYLE='font-size:12.0px'>Philip -<BR>
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i just checked out the latest version and tried to compile the project, but it didn't work. Very strange problem: <BR>
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</SPAN></FONT><SPAN STYLE='font-size:12.0px'><FONT FACE="Courier, Courier New"><I>BioCocoa_Prefix.h:6:38: Foundation/Foundation.h: No such file or directory <BR>
BioCocoa_Prefix.h:7:30: AppKit/AppKit.h: No such file or directory <BR>
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</I></FONT><FONT FACE="Verdana, Helvetica, Arial">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 :-) <BR>
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I just did a clean checkout, and switched to the new Framework target, and things worked without a hitch. Check that your target isn’t the “old format” one.<BR>
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NEXT <BR>
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I want to start with the BCAlignment stuff and there are many things to discuss: <BR>
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1. what exactly do we want an BCAlignment to be ? <BR>
A slim Datastructure for different Alignment algorithms <BR>
Or a comfortable datastructure, which is perhaps not very useful for programs concentrating on performance <BR>
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</FONT></SPAN></BLOCKQUOTE><SPAN STYLE='font-size:12.0px'><FONT FACE="Verdana, Helvetica, Arial">Both, obviously ;). From what I’ve seen of many alignment programs, they’re pretty processor intensive. I’d be willing to sacrifice using the full sequence classes in order to up the performance.<BR>
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2. We need a BCMatrix (protocol or class) for substitution matrices <BR>
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</FONT></SPAN></BLOCKQUOTE><SPAN STYLE='font-size:12.0px'><FONT FACE="Verdana, Helvetica, Arial">Could you explain what you need this for? Be gentle – I haven’t taken a math course in about 15 years, and I’m a developmental biologist now.<BR>
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3. A protocol for alignment generating algorithms <BR>
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</FONT></SPAN></BLOCKQUOTE><SPAN STYLE='font-size:12.0px'><FONT FACE="Verdana, Helvetica, Arial">Well, as the person writing the code, what would you need in order to set things up?<BR>
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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)?<BR>
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I'd like to know what you think about it and what you want to do with alignments in your application <BR>
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</FONT></SPAN></BLOCKQUOTE><SPAN STYLE='font-size:12.0px'><FONT FACE="Verdana, Helvetica, Arial">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 I’d think about it, I’m very excited!<BR>
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Cheers,<BR>
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JT<BR>
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