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Oops, forgot to add the mailing-list as recipient.<br><div><br><div>Anfang der weitergeleiteten E-Mail:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Von: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Stephan <<a href="mailto:stschiff80@googlemail.com">stschiff80@googlemail.com</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Datum: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">2. April 2009 09:26:50 MESZ</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>An: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Scott Christley <<a href="mailto:schristley@mac.com">schristley@mac.com</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Betreff: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><b>Re: [Biococoa-dev] read Fasta File with gap symbols</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Am 01.04.2009 um 21:34 schrieb Scott Christley:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On Apr 1, 2009, at 12:10 PM, Stephan wrote:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi Scott,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thank you for answering.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">In fact I looked through the code and found a workaround in the BioCocoa Source Code.</div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Ok, cool, I imagine you commented out some code?<span class="Apple-converted-space"> </span>I think a more permanent correct fix shouldn't be too difficult to implement.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">No, I actually just added the gap-character to lines 200 and 209 of BCSymbolSet.m. That is the definition of the dnaSymbolSet and the dnaStrictSymbolSet. I tried some more stuff before, such as defining my own symbolset and pushing it as parameter to the BCSequenceReader. I figured, however, as you guys already pointed out, we need something more general to change there, and this workaround was quick :-)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">One more question: The newest version of BioCocoa is not Mac OS X Tiger compatible... is that right?</div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I don't think there is anything preventing it, i.e. we are not using any Leopard specific functionality, it just may be how the current Xcode project settings are defined.<span class="Apple-converted-space"> </span>You might give it a try.</div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Well, it seems there are some errors. So on Tiger, first of all I had to modify the settings (the "architectures"-variable). When I then tried to compile, I have errors occurring in line 126 of BCUtilStrings.m. It does not understand the NSUIntger-type... I dont know why that is, I have been coding in Cocoa too recently. When I hacked around this by changing those lines to "unsigned int" or something, there were other mistakes. The BioCocoa-2.0 - branch does not have that issue. Any hints?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Actually, I wanted to ask how active the community is right now... I might be able to contribute something to the project. I am working in the bioinformatics field and just digging into Cocoa (coming from C++ and python). How easy/hard is it to get a developer account? Also I could help updating the webpage or writing some more tutorials...</div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Well, there was a flurry of activity in the beginning, before I joined the project, but most people have moved on to other projects, though many continue to lurk on the mailing list.<span class="Apple-converted-space"> </span>But no truthfully there really isn't much activity. <span class="Apple-converted-space"> </span>I too work in bioinformatics, and I love ObjC, so BioCocoa is perfect for me to place my code where others can use; however I spend about 80% of my time doing research and only 20% coding, so my contributions come in spurts.</div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Right, 80% - 20% is about the same for me.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">One thing I would like for BioCocoa is not for it to just re-implement much of what is in (say) bioperl or biopython, ok reading sequence files is fine, but some good analysis algorithms or data structures would help set BioCocoa apart.<span class="Apple-converted-space"> </span>But really that is my preference, any contributions are welcome, and getting a developer account is easy.<span class="Apple-converted-space"> </span>What area of bioinformatics do you work in?</div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I am actually a theoretical physicist, but I am doing my PhD in BioPhysics and currently working on Population genetics and -genomics. I am developing code for both simulation programs and data analysis tools.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">cheers,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Stephan</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">cheers</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Scott</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </blockquote></div><br></body></html>