[Biococoa-dev] Fwd: read Fasta File with gap symbols

Stephan stschiff80 at googlemail.com
Thu Apr 2 03:28:22 EDT 2009

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> Von: Stephan <stschiff80 at googlemail.com>
> Datum: 2. April 2009 09:26:50 MESZ
> An: Scott Christley <schristley at mac.com>
> Betreff: Re: [Biococoa-dev] read Fasta File with gap symbols
> Am 01.04.2009 um 21:34 schrieb Scott Christley:
>> On Apr 1, 2009, at 12:10 PM, Stephan wrote:
>>> Hi Scott,
>>> Thank you for answering.
>>> In fact I looked through the code and found a workaround in the  
>>> BioCocoa Source Code.
>> Ok, cool, I imagine you commented out some code?  I think a more  
>> permanent correct fix shouldn't be too difficult to implement.
> 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 :-)
>>> One more question: The newest version of BioCocoa is not Mac OS X  
>>> Tiger compatible... is that right?
>> 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.  You might give it a try.
> 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?
>>> 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...
>> 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.  But  
>> no truthfully there really isn't much activity.   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.
> Right, 80% - 20% is about the same for me.
>> 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.  But really that  
>> is my preference, any contributions are welcome, and getting a  
>> developer account is easy.  What area of bioinformatics do you  
>> work in?
> 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.
> cheers,
> Stephan
>> cheers
>> Scott

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