[Biococoa-dev] updated project in cvs

Charles Parnot charles.parnot at gmail.com
Mon Aug 15 00:30:29 EDT 2005

I know and I feel terribly sorry about that. I am really really  
caught up in a lot of different thins, and if I could work on it as  
much as I think about it (e.g. in traffic), all of this would be  
history now...

I tried to keep up with the discussions, as it is easier to write a  
little bit here and there. But writing code requires more  
consistentcy and continuity and I don't have that luxury right now.  
The only good side of it is I am working on some code where I learn a  
lot about CoreData and in particular, CoreData in the context of the  
framework, so it is like a run test for what could be done on BioCocoa.

I also want to thank you, Koen, for doing all the coding work and  
listening to the comments and being always responsive on it. I hope I  
will have time soon for more help on the coding side. I will however  
try to at least look more carefully at the code and make comments,  
which is easier to do too that the actual coding, and still helps...



On Aug 14, 2005, at 6:25 PM, Koen van der Drift wrote:

> Hi,
> I am a little bit surprised that there has been hardly any response  
> to the new framework setup. The WWDC meeting brought some great  
> ideas, which we extensively discussed on the list. It was good to  
> see some life back on the forum, and to see that people are still  
> interested in further developing BioCocoa. I then started  
> implementing some of the new ideas, more or less to compensate for  
> my absence at WWDC, but also because I think they are good  
> improvements. But after that it has been awfully quiet. Maybe  
> people are on vacation, or just plain busy, that is very well  
> possible.
> That being said, has anyone had a chance to look at the updated  
> project? Any comments, suggestions, ideas?
> As I posted a few days ago, I think that adding the code for  
> mutable sequences could be next. Also important is the  
> transformation of existing code to use the NSData sequence object,  
> instead of the symbolArray.
> cheers,
> - Koen.
> On Jul 19, 2005, at 11:19 PM, Koen van der Drift wrote:
>> Hi,
>> I took the plunge and have committed a lot of changes to the  
>> project. These changes now incorporate:
>> 1. The addition of NSData to hold the sequenceData
>> 2. Merging of BCSequence and BCAbstractSequence and removal of  
>> sequence subclasses
>> The new way to create a sequence is:
>> BCSequence *mySequence = [[BCSequence alloc] initWithString:  
>> @"ELVISLIVES" symbolSet: [BCSymbolSet proteinSymbolSet]];
>> The project compiles, with a few warnings, and the examples seem  
>> to work. There are of course still some parts that need attention.  
>> The most important are:
>> 1. Start using the NSData in more places to replace the  
>> symbolArray. A good example is the translation code, but also in  
>> other sections. BCSequenceCodon is still in the project.
>> 2. Implement the "type-guessing" code in BCSequence. See my notes  
>> in initWithString in BCSymbol. For now the examples use fasta  
>> files, and the code cannot yet see if it is a protein or dna. Make  
>> sure to un-comment the correct symbolSet in readFastaFile.
>> 3. Implementation of a mutable sequence class
>> 4. Update the documentation
>> 5. Update the Test code
>> cheers,
>> - Koen.
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Help science move fast forward:

Charles Parnot
charles.parnot at gmail.com

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