[Biococoa-dev] updated project in cvs

[Koen van der Drift]

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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