[Biococoa-dev] updated project in cvs

[Alexander Griekspoor]

Wooohooo!!! Great work Koen, I hope to have a good look at it before  
I leave for holidays on friday, well done!
Cheers,
Alex

On 20-jul-2005, at 5:19, 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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>
>

*********************************************************
                     ** Alexander Griekspoor **
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               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
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                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                   E-mail: a.griekspoor at nki.nl
             AIM: mekentosj at mac.com
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