[Biococoa-dev] updated project in cvs

[Koen van der Drift]

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.