[Biococoa-dev] Nomenclature

[John Timmer]

I've created a new account at bioinformatics, this time jrtimmer.
Hopefully, this time it'll work better.


> I am probably the oldest, so I will make the decision on the naming :)
Okay, I've got to ask - how old are you?


The following methods and their associated variables can probably be shifted
up to the BCSymbol class (I'll do this later today):
- (NSString *)symbolString;
- (NSString *) savableRepresentation;
- (NSString *) description;

If we're only going to be working with items that have single letter codes,
we could also move 
- (unichar) symbol;
As well.

The question I have is whether we'll ever allow anyone to rename the
symbols?  For the DNA nucleotides, I've overridden these methods to cause
them to have no effect them, since allowing a rename could lead to all sorts
of bizarre behavior.  Is there any case where it wouldn't?


Does anyone know a good class diagramming program?  It would be great to
have the following drawn out for the users.  It'll help them know where to
look for method documentation -

> BCSymbol
> |
> |
> -------------BCNucleotideDNA
> |
> |
> -------------BCNucleotideRNA
> |
> |
> -------------BCAminoAcid
> |
> |
> -------------???
> 
> 
> For the sequence we'll use:
> 
> BCSequence
> |
> |
> -------------BCSequenceDNA
> |
> |
> -------------BCSequenceRNA
> |
> |
> -------------BCSequenceProtein
> |
> |
> ---------???
>