[Biococoa-dev] BCSymbol Nomenclature

[Alexander Griekspoor]

John,

My comments as the youngest:

> symbol provides a 1 letter code as a unichar
> symbolString provides that as a string
> name provides the chemical name for the item

Ok by me!

> We move all initialization methods into the subclasses, since Koen and 
> I are
> writing them and handling them somewhat differently.

I'm not in favour of this one, can you identify what exactly you do 
differently? I would strongly ask you guys to agree on one of the two 
implementations as both classes are descendents of BCSymbol it would be 
not more than logical to keep implementations as similar as possible as 
well. The aminoacids are encoded through a plist as well aren't they?

> We'll drop the "setName:" method, since Koen doesn't want to do that 
> either.
Please leave the accessor methods, but make them private. This is the 
recommended way apple advises us to go. Things are more straight 
forward for people to read the code and prevents making mistakes. Thus 
in the .m file:

@private
-(void)setName:(NSString *)name;
@end

init...
  [self setName: @"blabla"];


> I'd like to create a standard "gap" and "non-chemical" symbol for the 
> bases,
> and thought they should parallel what's done with amino acids (the
> non-chemical is for situations where a long string is provided and 
> needs to
> be translated into objects - the user may need to know where problems 
> are).
> I also don't want them to conflict with a "stop" amino acid, which 
> would be
> needed for translating an entire frame.
>
> For stop, I propose:
> Symbol: X
> Name: stop

Commonly the symbol for stop is an asterix "*", please use that one.
Also a stop is kind of an ambiguous aminoacid like W is an ambiguous 
base. Do we provide this one in addition to the three stop codons we 
know? Also, how do we implement the fact that in one species something 
can be a stop codon, but in another not? This influences the symbol 
right?

> For gap:
> symbol: -
> name: gap

> For non-chemical:
> name: undefined
> symbol: ?

Both ok!

Cheers,
Alex
*********************************************************
                      ** Alexander Griekspoor **
*********************************************************
                The Netherlands Cancer Institute
                Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                  AIM: mekentosj at mac.com
                   E-mail: a.griekspoor at nki.nl
               Web: http://www.mekentosj.com

    The requirements said: Windows 2000 or better.
    So I got a Macintosh.

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*********************************************************
                     ** Alexander Griekspoor **
*********************************************************
               The Netherlands Cancer Institute
               Department of Tumorbiology (H4)
          Plesmanlaan 121, 1066 CX, Amsterdam
                   Tel:  + 31 20 - 512 2023
                   Fax:  + 31 20 - 512 2029
                   AIM: mekentosj at mac.com
                   E-mail: a.griekspoor at nki.nl
               Web: http://www.mekentosj.com

                           Mac vs Windows
	65 million years ago, there were more
                      dinosaurs than humans.
	     Where are the dinosaurs now?

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