[Biococoa-dev] BCSymbol Nomenclature
Alexander Griekspoor
mek at mekentosj.com
Fri Aug 20 14:17:21 EDT 2004
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.
*********************************************************
*********************************************************
** 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?
*********************************************************
More information about the Biococoa-dev
mailing list