Fwd: [Biococoa-dev] Nomenclature

[Alexander Griekspoor]

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

Welcome John! Kiddin' ;-)

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

That's unfair you should tell yours as well then ;-)
And to prevent the obvious, I'm from 1977, that would make me 27....

>
>
> 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;

Ok!

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

Shall we make that (unichar) token; to prevent the name circle you 
warned us for?

> 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?

I guess not. Which methods are you talking about? We don't implement 
the set methods do we, only the get ones. Perhaps I don't see the point 
your making here.

> 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 -

I believe Koen or Jim pointed me to Autograf: 
http://autograf.sourceforge.net/ which produces very nice results. 
Documentation will be something we have to look into quite some more... 
Autograf should work together with XCode I believe, haven't tested it 
though.

>
>> BCSymbol
>> |
>> |
>> -------------BCNucleotideDNA
>> |
>> |
>> -------------BCNucleotideRNA
>> |
>> |
>> -------------BCAminoAcid
>> |
>> |
>> -------------???
>>
>>
>> For the sequence we'll use:
>>
>> BCSequence
>> |
>> |
>> -------------BCSequenceDNA
>> |
>> |
>> -------------BCSequenceRNA
>> |
>> |
>> -------------BCSequenceProtein
>> |
>> |
>> ---------???
>>
>
>
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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
                   E-mail: a.griekspoor at nki.nl
	        AIM: mekentosj at mac.com
               Web: http://www.mekentosj.com

                  EnzymeX - To cut or not to cut
              http://www.mekentosj.com/enzymex

*********************************************************


*********************************************************
                     ** 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
                   E-mail: a.griekspoor at nki.nl
	        AIM: mekentosj at mac.com
               Web: http://www.mekentosj.com

                  EnzymeX - To cut or not to cut
              http://www.mekentosj.com/enzymex

*********************************************************