[Biococoa-dev] Nomenclature

[Alexander Griekspoor]

Reminded by the screenshot on the autograf homepage, XCode 2 from Tiger 
has some nice features as well.... (NDA)


Op 18-aug-04 om 15:07 heeft Alexander Griekspoor het volgende 
geschreven:

>> 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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>> Biococoa-dev at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>>
>>
> *********************************************************
>                     ** 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
>
> *********************************************************
>
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>
>
*********************************************************
                     ** 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

Windows is a 32-bit patch to a 16-bit shell for an 8-bit
operating system, written for a 4-bit processor by a 2-
bit company without 1 bit of sense.

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