[Biococoa-dev] ambiguous symbols

Alexander Griekspoor mek at mekentosj.com
Sat Nov 13 20:08:13 EST 2004


Hi Koen,

I think it makes perfectly sense to "upgrade" the code to the symbol 
class if both nucleotides and aminoacids contain ambiguous species... 
You're doing a great job in the recent days!
Cheers,
Alex

Op 14-nov-04 om 2:03 heeft Koen van der Drift het volgende geschreven:

> Hi,
>
> It turns out that there are some letters defined for ambiguous amino 
> acids, eg B for Asp and Asn and Z for Glu and Gln. I have already 
> added this in the amino acid plist including a Represents key for each 
> amino acid. So I need to add some code to BCSymbolAminoAcid that is 
> similar to the series of representsBase code in the nucleotide 
> classes. To make thing easier for ourselves, I suggest we rename the 
> following methods:
>
> - (void) initializeBaseRelationships;
> - (NSArray *) representedBases
> - (NSArray *) representingBases;
> - (BOOL) representsBase: (BCNucleotideRNA *) entry;
> - (BOOL) isRepresentedByBase: (BCNucleotideRNA *) entry;
> - (NSCharacterSet *) symbolsOfRepresentedBases;
>
> to:
>
> - (void) initializeSymbolRelationships;
> - (NSArray *) representedSymbols
> - (NSArray *) representingSymbols;
> - (BOOL) representsSymbol: (BCSymbol *) entry;
> - (BOOL) isRepresentedBySymbol: (BCSymbol *) entry;
> - (NSCharacterSet *) symbolsOfRepresentedSymbols;	
>
>
> And move them to BCSymbol. If needed the subclasses can still override 
> them, for instance in the case of initializeSymbolRelationships. We 
> could even merge representsSymbol with IsEqualToSymbol, using a 
> 'strict' flag.
>
>
> Let me know what you guys think, and I will implement if y'all agree.
>
>
> cheers,
>
> - Koen.
>
> _______________________________________________
> Biococoa-dev mailing list
> Biococoa-dev at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biococoa-dev
>
>
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                         ** Alexander Griekspoor **
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                  The Netherlands Cancer Institute
                  Department of Tumorbiology (H4)
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                       E-mail: a.griekspoor at nki.nl
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