[Biococoa-dev] ambiguous symbols

[Koen van der Drift]

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.