[Biococoa-dev] BCCodon bug (?)

John Timmer jtimmer at bellatlantic.net
Sun Sep 5 08:30:51 EDT 2004

> John,
> The method AminoAcidSymbolString in BCCodon returns the symbol '*'
> when theAminoAcid is nil. However, if you pass that in an NSString to
> BCSequenceProtein the code crashes, because '*' is not an entry in the
> amino acids plist. For gaps the entry in the plist is a hyphen. Maybe
> there is a specific reason to use the asterisk, in that case I will add
> a line to BCSequenceProtein to skip that symbol. Otherwise, can you
> change AminoAcidSymbolString to return an hyphen?
> Also, change the name of the method to aminoAcidSymbolString (first
> letter should be lowercase).

Sorry about that - that's a stop codon.  It was decided that we wouldn't
create a "stop" amino acid (I still think it would be convenient to do so),
so I used a nil amino acid reference as stop within a BCCodon.  Part of what
I need to do is to put the headerdoc in place, so this doesn't surprise
anyone, and to create a BCSequenceCodon in order to provide an interface for
generating BCSequenceProteins safely (ie - ending the sequence when it hits
a stop codon).

And go ahead and change the method name.

Sorry again -


This mind intentionally left blank

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