[Biojava-dev] Suggestion for Canonical Symbols

[Schreiber, Mark]

Would it be useful to use the Integer/ SubInteger model where protein
alphabet is a sub alphabet of protein-term?

> -----Original Message-----
> From: Thomas Down [mailto:td2@sanger.ac.uk] 
> Sent: Monday, 9 December 2002 1:00 p.m.
> To: Schreiber, Mark
> Cc: biojava-dev@biojava.org
> Subject: Re: [Biojava-dev] Suggestion for Canonical Symbols
> 
> 
> On Mon, Dec 09, 2002 at 11:59:01AM +1300, Schreiber, Mark wrote:
> > Hi -
> > 
> > If you translate and RNA SymbolList into Protein the Symbols in the 
> > protein SymbolList come from the alphabet referenced by the 
> > ProteinTools.getTAlphabet.
> > 
> > The Symbols from the Talphabet are not canonical with the 
> Symbols from 
> > the other protein Alphabet. This has lead to some very 
> surprising bugs 
> > in some stuff we were developing. Given that Integer 
> Symbols are now 
> > canonical even if they come from IntegerAlphabet or one of the 
> > Integer.SubAlphabets could the same happen for the protein 
> Alphabets?
> 
> *sigh*
> 
> That was actually the original behaviour.  I broke it
> (deliberately) a few weeks ago when fixing the knotty 
> question of serializing ambiguous symbols, so now you know
> who to blame.  At the time, requiring that all well-known 
> symbols should be scoped by Alphabet provided a sane way of 
> cleaning up the serialization code without having to write 
> totally new Symbol and Alphabet implementations for all the 
> well-known cases.  At least in the Protein/protein-term case 
> is probably does make sense to fix this.  I shall ponder -- 
> all suggestions welcome.
> 
> The division between protein and protein-term is really
> rather articificial.  As far as I can tell, the termination 
> symbol is a bit like the gap symbol, in that it never occurs 
> in "biologically real" sequences, but is a useful convenience 
> for computation.  Maybe we'll be able to build on that idea 
> for BJ2 and get rid of the annoying distinction.
> 
>      Thomas.
> 
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