[Biojava-dev] Suggestion for Canonical Symbols

[Schreiber, Mark]

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?

Thanks

Mark


Mark Schreiber PhD
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

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