[Biojava-l] Behavior of the createRegex() method (MotifTool class)

[Thomas Down]

On Mon, Dec 02, 2002 at 10:44:27AM +0000, Keith James wrote:
> 
> I don't think this method is behaving as expected. Passing the
> FiniteAlphabets from the following Symbols gets these results:
> 
> a -> getMatches() -> getAllSymbols -> tokenize -> -a
> c -> getMatches() -> getAllSymbols -> tokenize -> -c
> g -> getMatches() -> getAllSymbols -> tokenize -> -g
> t -> getMatches() -> getAllSymbols -> tokenize -> -t
> n -> getMatches() -> getAllSymbols -> tokenize -> tnn-nannnngncnnn

Okay, looks like I broke this when fixing serialization of
ambiguity-symbols.  Ugh, serialization...

It's fixed for now (see AlphabetManagerTest).  If we ever re-write
this code we *must* use some kind of globally unique names (URLs?)
for Symbols and Alphabets, otherwise we'll end up in this mess
again.

    Thomas.