[Biojava-dev] Gaps and EmptyAlphabet

[Matthew Pocock]

Mark, could you post some example code? This smells like it's a 
boundary-condition bug. The maths says it does match itself, so we have 
got the alphabet wrong.

We should have included a 'gap' Symbol sub-interface, but it's too late 
now. Symbols and alpphabets will be much cleaner next time around, but 
oopy programming realy doesn't make it easy to do very relational / 
group-theoretical things without jumping through hoops, as extention vs 
specialisation are both modelled by inheritance but are realy orthogonal 
processes.

Matthew

mark.schreiber at group.novartis.com wrote:

>The gap symbol getMatches method returns the EmptyAlphabet.
>
>This has the slightly weird result that the gap symbol doesn't match 
>itself!? I'm sure Bertrand Russell could write a book on that. I just 
>think it's plain weird. Wouldn't it be better if the getMatches for a gap 
>returned an FiniteAlphabet containing only the gap symbol??
>
>- Mark
>
>Mark Schreiber
>Principal Scientist (Bioinformatics)
>
>Novartis Institute for Tropical Diseases (NITD)
>1 Science Park Road
>#04-14 The Capricorn
>Singapore 117528
>
>phone +65 6722 2973
>fax  +65 6722 2910
>
>_______________________________________________
>biojava-dev mailing list
>biojava-dev at biojava.org
>http://biojava.org/mailman/listinfo/biojava-dev
>
>  
>