[Biojava-l] Gap: Basis Symbol vs Symbol

[Emig, Robin]

	I have some code that uses codons with ambiguous bases using
basissymbol. Problem is I also try to deal with gap symbols at the same
time. I thought the idea behind the gap symbol was that it would be
universal, ie gap or gapxgapxgap would be the same symbol. However, I can't
use my current code like that because I need to do a getsymbols, on standard
codons. This comes from the BasisSymbol. Since gap only implements Symbol,
my code blows up when a gap is thrown in.
	We could have gap implement BasisSymbol or AtomicSymbol, any ideas
why not?
	The workaround is that I will create a basis symbol which is
gapxgapxgap and try to deal with it differently elsewhere( I really liked
being able to just say AlphabetManager.getGapSymbol()) to deal with gaps.
	-Robin