[Biojava-l] Gap: Basis Symbol vs Symbol

Emig, Robin Robin.Emig@maxygen.com
Mon, 12 Feb 2001 06:16:42 -0800

>Hi Robin,
>I see what you mean. I've revised the docs to be more clear (and 
>accurate). At least this was spotted before release date. It turns out 
>that having gaps behave in the old way (gap == gap^n) causes lots of 
>problems. In your case, I think using gap^3 is the apropreate way to go 
>(should make all of your code work out seamlessly).
>Bother me if anything falls over.

	Well one thing that is annoying is that when I do a
AlphabetManger.getCrossProductAlphabet(list Degenerate DNA alphabet) I get
back an immutable Alphabet, so I cant add gap^3, unless I want to add
gapXDNAXDNA, gapXgapXDNA etc. To make matters worse it is a sparse alphabet
(~4000 symbols), which is an alphabet, not a finite alphabet, so I can't get
all the symbols to create a new alphabet that includes the gap^3. 
	ok, so I probably just have to create a new alphabet on my own, I
just didn't want to.