Tue, 27 Mar 2001 13:28:42 +0100
The latest round in the gap saga is that I have finaly added
Alphabet.getGapSymbol() which returns the apropreate BasisSymbol to
represent a null sub-space that spans the entire alphabet.
AlphabetManager.getGapSymbol() returns the basic gap entity that matches
nothing and spans nothing. DNA, RNA, Protein and all other order 1
alphabets have getGapSymbol methods that will return a BasisSymbol that
is a list of one copy of AlphabetManager.getGapSymbol(). The gap symbols
are all fly-weighted, so that asking for the apropreate gap symbol for
alphabets that are built from the same number of underlying alphabets
will return the same object.
Robin, could you see if this fixes the nasties you saw earlier? Have a
quick ganda at demos/symbol/TestGapSymbol.java to see an example of the
new gap syntax in action.
ps this may have unforseen knock-on effects, so please complain if
something suddenly stops working