[Biojava-l] gaps

[Matthew Pocock]

Hi all

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.

M

ps this may have unforseen knock-on effects, so please complain if 
something suddenly stops working