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 _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
