[Biojava-dev] More problems with gaps

[Lachlan Coin]

Hi,

I've been tracking down a bug to do with the use of gaps in cross product
alphabets.
The problem is that a gap symbol is not atomic, and hence when I use a cross product
alphabet, and I use the getSymbol(List syms) method of this cross product
alphabet, if any of the symbols in syms are gaps, the method returns a
SimpleSymbol with name "[]" (it should return a BasisSymbol).

I have commited a test in org.biojava.bio.symbol.AlphabetManagerTest which
demonstrates this:

public void testGapInCrossProductAlphabet() throws Exception{
	Alphabet alph = AlphabetManager.alphabetForName("(PROTEIN x
PROTEIN)");
	List s = new ArrayList();
	s.add(AlphabetManager.getGapSymbol());
	s.add(ProteinTools.createProtein("V").symbolAt(1));
	Symbol sym = alph.getSymbol(s);
	List l  = ((BasisSymbol)sym ).getSymbols();
	assertEquals(s.get(0), l.get(0));
	assertEquals(s.get(1), l.get(1));
    }


It falls over when it tries to cast to a BasisSymbol.

Any ideas on how to fix this?

The approach which makes most sense to me is to make the gap symbol
atomic.  Is this an option at all?

Thanks,

Lachlan