[Biojava-dev] Problems with cross-product alphabets and alignments

[Lachlan James Coin]

Hi,

I have a few more problems with alignments and cross-product alphabets, some of 
which I can fix, others for which the code is a bit impenetrable and I need 
some help.

The one which I can fix:  FlexibleAlignment has addSequence() and removeSequence
() methods which do not adjust the underlying cross-product alphabet.  Hence 
when you call align.symbolAt() it falls over.  I can fix this, and I will 
commit my changes if that is OK.

The on which I can't fix:  in the symbolAt() method of AbstractULAlignment 
there is the following line
 alphabet.getSymbol(list);

where alphabet is a cross-product alphabet list is a List of symbols.  However, 
if there is a gap symbol in this list, the symbol returned by the cross product 
alphabet is the gap symbol from the cross-product alphabet, not the BasisSymbol 
comprising all of the symbols in the list.

Any ideas on how to fix this?

Thanks a lot,

Lachlan