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

[Matthew Pocock]

Lachlan James Coin wrote:
> Hi,
> 
> The one which I can fix:  FlexibleAlignment has addSequence() and removeSequence

<snip/>

Go ahead and fix this.

> 
> 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.

That is a bug. the alphabet should be delegating to a method on 
AlphabetManager, which should handle this case. To track this down, we 
would need to know which alphabet impl is being used here, and trace its 
getSymbol() method.

Humph.

> 
> Any ideas on how to fix this?
> 
> Thanks a lot,
> 
> Lachlan
> 
> 
> 
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