[Biojava-dev] gaps and holes

[mark.schreiber at novartis.com]

>> So far it seems that if i take a small DNA SymbolList, 
>> write it to disk
>> and then read it. It no longer has the same symbols in it. So im fairly
>> sure this realy is
>> a serialization issue.
>
>Yup. It would be key to find out exactly which gaps where written out and 

>which where loaded in.

The serialization code seems to get confused during serialization of the 
basis gap symbol and ends up converting it to an n {a,c,g,t} rather than 
{}. Not entirely sure why, there is a very confusing 
if-else-then-but-except-onlyOnAMonday type loop in there.

- Mark