[Biojava-l] Getting a Slice of an Alignment

[Dexter Riley]

I have time to think about the problem of creating a subalignment again.  To
see if I understand Richard's solution, you:
Create a subalignment from the original alignment, at the desired location
Iterate through each SymbolList in the alignment, and 
     determine the offset of the SymbolList in the original alignment,
     determine the offset of the SymbolList in the subalignment,
     create a new SymbolList using these offsets.

My main problem with doing this is that you create an Alignment to get the
SymbolLists that represent the slice, which I then would use to...create an
Alignment.  Since all I really want is an Alignment view of a particular
location slice of an Alignment, I really think your original idea of
changing the behavior of
AbstractULAlignment.SubULAlignment.symbolListForLabel() would be much more
intuitive (at least to a new user like myself), and be at least one object
lighter, and possibly faster to boot (can't say for sure since I'm not
familiar with how AbstractULAlignment uses SubULAlignments.) 
Thanks,
Ed

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