[Biojava-l] Performance hit in OrderNSymbolList

[Matthew Pocock]

Dear all,

OrderNSymbolList was causing lots of objects to be allocated every time
you retrieved a symbol from it. This was bad for hotspot and killed the
alpha vm. I have refactored the symbolAt() method to avoid this and we
now have a dramatic improvement:

hotspot 1.3.0  110 -> 60 sec
alpha vm  still running after 1 1/2 days and gave up -> 20 sec

The new Symbol objects are now total API stable, and seem to work as
advertised. I have hammered them fairly hard. Still, if they do silly
things for you, then tell us.

Matthew