[Biojava-dev] LocationTools optimizations

[Thomas Down]

I've added various optimizations to the binary operators in
LocationTools (intersection, contains, overlaps).  These now
use binary searches and pruning strategies, rather than linear
searches, giving much better performance for complex
Locations.  I've been using this code heavily for the last few
days using locations with thousands of spans (in one case,
about 500,000).

There are some extra test methods in CompoundLocationTest
which exercise this code.

I've also written some new code for intersecting
CircularLocations -- the intersection of two circular
locations was previously returning a non-circular location
(!).

Let me know if this causes any trouble,

      Thomas.