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Copied the aglappe-jung branch into trunk.
Re-branching for JUNG2 development
Not creating anymore the score table
Cleaned up. More command line parameters
Now throwing all exceptions
Fixed bug: was outputing an empty column before the 'total' column
Now much faster thanks to hashing on pairs (separate script create the hash tables)
Faster version that writes to stdoutput, minor changes
Faster version that writes to stdoutput
Lame version that directly updates a table ... have to change to stdoutput
1st version scoring with pdb_reps_graph_4_2 and full nbhood string
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