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Copied the aglappe-jung branch into trunk.
New feature: now Pdb objects can be restricted to SCOP domains New member field sid in Pdb and ProtStructGraph if Pdb/ProtStructGraph is restricted to SCOP domain
Re-branching for JUNG2 development
Alignment and PairwiseAlignmentConverter now using Interval, IntervalSet and TreeSet<Integer> to replace Edge, EdgeSet and NodeSet New class IntervalSet
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