Fixing SymmRefiner

Tests were not functional. Fixing them revealed an additional
bug in SymmRefiner's handling of small loops, which is now fixed.
Refactoring replaceOptAln into Biojava

Now at AlignmentTools.replaceOptAln
Merge pull request #20 from sbliven/master

Merge latest SymmRefiner changes
As Spencer pointed out, using -DPDB_DIR is better than requiring an
explicit PDB dir everywhere. Also made Census and its subclasses print
usage messages.
Moving the census2.representatives package from protodomain-search to
symmetry. Also made significant improvements to
SuperfamilyRepresentatives: it now handles Sun Ids corresponding to
domains, species, and families.
Deprecated original symm.census.
Use ScopFactory methods instead.
Commented out extremely time-consuming tests.
Wrote ScopSupport. All the *ScopDescriptionCensus classes can now take
either Sun Ids or SCOP classification Ids. Deprecated
ScopDescriptionCensus.getDomainsUnder.
Updated TM-score cutoffs to 0.43 and 0.38.
Oops. Fixing compilation failure; forgot to commit.
Fixed mistake in main method: 2 arguments, not 3.
Added hooks for doing refinement (and made NamesCensus allow this).
Use ScopFactory.setScop(String). This is critical since the default
version of BerkeleyScopInstallation changed to 1.75B.
Temporarily commented out broken test since the functionality seems to
be working.
Fixed testBasic(), and finally wrote testWithPartialResult().
Download even if obsolete.
Determine significance after refinement.
Close files to prevent resource leaks
Merge pull request #21 from epeisach/master

Ensure that open files are closed to prevent resource leaks