Merge branch 'master', remote-tracking branch 'pwrose/master'
increasing version nr.
Merge pull request #18 from pwrose/master

Added parameter to limit number of combinations in local symmetry calculations.
Merge branch 'master' of https://github.com/pwrose/symmetry
Adding back old AxisTransformation constructor
upgrading version nr.
Merge branch 'master' of github.com:rcsb/symmetry
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).