Began to separate order-detection.
Include order 1 in ModeDecider (minor fix for most usage).
Include standard deviation.
Created AlignmentMapping, which is now a very optional component of a
Result.
Simplified some blocks of code, fixed variable names, and switched to a
simpler ConsensusDecider.
Print levels 1 and 2, not 0 and 1.
Removed debugging print statements.
Merge branch 'master' of https://github.com/rcsb/symmetry
Added a method CensusJob.runJob. Gave Census a storeAfpChain field.
Updated centroid ligand-finding tests. Made LigandFinder able to work
with structures other than domains.
Second iteration of AlignmentMapping, which doesn't use AFPChains.
Separated storeAfpChain and recordAlignmentMapping in CensusJob and
Census. Also uncommented CensusJob.getFractionHelical.
update
adding Peter's pull request plus some minor fixes