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.
updating to latest biojava - snapshot
Merge branch 'master' of github.com:rcsb/symmetry
Added CompareBioassemblies to compare bioassemblies create on the fly
vs. those provided by the PDB. Misc. improvements in the symmetry code
to avoid excessive number of local symmetry calculations.
updating to lastet biojava
Merge branch 'master' of https://github.com/rcsb/symmetry
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.
Downgraded vecmath methods to old version. Misc. code changes and
additions to check creation of bioassemblies on the fly.
Merge branch 'master' of https://github.com/pwrose/symmetry into pwrose-master
fixing broken imports