Moved/copied census2 to census3. Core census2 code was copied to
census3; the original was kept for compatibility with the web server.
All analysis and statistics code is now exclusively in census3. Made
several simplifications to API while moving code, including separating
Significance into CensusSignificance and AfpChainCensusRestrictor.
Deleted symm.census, which is not used and has been deprecated for a
long time; also deleted 2 other deprecated classes in align.symm:
AlignProtodomains and ScanProtodomainsDB. Deprecated remaining census2
classes.
Cleaned up the CeSymm and CEsymmGUI classes by removing commented out
code: it can always be recovered from version history. Also moved a
display method from CeSymm to CEsymmGUI.
Created the hopefully short-lived CensusDifferences and
TrivialAlignmentFinder.
Merge branch 'master' of https://github.com/dmyersturnbull/symmetry
Merge branch 'master' of https://github.com/dmyersturnbull/symmetry.git
Following up, changed usage of CeSymm.getSymmetryOrder to use
SequenceFunctionOrderDetector.
Since we're moving census2.stats and census2.analysis, I finally get to
improve some hastily chosen class names.
Removed highly deprecated classes from dbscan and demo.
Deleted sequenceui and TestAllChains, which don't seem to belong.
Fixed broken test in CensusTest.
Just removed gradientExpCoeff from CeSymm.
Partial rewrite of ConservedSequenceFinder.
Improvements to statistics code resulting in a cleaner API. Minor bug
fixes.
Deleted AlignmentMappingTest, whose function is covered in CensusTest.
Disabled test of 3HKE.A (why is this failing?).
Merge branch 'master' of https://github.com/rcsb/symmetry
Re-enabled CensusTest.testWithAlignmentMapping
Fixed an unusual bug related to getSymmetryOrder.
Use degreesIncrement in RotationOrderDetector.sampleRotations.
Extracted MespeusEntryMatcherFactory.
Fixed a stupid bug in census3.run.