Added -start and -stop options to census2.CLI.
Improved logging in census2 and made LogManagers class-level.
Made Results.fromXML(File[]) remove results for redundant SCOP Ids, and
made it set the mean time taken. Added -reverse and -names options to
census2.CLI.
Made ScopSupport.getAllDomainsUnder attempt to read results in
resources/scop_domains, greatly enhancing performance.
Wrote census2.utils.CensusChecker, which looks for extra and missing
SCOP Ids.
Made AlignmentMapping replace ">" with "-" from
to/fromConciseAlignmentString in the XML. Prevents escaping,
significantly reducing file size.
Wrote symm.census3, which will probably exist alongside census2 for some
time.
Fixed a couple tests so the project will build.
Small changes to Census2Adaptor.
Set setFetchFileEvenIfObsolete to true in census2.
Moved census3 utilities to a new package census3.utils. Starting to
mirror census2.
adding a fake test to prevent this from failing under cruisecontrol
Merge branch 'master' of https://github.com/rcsb/symmetry
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.