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Author: duarte
Date: Fri Jan 29 11:57:38 2010 UTC (9 years, 7 months ago)
Log Message:
Major refactoring and clean-up.
Most important changes are some methods in Pdb class: get_graph->getRIGraph and dump2pdb->writeToPDBFile
Removed all specific FileFormatError exception classes, now using only the generic FileFormatError.
All tests passed.

Changed paths

Path Details
Directorytrunk/alignSeq.java modified , text changed
Directorytrunk/averageGraph.java modified , text changed
Directorytrunk/benchmarkGraphAlgorithm.java modified , text changed
Directorytrunk/compareCMs.java modified , text changed
Directorytrunk/dumppdb.java modified , text changed
Directorytrunk/embed/Distiller.java modified , text changed
Directorytrunk/embed/Embedder.java modified , text changed
Directorytrunk/embed/Reconstructer.java modified , text changed
Directorytrunk/embed/Scorer.java modified , text changed
Directorytrunk/embed/contactmaps/CMGrabber.java modified , text changed
Directorytrunk/embed/contactmaps/CompareIndis.java modified , text changed
Directorytrunk/embed/contactmaps/CorrelationFunction.java modified , text changed
Directorytrunk/embed/contactmaps/Demes.java modified , text changed
Directorytrunk/embed/contactmaps/Individuals.java modified , text changed
Directorytrunk/embed/contactmaps/Stripper.java modified , text changed
Directorytrunk/genDbGraph.java modified , text changed
Directorytrunk/genGraph.java modified , text changed
Directorytrunk/mapMutations.java modified , text changed
Directorytrunk/mirrorIt.java modified , text changed
Directorytrunk/proteinstructure/Alignment.java modified , text changed
Directorytrunk/proteinstructure/CaspRRFileRIGraph.java modified , text changed
Directorytrunk/proteinstructure/CiffileFormatError.java deleted
Directorytrunk/proteinstructure/CiffilePdb.java modified , text changed
Directorytrunk/proteinstructure/DaliRunner.java modified , text changed
Directorytrunk/proteinstructure/DecoyScoring/ deleted
Directorytrunk/proteinstructure/FastaFileFormatError.java deleted
Directorytrunk/proteinstructure/FileFormatError.java modified , text changed
Directorytrunk/proteinstructure/FileRIGraph.java modified , text changed
Directorytrunk/proteinstructure/GraphFileFormatError.java deleted
Directorytrunk/proteinstructure/GraphIOGDLFile.java modified , text changed
Directorytrunk/proteinstructure/PaulStructAligner.java modified , text changed
Directorytrunk/proteinstructure/Pdb.java modified , text changed
Directorytrunk/proteinstructure/PdbfileFormatError.java deleted
Directorytrunk/proteinstructure/PdbfilePdb.java modified , text changed
Directorytrunk/proteinstructure/PirFileFormatError.java deleted
Directorytrunk/proteinstructure/PolyposeRunner.java modified , text changed
Directorytrunk/proteinstructure/RIGEnsemble.java modified , text changed
Directorytrunk/proteinstructure/RIGraphMinSpanningTree.java modified , text changed
Directorytrunk/proteinstructure/Template.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/
(Copied from trunk/proteinstructure/DecoyScoring, r948)
added
Directorytrunk/proteinstructure/decoyScoring/AtomCombinedScorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/AtomCountScorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/AtomTripletScorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/AtomTypeScorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/CountScorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/DecoyScore.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/DecoyScoreSet.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/DecoyScoreSetsGroup.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/DistanceScorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/GenerateSummaries.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/ResCombinedScorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/ResCountScorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/ResTripletScorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/ResTypeScorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/Scorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/ScoringMethod.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/TripletScorer.java modified , text changed
Directorytrunk/proteinstructure/decoyScoring/TypeScorer.java modified , text changed
Directorytrunk/reconstruct.java modified , text changed
Directorytrunk/scoreDecoys.java modified , text changed
Directorytrunk/sequence/BlastUtils.java modified , text changed
Directorytrunk/sequence/Sequence.java modified , text changed
Directorytrunk/superimposeMult.java modified , text changed
Directorytrunk/testJUNGframework.java modified , text changed
Directorytrunk/testPdb.java modified , text changed
Directorytrunk/tests/proteinstructure/PdbParsersTest.java modified , text changed
Directorytrunk/tests/proteinstructure/PdbTest.java modified , text changed
Directorytrunk/tests/tinker/TinkerRunnerTest.java modified , text changed
Directorytrunk/tests/tools/ColoredStringsTest.java modified , text changed
Directorytrunk/tests/tools/MultiOutputStreamTest.java modified , text changed
Directorytrunk/tests/tools/PymolServerOutputStreamTest.java modified , text changed
Directorytrunk/tinker/TinkerRunner.java modified , text changed
Directorytrunk/writePerAtomDistancesToBFactor.java modified , text changed
Directorytrunk/writeSASAtoBFactor.java modified , text changed