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Author: jmduarteg
Date: Thu Mar 3 13:21:18 2011 UTC (8 years, 9 months ago)
Log Message:
Renamed xxxxError classes to xxxxException as they should be.

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Directorytrunk/src/addSeq2Mcma.java modified , text changed
Directorytrunk/src/alignSeq.java modified , text changed
Directorytrunk/src/benchmarkGraphAlgorithm.java modified , text changed
Directorytrunk/src/calculateGridDensity.java modified , text changed
Directorytrunk/src/compareAlignments.java modified , text changed
Directorytrunk/src/dumppdb.java modified , text changed
Directorytrunk/src/dumpseq.java modified , text changed
Directorytrunk/src/examples/ContactMapHelloWorld.java modified , text changed
Directorytrunk/src/examples/ContactMapOverDir.java modified , text changed
Directorytrunk/src/examples/HelloAGLappe.java modified , text changed
Directorytrunk/src/genDbGraph.java modified , text changed
Directorytrunk/src/genGraph.java modified , text changed
Directorytrunk/src/mapMutations.java modified , text changed
Directorytrunk/src/owl/casp/benchmarking/Benchmarking.java modified , text changed
Directorytrunk/src/owl/casp/benchmarking/scoreAllModelsWithRanks.java modified , text changed
Directorytrunk/src/owl/casp/pipeline/RunAll.java modified , text changed
Directorytrunk/src/owl/casp/pipeline/TargetToTemplatesAlignment.java modified , text changed
Directorytrunk/src/owl/casp/pipeline/TemplateSelection.java modified , text changed
Directorytrunk/src/owl/casp/pipeline/TemplatesAlignment.java modified , text changed
Directorytrunk/src/owl/casp/tools/MapStru2Seq.java modified , text changed
Directorytrunk/src/owl/core/connections/EmblWSDBfetchConnection.java modified , text changed
Directorytrunk/src/owl/core/connections/GTGHit.java modified , text changed
Directorytrunk/src/owl/core/connections/GTGHitList.java modified , text changed
Directorytrunk/src/owl/core/connections/GTGParser.java modified , text changed
Directorytrunk/src/owl/core/runners/DaliRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/PolyposeRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/SelectonRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/TcoffeeRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/blast/BlastTabularParser.java modified , text changed
Directorytrunk/src/owl/core/runners/blast/BlastUtils.java modified , text changed
Directorytrunk/src/owl/core/runners/tinker/ConstraintsMaker.java modified , text changed
Directorytrunk/src/owl/core/runners/tinker/TinkerRunner.java modified , text changed
Directorytrunk/src/owl/core/sequence/Sequence.java modified , text changed
Directorytrunk/src/owl/core/sequence/UniprotHomologList.java modified , text changed
Directorytrunk/src/owl/core/sequence/alignment/MultipleSequenceAlignment.java modified , text changed
Directorytrunk/src/owl/core/structure/CiffilePdb.java modified , text changed
Directorytrunk/src/owl/core/structure/Pdb.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbAsymUnit.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbLoadError.java deleted
Directorytrunk/src/owl/core/structure/PdbLoadException.java
(Copied from trunk/src/owl/core/structure/PdbLoadError.java, r1322)
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Directorytrunk/src/owl/core/structure/PdbSet.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbasePdb.java modified , text changed
Directorytrunk/src/owl/core/structure/PdbfilePdb.java modified , text changed
Directorytrunk/src/owl/core/structure/Template.java modified , text changed
Directorytrunk/src/owl/core/structure/TemplateList.java modified , text changed
Directorytrunk/src/owl/core/structure/alignment/PaulStructAligner.java modified , text changed
Directorytrunk/src/owl/core/structure/alignment/StructureAlignmentEvaluator.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/CaspRRFileRIGraph.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/FileRIGraph.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/GraphIOGDLFile.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/RIGEnsemble.java modified , text changed
Directorytrunk/src/owl/core/structure/graphs/RIGMatrix.java modified , text changed
Directorytrunk/src/owl/core/util/FileFormatError.java deleted
Directorytrunk/src/owl/core/util/FileFormatException.java
(Copied from trunk/src/owl/core/util/FileFormatError.java, r1322)
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Directorytrunk/src/owl/decoyScoring/AtomCombinedScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/AtomCountScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/AtomTripletScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/AtomTypeScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/CountScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/DecoyScoreSet.java modified , text changed
Directorytrunk/src/owl/decoyScoring/DecoyScoreSetsGroup.java modified , text changed
Directorytrunk/src/owl/decoyScoring/DistanceScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/GenerateSummaries.java modified , text changed
Directorytrunk/src/owl/decoyScoring/ResCombinedScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/ResCountScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/ResTripletScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/ResTypeScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/Scorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/TripletScorer.java modified , text changed
Directorytrunk/src/owl/decoyScoring/TypeScorer.java modified , text changed
Directorytrunk/src/owl/embed/ConePeeler.java modified , text changed
Directorytrunk/src/owl/embed/Distiller.java modified , text changed
Directorytrunk/src/owl/embed/Scorer.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/CMDMErrorEvaluator.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/CMGrabber.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/CompareIndis.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/ContactMap.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/ContactMapEvolver.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/ContactMapWeighted.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/ContactMatrix.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/Demes.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/DistMatrix.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/Individuals.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/Metric2.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/NbhStringRanker.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/NeighbourhoodString.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/Species.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/Stripper.java modified , text changed
Directorytrunk/src/owl/gmbp/CMPdb_sphoxel_greedy.java modified , text changed
Directorytrunk/src/owl/gmbp/Gmbp_Geom.java modified , text changed
Directorytrunk/src/owl/tests/core/connections/SiftsConnectionTest.java modified , text changed
Directorytrunk/src/owl/tests/core/runners/tinker/TinkerRunnerTest.java modified , text changed
Directorytrunk/src/owl/tests/core/structure/PdbAsymUnitTest.java modified , text changed
Directorytrunk/src/owl/tests/core/structure/PdbParsersTest.java modified , text changed
Directorytrunk/src/owl/tests/core/structure/PdbTest.java modified , text changed
Directorytrunk/src/reconstruct.java modified , text changed
Directorytrunk/src/scoreDecoys.java modified , text changed
Directorytrunk/src/scoreGeomOfPdbs.java modified , text changed
Directorytrunk/src/scorePdbSet.java modified , text changed
Directorytrunk/src/superimposeMult.java modified , text changed