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Author: hstehr
Date: Wed Mar 31 12:29:26 2010 UTC (12 years, 1 month ago)
Log Message:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core

Changed paths

Show only first 100 changes...
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Directorytrunk/src/addSeq2Mcma.java modified , text changed
Directorytrunk/src/alignSeq.java modified , text changed
Directorytrunk/src/analyseHistone.java modified , text changed
Directorytrunk/src/averageGraph.java modified , text changed
Directorytrunk/src/benchmarkGraphAlgorithm.java modified , text changed
Directorytrunk/src/calcVolsAndSurfs.java modified , text changed
Directorytrunk/src/calculateGridDensity.java modified , text changed
Directorytrunk/src/casp/benchmarking/Benchmarking.java modified , text changed
Directorytrunk/src/casp/pipeline/RunAll.java modified , text changed
Directorytrunk/src/casp/pipeline/TargetToTemplatesAlignment.java modified , text changed
Directorytrunk/src/casp/pipeline/TemplateSelection.java modified , text changed
Directorytrunk/src/casp/pipeline/TemplatesAlignment.java modified , text changed
Directorytrunk/src/casp/tools/DisplaySecStructMatching.java modified , text changed
Directorytrunk/src/casp/tools/MapStru2Seq.java modified , text changed
Directorytrunk/src/checkChirality.java modified , text changed
Directorytrunk/src/compareAlignments.java modified , text changed
Directorytrunk/src/compareCMs.java modified , text changed
Directorytrunk/src/computeEnergies.java modified , text changed
Directorytrunk/src/connections/ deleted
Directorytrunk/src/deltaRank/DeltaRank.java modified , text changed
Directorytrunk/src/dumppdb.java modified , text changed
Directorytrunk/src/dumpseq.java modified , text changed
Directorytrunk/src/embed/BoundsSmoother.java modified , text changed
Directorytrunk/src/embed/Distiller.java modified , text changed
Directorytrunk/src/embed/Embedder.java modified , text changed
Directorytrunk/src/embed/Reconstructer.java modified , text changed
Directorytrunk/src/embed/Scorer.java modified , text changed
Directorytrunk/src/embed/SetScore.java modified , text changed
Directorytrunk/src/embed/contactmaps/CMDMErrorEvaluator.java modified , text changed
Directorytrunk/src/embed/contactmaps/CMGrabber.java modified , text changed
Directorytrunk/src/embed/contactmaps/CompareIndis.java modified , text changed
Directorytrunk/src/embed/contactmaps/ContactMap.java modified , text changed
Directorytrunk/src/embed/contactmaps/ContactMapEvolver.java modified , text changed
Directorytrunk/src/embed/contactmaps/ContactMapWeighted.java modified , text changed
Directorytrunk/src/embed/contactmaps/ContactMatrix.java modified , text changed
Directorytrunk/src/embed/contactmaps/ConvertErrorsToTextFile.java modified , text changed
Directorytrunk/src/embed/contactmaps/CorrelationFunction.java modified , text changed
Directorytrunk/src/embed/contactmaps/Demes.java modified , text changed
Directorytrunk/src/embed/contactmaps/DistMatrix.java modified , text changed
Directorytrunk/src/embed/contactmaps/Individuals.java modified , text changed
Directorytrunk/src/embed/contactmaps/MergeOutPut.java modified , text changed
Directorytrunk/src/embed/contactmaps/Metric2.java modified , text changed
Directorytrunk/src/embed/contactmaps/NbhStringRanker.java modified , text changed
Directorytrunk/src/embed/contactmaps/NeighbourhoodString.java modified , text changed
Directorytrunk/src/embed/contactmaps/Population1.java modified , text changed
Directorytrunk/src/embed/contactmaps/Species.java modified , text changed
Directorytrunk/src/embed/contactmaps/Stripper.java modified , text changed
Directorytrunk/src/features/ deleted
Directorytrunk/src/genDbGraph.java modified , text changed
Directorytrunk/src/genGraph.java modified , text changed
Directorytrunk/src/graphAveraging/ConsensusInterval.java modified , text changed
Directorytrunk/src/graphAveraging/GraphAverager.java modified , text changed
Directorytrunk/src/graphAveraging/PhiPsiAverager.java modified , text changed
Directorytrunk/src/litNet/LiteratureGraph.java modified , text changed
Directorytrunk/src/mapMutations.java modified , text changed
Directorytrunk/src/mirrorIt.java modified , text changed
Directorytrunk/src/owl/core/connections/
(Copied from trunk/src/connections, r1002)
added
Directorytrunk/src/owl/core/connections/ConsurfConnection.java modified , text changed
Directorytrunk/src/owl/core/connections/PDomainsConnection.java modified , text changed
Directorytrunk/src/owl/core/connections/PhosphoSitePlusConnection.java modified , text changed
Directorytrunk/src/owl/core/connections/package-info.java modified , text changed
Directorytrunk/src/owl/core/features/
(Copied from trunk/src/features, r1002)
added
Directorytrunk/src/owl/core/features/CsaFeature.java modified , text changed
Directorytrunk/src/owl/core/features/Feature.java modified , text changed
Directorytrunk/src/owl/core/features/FeatureType.java modified , text changed
Directorytrunk/src/owl/core/features/GeneralFeature.java modified , text changed
Directorytrunk/src/owl/core/features/HasFeatures.java modified , text changed
Directorytrunk/src/owl/core/features/InvalidFeatureCoordinatesException.java modified , text changed
Directorytrunk/src/owl/core/features/OverlappingFeatureException.java modified , text changed
Directorytrunk/src/owl/core/features/PhosphoSitePlusFeature.java modified , text changed
Directorytrunk/src/owl/core/features/PrositeFeature.java modified , text changed
Directorytrunk/src/owl/core/features/ProteinModificationType.java modified , text changed
Directorytrunk/src/owl/core/features/StructuralDomainFeature.java modified , text changed
Directorytrunk/src/owl/core/features/StructuralDomainType.java modified , text changed
Directorytrunk/src/owl/core/features/UniprotFeature.java modified , text changed
Directorytrunk/src/owl/core/runners/
(Copied from trunk/src/runners, r1002)
added
Directorytrunk/src/owl/core/runners/DsspRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/NaccessRunner.java modified , text changed
Directorytrunk/src/owl/core/sequence/
(Copied from trunk/src/sequence, r1002)
added
Directorytrunk/src/owl/core/sequence/BlastError.java modified , text changed
Directorytrunk/src/owl/core/sequence/BlastHit.java modified , text changed
Directorytrunk/src/owl/core/sequence/BlastHitList.java modified , text changed
Directorytrunk/src/owl/core/sequence/BlastRunner.java modified , text changed
Directorytrunk/src/owl/core/sequence/BlastTabularParser.java modified , text changed
Directorytrunk/src/owl/core/sequence/BlastUtils.java modified , text changed
Directorytrunk/src/owl/core/sequence/BlastXMLParser.java modified , text changed
Directorytrunk/src/owl/core/sequence/GTGHit.java modified , text changed
Directorytrunk/src/owl/core/sequence/GTGHitList.java modified , text changed
Directorytrunk/src/owl/core/sequence/GTGParser.java modified , text changed
Directorytrunk/src/owl/core/sequence/PsipredError.java modified , text changed
Directorytrunk/src/owl/core/sequence/PsipredRunner.java modified , text changed
Directorytrunk/src/owl/core/sequence/Sequence.java modified , text changed
Directorytrunk/src/owl/core/sequence/TcoffeeError.java modified , text changed
Directorytrunk/src/owl/core/sequence/TcoffeeRunner.java modified , text changed
Directorytrunk/src/owl/core/structure/ added
Directorytrunk/src/owl/core/structure/AAinfo.java
(Copied from trunk/src/proteinstructure/AAinfo.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/AIGEdge.java
(Copied from trunk/src/proteinstructure/AIGEdge.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/AIGNode.java
(Copied from trunk/src/proteinstructure/AIGNode.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/AIGraph.java
(Copied from trunk/src/proteinstructure/AIGraph.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/Alignment.java
(Copied from trunk/src/proteinstructure/Alignment.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/AlignmentConstructionError.java
(Copied from trunk/src/proteinstructure/AlignmentConstructionError.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/AlignmentEvaluator.java
(Copied from trunk/src/proteinstructure/AlignmentEvaluator.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/AminoAcid.java
(Copied from trunk/src/proteinstructure/AminoAcid.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/Atom.java
(Copied from trunk/src/proteinstructure/Atom.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/AtomType.java
(Copied from trunk/src/proteinstructure/AtomType.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/BackboneCoords.java
(Copied from trunk/src/proteinstructure/BackboneCoords.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/Box.java
(Copied from trunk/src/proteinstructure/Box.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/CaspRRFileData.java
(Copied from trunk/src/proteinstructure/CaspRRFileData.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/CaspRRFileRIGraph.java
(Copied from trunk/src/proteinstructure/CaspRRFileRIGraph.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/CatalSiteSet.java
(Copied from trunk/src/proteinstructure/CatalSiteSet.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/CatalyticSite.java
(Copied from trunk/src/proteinstructure/CatalyticSite.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/CiffilePdb.java
(Copied from trunk/src/proteinstructure/CiffilePdb.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/ConformationsNotSameSizeError.java
(Copied from trunk/src/proteinstructure/ConformationsNotSameSizeError.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/ContactType.java
(Copied from trunk/src/proteinstructure/ContactType.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/DaliRunner.java
(Copied from trunk/src/proteinstructure/DaliRunner.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/DbRIGraph.java
(Copied from trunk/src/proteinstructure/DbRIGraph.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/EC.java
(Copied from trunk/src/proteinstructure/EC.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/ECRegion.java
(Copied from trunk/src/proteinstructure/ECRegion.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/FileFormatError.java
(Copied from trunk/src/proteinstructure/FileFormatError.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/FileRIGraph.java
(Copied from trunk/src/proteinstructure/FileRIGraph.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/FileTypeGuesser.java
(Copied from trunk/src/proteinstructure/FileTypeGuesser.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/GeometryTools.java
(Copied from trunk/src/proteinstructure/GeometryTools.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/GraphIODb.java
(Copied from trunk/src/proteinstructure/GraphIODb.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/GraphIOGDLFile.java
(Copied from trunk/src/proteinstructure/GraphIOGDLFile.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/GraphIdNotFoundError.java
(Copied from trunk/src/proteinstructure/GraphIdNotFoundError.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/HashGrid.java
(Copied from trunk/src/proteinstructure/HashGrid.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/MaxClusterRunner.java
(Copied from trunk/src/proteinstructure/MaxClusterRunner.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/NbhProbDistribution.java
(Copied from trunk/src/proteinstructure/NbhProbDistribution.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/NbhoodBackgrnd.java
(Copied from trunk/src/proteinstructure/NbhoodBackgrnd.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/OligomericState.java
(Copied from trunk/src/proteinstructure/OligomericState.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PairwiseAlignmentConverter.java
(Copied from trunk/src/proteinstructure/PairwiseAlignmentConverter.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PairwiseSequenceAlignment.java
(Copied from trunk/src/proteinstructure/PairwiseSequenceAlignment.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PaulStructAligner.java
(Copied from trunk/src/proteinstructure/PaulStructAligner.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/Pdb.java
(Copied from trunk/src/proteinstructure/Pdb.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PdbChainCodeNotFoundError.java
(Copied from trunk/src/proteinstructure/PdbChainCodeNotFoundError.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PdbCodeNotFoundError.java
(Copied from trunk/src/proteinstructure/PdbCodeNotFoundError.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PdbLoadError.java
(Copied from trunk/src/proteinstructure/PdbLoadError.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PdbSet.java
(Copied from trunk/src/proteinstructure/PdbSet.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PdbaseInconsistencyError.java
(Copied from trunk/src/proteinstructure/PdbaseInconsistencyError.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PdbasePdb.java
(Copied from trunk/src/proteinstructure/PdbasePdb.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PdbfilePdb.java
(Copied from trunk/src/proteinstructure/PdbfilePdb.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PolResidue.java
(Copied from trunk/src/proteinstructure/PolResidue.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/Polymer.java
(Copied from trunk/src/proteinstructure/Polymer.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PolyposeRunner.java
(Copied from trunk/src/proteinstructure/PolyposeRunner.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PredEval.java
(Copied from trunk/src/proteinstructure/PredEval.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PrositeHit.java
(Copied from trunk/src/proteinstructure/PrositeHit.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/PrositeScanner.java
(Copied from trunk/src/proteinstructure/PrositeScanner.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/ProtStructGraph.java
(Copied from trunk/src/proteinstructure/ProtStructGraph.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/RIGCommonNbhood.java
(Copied from trunk/src/proteinstructure/RIGCommonNbhood.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/RIGEdge.java
(Copied from trunk/src/proteinstructure/RIGEdge.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/RIGEnsemble.java
(Copied from trunk/src/proteinstructure/RIGEnsemble.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/RIGNbhood.java
(Copied from trunk/src/proteinstructure/RIGNbhood.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/RIGNode.java
(Copied from trunk/src/proteinstructure/RIGNode.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/RIGraph.java
(Copied from trunk/src/proteinstructure/RIGraph.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/RIGraphMinSpanningTree.java
(Copied from trunk/src/proteinstructure/RIGraphMinSpanningTree.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/Residue.java
(Copied from trunk/src/proteinstructure/Residue.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/Scop.java
(Copied from trunk/src/proteinstructure/Scop.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/ScopRegion.java
(Copied from trunk/src/proteinstructure/ScopRegion.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/SecStrucElement.java
(Copied from trunk/src/proteinstructure/SecStrucElement.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/SecondaryStructure.java
(Copied from trunk/src/proteinstructure/SecondaryStructure.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/StructAligner.java
(Copied from trunk/src/proteinstructure/StructAligner.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/StructAlignmentError.java
(Copied from trunk/src/proteinstructure/StructAlignmentError.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/Template.java
(Copied from trunk/src/proteinstructure/Template.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/TemplateList.java
(Copied from trunk/src/proteinstructure/TemplateList.java, r1002)
added , text changed
Directorytrunk/src/owl/core/structure/aapairsBounds.dat
(Copied from trunk/src/proteinstructure/aapairsBounds.dat, r1002)
added
Directorytrunk/src/owl/core/structure/contactTypes.dat
(Copied from trunk/src/proteinstructure/contactTypes.dat, r1002)
added
Directorytrunk/src/owl/core/structure/decoyScoring/
(Copied from trunk/src/proteinstructure/decoyScoring, r1002)
added
Directorytrunk/src/owl/core/structure/decoyScoring/AtomCombinedScorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/AtomCountScorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/AtomTripletScorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/AtomTypeScorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/CountScorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/DecoyScore.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/DecoyScoreSet.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/DecoyScoreSetsGroup.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/DistanceScorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/GenerateSummaries.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/ResCombinedScorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/ResCountScorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/ResTripletScorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/ResTypeScorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/Scorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/ScoringMethod.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/TripletScorer.java modified , text changed
Directorytrunk/src/owl/core/structure/decoyScoring/TypeScorer.java modified , text changed
Directorytrunk/src/owl/core/util/
(Copied from trunk/src/tools, r1002)
added
Directorytrunk/src/owl/core/util/ClusterConnection.java modified , text changed
Directorytrunk/src/owl/core/util/ColoredStrings.java modified , text changed
Directorytrunk/src/owl/core/util/DataDistributer.java modified , text changed
Directorytrunk/src/owl/core/util/DataDistribution.java modified , text changed
Directorytrunk/src/owl/core/util/Goodies.java modified , text changed
Directorytrunk/src/owl/core/util/Graph2Pml.java modified , text changed
Directorytrunk/src/owl/core/util/IntPairComparator.java modified , text changed
Directorytrunk/src/owl/core/util/IntPairSet.java modified , text changed
Directorytrunk/src/owl/core/util/Interval.java modified , text changed
Directorytrunk/src/owl/core/util/IntervalSet.java modified , text changed
Directorytrunk/src/owl/core/util/Machine.java modified , text changed
Directorytrunk/src/owl/core/util/MultiOutputStream.java modified , text changed
Directorytrunk/src/owl/core/util/MySQLConnection.java modified , text changed
Directorytrunk/src/owl/core/util/MySQLConnectionCheck.java modified , text changed
Directorytrunk/src/owl/core/util/Pair.java modified , text changed
Directorytrunk/src/owl/core/util/PyMol.java modified , text changed
Directorytrunk/src/owl/core/util/PymolServerOutputStream.java modified , text changed
Directorytrunk/src/owl/core/util/QueryThread.java modified , text changed
Directorytrunk/src/owl/core/util/R.java modified , text changed
Directorytrunk/src/owl/core/util/RegexFileFilter.java modified , text changed
Directorytrunk/src/owl/core/util/Statistics.java modified , text changed
Directorytrunk/src/owl/core/util/StreamGobbler.java modified , text changed
Directorytrunk/src/owl/core/util/SystemCmd.java modified , text changed
Directorytrunk/src/owl/core/util/TableSorter.java modified , text changed
Directorytrunk/src/owl/core/util/Triplet.java modified , text changed
Directorytrunk/src/owl/core/util/utils4DB.java modified , text changed
Directorytrunk/src/owl/core/util/utils4lh.java modified , text changed
Directorytrunk/src/pairwiseSeqId.java modified , text changed
Directorytrunk/src/ppi/PPIGraph.java modified , text changed
Directorytrunk/src/proteinstructure/AAinfo.java deleted
Directorytrunk/src/proteinstructure/AIGEdge.java deleted
Directorytrunk/src/proteinstructure/AIGNode.java deleted
Directorytrunk/src/proteinstructure/AIGraph.java deleted
Directorytrunk/src/proteinstructure/Alignment.java deleted
Directorytrunk/src/proteinstructure/AlignmentConstructionError.java deleted
Directorytrunk/src/proteinstructure/AlignmentEvaluator.java deleted
Directorytrunk/src/proteinstructure/AminoAcid.java deleted
Directorytrunk/src/proteinstructure/Atom.java deleted
Directorytrunk/src/proteinstructure/AtomType.java deleted
Directorytrunk/src/proteinstructure/BackboneCoords.java deleted
Directorytrunk/src/proteinstructure/Box.java deleted
Directorytrunk/src/proteinstructure/CaspRRFileData.java deleted
Directorytrunk/src/proteinstructure/CaspRRFileRIGraph.java deleted
Directorytrunk/src/proteinstructure/CatalSiteSet.java deleted
Directorytrunk/src/proteinstructure/CatalyticSite.java deleted
Directorytrunk/src/proteinstructure/CiffilePdb.java deleted
Directorytrunk/src/proteinstructure/ConformationsNotSameSizeError.java deleted
Directorytrunk/src/proteinstructure/ContactType.java deleted
Directorytrunk/src/proteinstructure/DaliRunner.java deleted
Directorytrunk/src/proteinstructure/DbRIGraph.java deleted
Directorytrunk/src/proteinstructure/EC.java deleted
Directorytrunk/src/proteinstructure/ECRegion.java deleted
Directorytrunk/src/proteinstructure/FileFormatError.java deleted
Directorytrunk/src/proteinstructure/FileRIGraph.java deleted
Directorytrunk/src/proteinstructure/FileTypeGuesser.java deleted
Directorytrunk/src/proteinstructure/GeometryTools.java deleted
Directorytrunk/src/proteinstructure/GraphIODb.java deleted
Directorytrunk/src/proteinstructure/GraphIOGDLFile.java deleted
Directorytrunk/src/proteinstructure/GraphIdNotFoundError.java deleted
Directorytrunk/src/proteinstructure/HashGrid.java deleted
Directorytrunk/src/proteinstructure/MaxClusterRunner.java deleted
Directorytrunk/src/proteinstructure/NbhProbDistribution.java deleted
Directorytrunk/src/proteinstructure/NbhoodBackgrnd.java deleted
Directorytrunk/src/proteinstructure/OligomericState.java deleted
Directorytrunk/src/proteinstructure/PairwiseAlignmentConverter.java deleted
Directorytrunk/src/proteinstructure/PairwiseSequenceAlignment.java deleted
Directorytrunk/src/proteinstructure/PaulStructAligner.java deleted
Directorytrunk/src/proteinstructure/Pdb.java deleted
Directorytrunk/src/proteinstructure/PdbChainCodeNotFoundError.java deleted
Directorytrunk/src/proteinstructure/PdbCodeNotFoundError.java deleted
Directorytrunk/src/proteinstructure/PdbLoadError.java deleted
Directorytrunk/src/proteinstructure/PdbSet.java deleted
Directorytrunk/src/proteinstructure/PdbaseInconsistencyError.java deleted
Directorytrunk/src/proteinstructure/PdbasePdb.java deleted
Directorytrunk/src/proteinstructure/PdbfilePdb.java deleted
Directorytrunk/src/proteinstructure/PolResidue.java deleted
Directorytrunk/src/proteinstructure/Polymer.java deleted
Directorytrunk/src/proteinstructure/PolyposeRunner.java deleted
Directorytrunk/src/proteinstructure/PredEval.java deleted
Directorytrunk/src/proteinstructure/PrositeHit.java deleted
Directorytrunk/src/proteinstructure/PrositeScanner.java deleted
Directorytrunk/src/proteinstructure/ProtStructGraph.java deleted
Directorytrunk/src/proteinstructure/RIGCommonNbhood.java deleted
Directorytrunk/src/proteinstructure/RIGEdge.java deleted
Directorytrunk/src/proteinstructure/RIGEnsemble.java deleted
Directorytrunk/src/proteinstructure/RIGNbhood.java deleted
Directorytrunk/src/proteinstructure/RIGNode.java deleted
Directorytrunk/src/proteinstructure/RIGraph.java deleted
Directorytrunk/src/proteinstructure/RIGraphMinSpanningTree.java deleted
Directorytrunk/src/proteinstructure/Residue.java deleted
Directorytrunk/src/proteinstructure/Scop.java deleted
Directorytrunk/src/proteinstructure/ScopRegion.java deleted
Directorytrunk/src/proteinstructure/SecStrucElement.java deleted
Directorytrunk/src/proteinstructure/SecondaryStructure.java deleted
Directorytrunk/src/proteinstructure/StructAligner.java deleted
Directorytrunk/src/proteinstructure/StructAlignmentError.java deleted
Directorytrunk/src/proteinstructure/Template.java deleted
Directorytrunk/src/proteinstructure/TemplateList.java deleted
Directorytrunk/src/proteinstructure/aapairsBounds.dat deleted
Directorytrunk/src/proteinstructure/contactTypes.dat deleted
Directorytrunk/src/proteinstructure/decoyScoring/ deleted
Directorytrunk/src/reconstruct.java modified , text changed
Directorytrunk/src/runners/ deleted
Directorytrunk/src/sadp/ContactMap.java modified , text changed
Directorytrunk/src/sadp/SADP.java modified , text changed
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