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Author: hstehr
Date: Wed Mar 31 15:50:04 2010 UTC (10 years ago)
Log Message:
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features

Changed paths

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Directorytrunk/src/addSeq2Mcma.java modified , text changed
Directorytrunk/src/alignSeq.java modified , text changed
Directorytrunk/src/averageGraph.java modified , text changed
Directorytrunk/src/benchmarkGraphAlgorithm.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/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/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/DisplaySecStructMatching.java modified , text changed
Directorytrunk/src/owl/casp/tools/MapStru2Seq.java modified , text changed
Directorytrunk/src/owl/core/connections/GTGHit.java
(Copied from trunk/src/owl/core/sequence/GTGHit.java, r1007)
added , text changed
Directorytrunk/src/owl/core/connections/GTGHitList.java
(Copied from trunk/src/owl/core/sequence/GTGHitList.java, r1007)
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Directorytrunk/src/owl/core/connections/GTGParser.java
(Copied from trunk/src/owl/core/sequence/GTGParser.java, r1007)
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Directorytrunk/src/owl/core/connections/PrositeHit.java
(Copied from trunk/src/owl/core/structure/PrositeHit.java, r1007)
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Directorytrunk/src/owl/core/connections/PrositeScanner.java
(Copied from trunk/src/owl/core/structure/PrositeScanner.java, r1007)
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Directorytrunk/src/owl/core/features/CsaFeature.java modified , text changed
Directorytrunk/src/owl/core/features/PrositeFeature.java modified , text changed
Directorytrunk/src/owl/core/runners/DaliRunner.java
(Copied from trunk/src/owl/core/structure/DaliRunner.java, r1007)
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Directorytrunk/src/owl/core/runners/DsspRunner.java modified , text changed
Directorytrunk/src/owl/core/runners/MaxClusterRunner.java
(Copied from trunk/src/owl/core/structure/MaxClusterRunner.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/PolyposeRunner.java
(Copied from trunk/src/owl/core/structure/PolyposeRunner.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/PsipredError.java
(Copied from trunk/src/owl/core/sequence/PsipredError.java, r1007)
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Directorytrunk/src/owl/core/runners/PsipredRunner.java
(Copied from trunk/src/owl/core/sequence/PsipredRunner.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/TcoffeeError.java
(Copied from trunk/src/owl/core/sequence/TcoffeeError.java, r1007)
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Directorytrunk/src/owl/core/runners/TcoffeeRunner.java
(Copied from trunk/src/owl/core/sequence/TcoffeeRunner.java, r1007)
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Directorytrunk/src/owl/core/runners/blast/BlastError.java
(Copied from trunk/src/owl/core/sequence/BlastError.java, r1007)
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Directorytrunk/src/owl/core/runners/blast/BlastHit.java
(Copied from trunk/src/owl/core/sequence/BlastHit.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/blast/BlastHitList.java
(Copied from trunk/src/owl/core/sequence/BlastHitList.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/blast/BlastRunner.java
(Copied from trunk/src/owl/core/sequence/BlastRunner.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/blast/BlastTabularParser.java
(Copied from trunk/src/owl/core/sequence/BlastTabularParser.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/blast/BlastUtils.java
(Copied from trunk/src/owl/core/sequence/BlastUtils.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/blast/BlastXMLParser.java
(Copied from trunk/src/owl/core/sequence/BlastXMLParser.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/gromacs/GromacsError.java
(Copied from trunk/src/owl/core/runners/tinker/GromacsError.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/gromacs/GromacsMDP.java
(Copied from trunk/src/owl/core/runners/tinker/GromacsMDP.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/gromacs/GromacsRunner.java
(Copied from trunk/src/owl/core/runners/tinker/GromacsRunner.java, r1007)
added , text changed
Directorytrunk/src/owl/core/runners/tinker/ConstraintsMaker.java modified , text changed
Directorytrunk/src/owl/core/runners/tinker/GromacsError.java deleted
Directorytrunk/src/owl/core/runners/tinker/GromacsMDP.java deleted
Directorytrunk/src/owl/core/runners/tinker/GromacsRunner.java deleted
Directorytrunk/src/owl/core/runners/tinker/TinkerRunner.java modified , text changed
Directorytrunk/src/owl/core/sequence/BlastError.java deleted
Directorytrunk/src/owl/core/sequence/BlastHit.java deleted
Directorytrunk/src/owl/core/sequence/BlastHitList.java deleted
Directorytrunk/src/owl/core/sequence/BlastRunner.java deleted
Directorytrunk/src/owl/core/sequence/BlastTabularParser.java deleted
Directorytrunk/src/owl/core/sequence/BlastUtils.java deleted
Directorytrunk/src/owl/core/sequence/BlastXMLParser.java deleted
Directorytrunk/src/owl/core/sequence/GTGHit.java deleted
Directorytrunk/src/owl/core/sequence/GTGHitList.java deleted
Directorytrunk/src/owl/core/sequence/GTGParser.java deleted
Directorytrunk/src/owl/core/sequence/PsipredError.java deleted
Directorytrunk/src/owl/core/sequence/PsipredRunner.java deleted
Directorytrunk/src/owl/core/sequence/Sequence.java modified , text changed
Directorytrunk/src/owl/core/sequence/TcoffeeError.java deleted
Directorytrunk/src/owl/core/sequence/TcoffeeRunner.java deleted
Directorytrunk/src/owl/core/sequence/alignment/ added
Directorytrunk/src/owl/core/sequence/alignment/AlignmentConstructionError.java
(Copied from trunk/src/owl/core/structure/AlignmentConstructionError.java, r1007)
added , text changed
Directorytrunk/src/owl/core/sequence/alignment/MultipleSequenceAlignment.java
(Copied from trunk/src/owl/core/structure/Alignment.java, r1007)
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Directorytrunk/src/owl/core/sequence/alignment/PairwiseAlignmentConverter.java
(Copied from trunk/src/owl/core/structure/PairwiseAlignmentConverter.java, r1007)
added , text changed
Directorytrunk/src/owl/core/sequence/alignment/PairwiseSequenceAlignment.java
(Copied from trunk/src/owl/core/structure/PairwiseSequenceAlignment.java, r1007)
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Directorytrunk/src/owl/core/structure/AIGEdge.java deleted
Directorytrunk/src/owl/core/structure/AIGNode.java deleted
Directorytrunk/src/owl/core/structure/AIGraph.java deleted
Directorytrunk/src/owl/core/structure/Alignment.java deleted
Directorytrunk/src/owl/core/structure/AlignmentConstructionError.java deleted
Directorytrunk/src/owl/core/structure/AlignmentEvaluator.java deleted
Directorytrunk/src/owl/core/structure/BackboneCoords.java modified , text changed
Directorytrunk/src/owl/core/structure/Box.java deleted
Directorytrunk/src/owl/core/structure/CaspRRFileData.java deleted
Directorytrunk/src/owl/core/structure/CaspRRFileRIGraph.java deleted
Directorytrunk/src/owl/core/structure/CatalSiteSet.java deleted
Directorytrunk/src/owl/core/structure/CatalyticSite.java deleted
Directorytrunk/src/owl/core/structure/CiffilePdb.java modified , text changed
Directorytrunk/src/owl/core/structure/DaliRunner.java deleted
Directorytrunk/src/owl/core/structure/DbRIGraph.java deleted
Directorytrunk/src/owl/core/structure/EC.java deleted
Directorytrunk/src/owl/core/structure/ECRegion.java deleted
Directorytrunk/src/owl/core/structure/FileFormatError.java deleted
Directorytrunk/src/owl/core/structure/FileRIGraph.java deleted
Directorytrunk/src/owl/core/structure/FileTypeGuesser.java deleted
Directorytrunk/src/owl/core/structure/GeometryTools.java deleted
Directorytrunk/src/owl/core/structure/GraphIODb.java deleted
Directorytrunk/src/owl/core/structure/GraphIOGDLFile.java deleted
Directorytrunk/src/owl/core/structure/GraphIdNotFoundError.java deleted
Directorytrunk/src/owl/core/structure/HashGrid.java deleted
Directorytrunk/src/owl/core/structure/MaxClusterRunner.java deleted
Directorytrunk/src/owl/core/structure/NbhProbDistribution.java deleted
Directorytrunk/src/owl/core/structure/NbhoodBackgrnd.java deleted
Directorytrunk/src/owl/core/structure/PairwiseAlignmentConverter.java deleted
Directorytrunk/src/owl/core/structure/PairwiseSequenceAlignment.java deleted
Directorytrunk/src/owl/core/structure/PaulStructAligner.java deleted
Directorytrunk/src/owl/core/structure/Pdb.java modified , text changed
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/PolyposeRunner.java deleted
Directorytrunk/src/owl/core/structure/PredEval.java deleted
Directorytrunk/src/owl/core/structure/PrositeHit.java deleted
Directorytrunk/src/owl/core/structure/PrositeScanner.java deleted
Directorytrunk/src/owl/core/structure/ProtStructGraph.java deleted
Directorytrunk/src/owl/core/structure/RIGCommonNbhood.java deleted
Directorytrunk/src/owl/core/structure/RIGEdge.java deleted
Directorytrunk/src/owl/core/structure/RIGEnsemble.java deleted
Directorytrunk/src/owl/core/structure/RIGNbhood.java deleted
Directorytrunk/src/owl/core/structure/RIGNode.java deleted
Directorytrunk/src/owl/core/structure/RIGraph.java deleted
Directorytrunk/src/owl/core/structure/RIGraphMinSpanningTree.java deleted
Directorytrunk/src/owl/core/structure/Residue.java modified , text changed
Directorytrunk/src/owl/core/structure/Scop.java deleted
Directorytrunk/src/owl/core/structure/ScopRegion.java deleted
Directorytrunk/src/owl/core/structure/SecStrucElement.java deleted
Directorytrunk/src/owl/core/structure/SecondaryStructure.java deleted
Directorytrunk/src/owl/core/structure/StructAligner.java deleted
Directorytrunk/src/owl/core/structure/StructAlignmentError.java deleted
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/ added
Directorytrunk/src/owl/core/structure/alignment/PaulStructAligner.java
(Copied from trunk/src/owl/core/structure/PaulStructAligner.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/alignment/StructAligner.java
(Copied from trunk/src/owl/core/structure/StructAligner.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/alignment/StructAlignmentError.java
(Copied from trunk/src/owl/core/structure/StructAlignmentError.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/alignment/StructureAlignmentEvaluator.java
(Copied from trunk/src/owl/core/structure/AlignmentEvaluator.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/features/ added
Directorytrunk/src/owl/core/structure/features/CatalSiteSet.java
(Copied from trunk/src/owl/core/structure/CatalSiteSet.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/features/CatalyticSite.java
(Copied from trunk/src/owl/core/structure/CatalyticSite.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/features/EC.java
(Copied from trunk/src/owl/core/structure/EC.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/features/ECRegion.java
(Copied from trunk/src/owl/core/structure/ECRegion.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/features/Scop.java
(Copied from trunk/src/owl/core/structure/Scop.java, r1007)
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Directorytrunk/src/owl/core/structure/features/ScopRegion.java
(Copied from trunk/src/owl/core/structure/ScopRegion.java, r1007)
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Directorytrunk/src/owl/core/structure/features/SecStrucElement.java
(Copied from trunk/src/owl/core/structure/SecStrucElement.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/features/SecondaryStructure.java
(Copied from trunk/src/owl/core/structure/SecondaryStructure.java, r1007)
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Directorytrunk/src/owl/core/structure/graphs/AIGEdge.java
(Copied from trunk/src/owl/core/structure/AIGEdge.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/graphs/AIGNode.java
(Copied from trunk/src/owl/core/structure/AIGNode.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/graphs/AIGraph.java
(Copied from trunk/src/owl/core/structure/AIGraph.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/graphs/CaspRRFileData.java
(Copied from trunk/src/owl/core/structure/CaspRRFileData.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/graphs/CaspRRFileRIGraph.java
(Copied from trunk/src/owl/core/structure/CaspRRFileRIGraph.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/graphs/DbRIGraph.java
(Copied from trunk/src/owl/core/structure/DbRIGraph.java, r1007)
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Directorytrunk/src/owl/core/structure/graphs/FileRIGraph.java
(Copied from trunk/src/owl/core/structure/FileRIGraph.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/graphs/GraphComparisonResult.java
(Copied from trunk/src/owl/core/structure/PredEval.java, r1007)
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Directorytrunk/src/owl/core/structure/graphs/GraphIODb.java
(Copied from trunk/src/owl/core/structure/GraphIODb.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/graphs/GraphIOGDLFile.java
(Copied from trunk/src/owl/core/structure/GraphIOGDLFile.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/graphs/GraphIdNotFoundError.java
(Copied from trunk/src/owl/core/structure/GraphIdNotFoundError.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/graphs/NbhProbDistribution.java
(Copied from trunk/src/owl/core/structure/NbhProbDistribution.java, r1007)
added , text changed
Directorytrunk/src/owl/core/structure/graphs/NbhoodBackgrnd.java
(Copied from trunk/src/owl/core/structure/NbhoodBackgrnd.java, r1007)
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Directorytrunk/src/owl/core/structure/graphs/ProtStructGraph.java
(Copied from trunk/src/owl/core/structure/ProtStructGraph.java, r1007)
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Directorytrunk/src/owl/core/structure/graphs/RIGCommonNbhood.java
(Copied from trunk/src/owl/core/structure/RIGCommonNbhood.java, r1007)
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Directorytrunk/src/owl/core/structure/graphs/RIGEdge.java
(Copied from trunk/src/owl/core/structure/RIGEdge.java, r1007)
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Directorytrunk/src/owl/core/structure/graphs/RIGEnsemble.java
(Copied from trunk/src/owl/core/structure/RIGEnsemble.java, r1007)
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Directorytrunk/src/owl/core/structure/graphs/RIGNbhood.java
(Copied from trunk/src/owl/core/structure/RIGNbhood.java, r1007)
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Directorytrunk/src/owl/core/structure/graphs/RIGNode.java
(Copied from trunk/src/owl/core/structure/RIGNode.java, r1007)
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Directorytrunk/src/owl/core/structure/graphs/RIGraph.java
(Copied from trunk/src/owl/core/structure/RIGraph.java, r1007)
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Directorytrunk/src/owl/core/structure/graphs/RIGraphMinSpanningTree.java
(Copied from trunk/src/owl/core/structure/RIGraphMinSpanningTree.java, r1007)
added , text changed
Directorytrunk/src/owl/core/util/Box.java
(Copied from trunk/src/owl/core/structure/Box.java, r1007)
added , text changed
Directorytrunk/src/owl/core/util/FileFormatError.java
(Copied from trunk/src/owl/core/structure/FileFormatError.java, r1007)
added , text changed
Directorytrunk/src/owl/core/util/FileTypeGuesser.java
(Copied from trunk/src/owl/core/structure/FileTypeGuesser.java, r1007)
added , text changed
Directorytrunk/src/owl/core/util/GeometryTools.java
(Copied from trunk/src/owl/core/structure/GeometryTools.java, r1007)
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Directorytrunk/src/owl/core/util/HashGrid.java
(Copied from trunk/src/owl/core/structure/HashGrid.java, r1007)
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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/deltaRank/DeltaRank.java modified , text changed
Directorytrunk/src/owl/embed/Distiller.java modified , text changed
Directorytrunk/src/owl/embed/Reconstructer.java modified , text changed
Directorytrunk/src/owl/embed/Scorer.java modified , text changed
Directorytrunk/src/owl/embed/SetScore.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/ContactMatrix.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/CorrelationFunction.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/Demes.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/Individuals.java modified , text changed
Directorytrunk/src/owl/embed/contactmaps/Stripper.java modified , text changed
Directorytrunk/src/owl/graphAveraging/GraphAverager.java modified , text changed
Directorytrunk/src/owl/graphAveraging/PhiPsiAverager.java modified , text changed
Directorytrunk/src/owl/sadp/ContactMap.java modified , text changed
Directorytrunk/src/owl/sadp/SADP.java modified , text changed
Directorytrunk/src/owl/tests/TestsSetup.java modified , text changed
Directorytrunk/src/owl/tests/core/runners/blast/
(Copied from trunk/src/owl/tests/core/sequence, r1008)
added
Directorytrunk/src/owl/tests/core/runners/blast/BlastParsersTest.java modified , text changed
Directorytrunk/src/owl/tests/core/runners/tinker/TinkerRunnerTest.java modified , text changed
Directorytrunk/src/owl/tests/core/sequence/ deleted
Directorytrunk/src/owl/tests/core/structure/PdbParsersTest.java modified , text changed
Directorytrunk/src/owl/tests/core/structure/PdbTest.java modified , text changed
Directorytrunk/src/pairwiseSeqId.java modified , text changed
Directorytrunk/src/reconstruct.java modified , text changed
Directorytrunk/src/runMD.java modified , text changed
Directorytrunk/src/scoreDecoys.java modified , text changed
Directorytrunk/src/scorePdbSet.java modified , text changed
Directorytrunk/src/superimposeMult.java modified , text changed
Directorytrunk/src/testDbRIGraph.java modified , text changed
Directorytrunk/src/testJUNGframework.java modified , text changed
Directorytrunk/src/testPdb.java modified , text changed
Directorytrunk/src/tests/proteinstructure/ deleted