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Author: hstehr
Date: Wed Mar 31 12:29:26 2010 UTC (9 years, 4 months ago)
Log Message:
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core

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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