[ViewVC] Revision 1005 of: owl

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Author:	hstehr
Date:	Wed Mar 31 12:29:26 2010 UTC (11 years 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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Path	Details
trunk/src/addSeq2Mcma.java	modified , text changed
trunk/src/alignSeq.java	modified , text changed
trunk/src/analyseHistone.java	modified , text changed
trunk/src/averageGraph.java	modified , text changed
trunk/src/benchmarkGraphAlgorithm.java	modified , text changed
trunk/src/calcVolsAndSurfs.java	modified , text changed
trunk/src/calculateGridDensity.java	modified , text changed
trunk/src/casp/benchmarking/Benchmarking.java	modified , text changed
trunk/src/casp/pipeline/RunAll.java	modified , text changed
trunk/src/casp/pipeline/TargetToTemplatesAlignment.java	modified , text changed
trunk/src/casp/pipeline/TemplateSelection.java	modified , text changed
trunk/src/casp/pipeline/TemplatesAlignment.java	modified , text changed
trunk/src/casp/tools/DisplaySecStructMatching.java	modified , text changed
trunk/src/casp/tools/MapStru2Seq.java	modified , text changed
trunk/src/checkChirality.java	modified , text changed
trunk/src/compareAlignments.java	modified , text changed
trunk/src/compareCMs.java	modified , text changed
trunk/src/computeEnergies.java	modified , text changed
trunk/src/connections/	deleted
trunk/src/deltaRank/DeltaRank.java	modified , text changed
trunk/src/dumppdb.java	modified , text changed
trunk/src/dumpseq.java	modified , text changed
trunk/src/embed/BoundsSmoother.java	modified , text changed
trunk/src/embed/Distiller.java	modified , text changed
trunk/src/embed/Embedder.java	modified , text changed
trunk/src/embed/Reconstructer.java	modified , text changed
trunk/src/embed/Scorer.java	modified , text changed
trunk/src/embed/SetScore.java	modified , text changed
trunk/src/embed/contactmaps/CMDMErrorEvaluator.java	modified , text changed
trunk/src/embed/contactmaps/CMGrabber.java	modified , text changed
trunk/src/embed/contactmaps/CompareIndis.java	modified , text changed
trunk/src/embed/contactmaps/ContactMap.java	modified , text changed
trunk/src/embed/contactmaps/ContactMapEvolver.java	modified , text changed
trunk/src/embed/contactmaps/ContactMapWeighted.java	modified , text changed
trunk/src/embed/contactmaps/ContactMatrix.java	modified , text changed
trunk/src/embed/contactmaps/ConvertErrorsToTextFile.java	modified , text changed
trunk/src/embed/contactmaps/CorrelationFunction.java	modified , text changed
trunk/src/embed/contactmaps/Demes.java	modified , text changed
trunk/src/embed/contactmaps/DistMatrix.java	modified , text changed
trunk/src/embed/contactmaps/Individuals.java	modified , text changed
trunk/src/embed/contactmaps/MergeOutPut.java	modified , text changed
trunk/src/embed/contactmaps/Metric2.java	modified , text changed
trunk/src/embed/contactmaps/NbhStringRanker.java	modified , text changed
trunk/src/embed/contactmaps/NeighbourhoodString.java	modified , text changed
trunk/src/embed/contactmaps/Population1.java	modified , text changed
trunk/src/embed/contactmaps/Species.java	modified , text changed
trunk/src/embed/contactmaps/Stripper.java	modified , text changed
trunk/src/features/	deleted
trunk/src/genDbGraph.java	modified , text changed
trunk/src/genGraph.java	modified , text changed
trunk/src/graphAveraging/ConsensusInterval.java	modified , text changed
trunk/src/graphAveraging/GraphAverager.java	modified , text changed
trunk/src/graphAveraging/PhiPsiAverager.java	modified , text changed
trunk/src/litNet/LiteratureGraph.java	modified , text changed
trunk/src/mapMutations.java	modified , text changed
trunk/src/mirrorIt.java	modified , text changed
trunk/src/owl/core/connections/ (Copied from trunk/src/connections, r1002)	added
trunk/src/owl/core/connections/ConsurfConnection.java	modified , text changed
trunk/src/owl/core/connections/PDomainsConnection.java	modified , text changed
trunk/src/owl/core/connections/PhosphoSitePlusConnection.java	modified , text changed
trunk/src/owl/core/connections/package-info.java	modified , text changed
trunk/src/owl/core/features/ (Copied from trunk/src/features, r1002)	added
trunk/src/owl/core/features/CsaFeature.java	modified , text changed
trunk/src/owl/core/features/Feature.java	modified , text changed
trunk/src/owl/core/features/FeatureType.java	modified , text changed
trunk/src/owl/core/features/GeneralFeature.java	modified , text changed
trunk/src/owl/core/features/HasFeatures.java	modified , text changed
trunk/src/owl/core/features/InvalidFeatureCoordinatesException.java	modified , text changed
trunk/src/owl/core/features/OverlappingFeatureException.java	modified , text changed
trunk/src/owl/core/features/PhosphoSitePlusFeature.java	modified , text changed
trunk/src/owl/core/features/PrositeFeature.java	modified , text changed
trunk/src/owl/core/features/ProteinModificationType.java	modified , text changed
trunk/src/owl/core/features/StructuralDomainFeature.java	modified , text changed
trunk/src/owl/core/features/StructuralDomainType.java	modified , text changed
trunk/src/owl/core/features/UniprotFeature.java	modified , text changed
trunk/src/owl/core/runners/ (Copied from trunk/src/runners, r1002)	added
trunk/src/owl/core/runners/DsspRunner.java	modified , text changed
trunk/src/owl/core/runners/NaccessRunner.java	modified , text changed
trunk/src/owl/core/sequence/ (Copied from trunk/src/sequence, r1002)	added
trunk/src/owl/core/sequence/BlastError.java	modified , text changed
trunk/src/owl/core/sequence/BlastHit.java	modified , text changed
trunk/src/owl/core/sequence/BlastHitList.java	modified , text changed
trunk/src/owl/core/sequence/BlastRunner.java	modified , text changed
trunk/src/owl/core/sequence/BlastTabularParser.java	modified , text changed
trunk/src/owl/core/sequence/BlastUtils.java	modified , text changed
trunk/src/owl/core/sequence/BlastXMLParser.java	modified , text changed
trunk/src/owl/core/sequence/GTGHit.java	modified , text changed
trunk/src/owl/core/sequence/GTGHitList.java	modified , text changed
trunk/src/owl/core/sequence/GTGParser.java	modified , text changed
trunk/src/owl/core/sequence/PsipredError.java	modified , text changed
trunk/src/owl/core/sequence/PsipredRunner.java	modified , text changed
trunk/src/owl/core/sequence/Sequence.java	modified , text changed
trunk/src/owl/core/sequence/TcoffeeError.java	modified , text changed
trunk/src/owl/core/sequence/TcoffeeRunner.java	modified , text changed
trunk/src/owl/core/structure/	added
trunk/src/owl/core/structure/AAinfo.java (Copied from trunk/src/proteinstructure/AAinfo.java, r1002)	added , text changed
trunk/src/owl/core/structure/AIGEdge.java (Copied from trunk/src/proteinstructure/AIGEdge.java, r1002)	added , text changed
trunk/src/owl/core/structure/AIGNode.java (Copied from trunk/src/proteinstructure/AIGNode.java, r1002)	added , text changed
trunk/src/owl/core/structure/AIGraph.java (Copied from trunk/src/proteinstructure/AIGraph.java, r1002)	added , text changed
trunk/src/owl/core/structure/Alignment.java (Copied from trunk/src/proteinstructure/Alignment.java, r1002)	added , text changed