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Author: hstehr
Date: Wed Mar 31 15:50:04 2010 UTC (9 years, 5 months 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

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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)
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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)
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Directorytrunk/src/owl/core/runners/PolyposeRunner.java
(Copied from trunk/src/owl/core/structure/PolyposeRunner.java, r1007)
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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)
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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)
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Directorytrunk/src/owl/core/runners/blast/BlastHitList.java
(Copied from trunk/src/owl/core/sequence/BlastHitList.java, r1007)
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Directorytrunk/src/owl/core/runners/blast/BlastRunner.java
(Copied from trunk/src/owl/core/sequence/BlastRunner.java, r1007)
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Directorytrunk/src/owl/core/runners/blast/BlastTabularParser.java
(Copied from trunk/src/owl/core/sequence/BlastTabularParser.java, r1007)
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Directorytrunk/src/owl/core/runners/blast/BlastUtils.java
(Copied from trunk/src/owl/core/sequence/BlastUtils.java, r1007)
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Directorytrunk/src/owl/core/runners/blast/BlastXMLParser.java
(Copied from trunk/src/owl/core/sequence/BlastXMLParser.java, r1007)
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Directorytrunk/src/owl/core/runners/gromacs/GromacsError.java
(Copied from trunk/src/owl/core/runners/tinker/GromacsError.java, r1007)
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Directorytrunk/src/owl/core/runners/gromacs/GromacsMDP.java
(Copied from trunk/src/owl/core/runners/tinker/GromacsMDP.java, r1007)
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Directorytrunk/src/owl/core/runners/gromacs/GromacsRunner.java
(Copied from trunk/src/owl/core/runners/tinker/GromacsRunner.java, r1007)
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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)
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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)
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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