trunk/.classpath
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trunk/.project
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trunk/actionTools/
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trunk/addSeq2Mcma.java
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trunk/alignSeq.java
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trunk/analyseHistone.java
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trunk/averageGraph.java
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trunk/benchmarkGraphAlgorithm.java
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trunk/calculateGridDensity.java
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trunk/compareAlignments.java
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trunk/compareCMs.java
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trunk/computeEnergies.java
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trunk/deltaRank/
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trunk/dumppdb.java
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trunk/dumpseq.java
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trunk/embed/
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trunk/features/
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trunk/genDbGraph.java
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trunk/genGraph.java
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trunk/graphAveraging/
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trunk/jars/
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trunk/jars/JRclient-RE817.jar
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trunk/jars/Jama-1.0.2.jar
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trunk/jars/collections-generic-4.01.jar
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trunk/jars/commons-codec-1.3.jar
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trunk/jars/drmaa.jar
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trunk/jars/jaligner.jar
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trunk/jars/java-getopt-1.0.13.jar
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trunk/jars/jung-algorithms-2.0-beta1.jar
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trunk/jars/jung-api-2.0-beta1.jar
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trunk/jars/jung-graph-impl-2.0-beta1.jar
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trunk/jars/mysql-connector-java-5.0.5-bin.jar
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trunk/jars/vecmath.jar
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trunk/jars/ws-commons-util-1.0.2.jar
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trunk/jars/xmlrpc-client-3.1.jar
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trunk/jars/xmlrpc-common-3.1.jar
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trunk/litNet/
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trunk/mapMutations.java
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trunk/mirrorIt.java
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trunk/pairwiseSeqId.java
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trunk/ppi/
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trunk/proteinstructure/
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trunk/reconstruct.java
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trunk/runMD.java
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trunk/sadp/
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trunk/scoreDecoys.java
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trunk/sequence/
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trunk/src/
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trunk/src/actionTools/
(Copied from trunk/actionTools, r949)
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added
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trunk/src/addSeq2Mcma.java
(Copied from trunk/addSeq2Mcma.java, r949)
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added
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trunk/src/alignSeq.java
(Copied from trunk/alignSeq.java, r950)
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added
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trunk/src/analyseHistone.java
(Copied from trunk/analyseHistone.java, r949)
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added
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trunk/src/averageGraph.java
(Copied from trunk/averageGraph.java, r950)
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trunk/src/benchmarkGraphAlgorithm.java
(Copied from trunk/benchmarkGraphAlgorithm.java, r950)
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added
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trunk/src/calculateGridDensity.java
(Copied from trunk/calculateGridDensity.java, r949)
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added
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trunk/src/compareAlignments.java
(Copied from trunk/compareAlignments.java, r949)
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added
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trunk/src/compareCMs.java
(Copied from trunk/compareCMs.java, r950)
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trunk/src/computeEnergies.java
(Copied from trunk/computeEnergies.java, r949)
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trunk/src/deltaRank/
(Copied from trunk/deltaRank, r949)
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added
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trunk/src/dumppdb.java
(Copied from trunk/dumppdb.java, r950)
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added
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trunk/src/dumpseq.java
(Copied from trunk/dumpseq.java, r949)
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added
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trunk/src/embed/
(Copied from trunk/embed, r949)
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added
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trunk/src/embed/Distiller.java
(Copied from trunk/embed/Distiller.java, r950)
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replaced
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trunk/src/embed/Embedder.java
(Copied from trunk/embed/Embedder.java, r950)
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replaced
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trunk/src/embed/Reconstructer.java
(Copied from trunk/embed/Reconstructer.java, r950)
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trunk/src/embed/Scorer.java
(Copied from trunk/embed/Scorer.java, r950)
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trunk/src/embed/contactmaps/CMGrabber.java
(Copied from trunk/embed/contactmaps/CMGrabber.java, r950)
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replaced
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trunk/src/embed/contactmaps/CompareIndis.java
(Copied from trunk/embed/contactmaps/CompareIndis.java, r950)
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replaced
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trunk/src/embed/contactmaps/CorrelationFunction.java
(Copied from trunk/embed/contactmaps/CorrelationFunction.java, r950)
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replaced
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trunk/src/embed/contactmaps/Demes.java
(Copied from trunk/embed/contactmaps/Demes.java, r950)
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replaced
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trunk/src/embed/contactmaps/Individuals.java
(Copied from trunk/embed/contactmaps/Individuals.java, r950)
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replaced
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trunk/src/embed/contactmaps/Stripper.java
(Copied from trunk/embed/contactmaps/Stripper.java, r950)
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replaced
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trunk/src/features/
(Copied from trunk/features, r949)
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added
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trunk/src/genDbGraph.java
(Copied from trunk/genDbGraph.java, r950)
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added
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trunk/src/genGraph.java
(Copied from trunk/genGraph.java, r950)
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added
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trunk/src/graphAveraging/
(Copied from trunk/graphAveraging, r949)
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added
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trunk/src/litNet/
(Copied from trunk/litNet, r949)
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added
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trunk/src/mapMutations.java
(Copied from trunk/mapMutations.java, r950)
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added
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trunk/src/mirrorIt.java
(Copied from trunk/mirrorIt.java, r950)
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added
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trunk/src/pairwiseSeqId.java
(Copied from trunk/pairwiseSeqId.java, r949)
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added
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trunk/src/ppi/
(Copied from trunk/ppi, r949)
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added
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trunk/src/proteinstructure/
(Copied from trunk/proteinstructure, r949)
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added
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trunk/src/proteinstructure/Alignment.java
(Copied from trunk/proteinstructure/Alignment.java, r950)
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replaced
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trunk/src/proteinstructure/CaspRRFileRIGraph.java
(Copied from trunk/proteinstructure/CaspRRFileRIGraph.java, r950)
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replaced
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trunk/src/proteinstructure/CiffileFormatError.java
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deleted
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trunk/src/proteinstructure/CiffilePdb.java
(Copied from trunk/proteinstructure/CiffilePdb.java, r950)
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replaced
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trunk/src/proteinstructure/DaliRunner.java
(Copied from trunk/proteinstructure/DaliRunner.java, r950)
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replaced
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trunk/src/proteinstructure/DecoyScoring/
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deleted
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trunk/src/proteinstructure/FastaFileFormatError.java
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deleted
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trunk/src/proteinstructure/FileFormatError.java
(Copied from trunk/proteinstructure/FileFormatError.java, r950)
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replaced
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trunk/src/proteinstructure/FileRIGraph.java
(Copied from trunk/proteinstructure/FileRIGraph.java, r950)
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replaced
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trunk/src/proteinstructure/GraphFileFormatError.java
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deleted
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trunk/src/proteinstructure/GraphIOGDLFile.java
(Copied from trunk/proteinstructure/GraphIOGDLFile.java, r950)
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replaced
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trunk/src/proteinstructure/PaulStructAligner.java
(Copied from trunk/proteinstructure/PaulStructAligner.java, r950)
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replaced
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trunk/src/proteinstructure/Pdb.java
(Copied from trunk/proteinstructure/Pdb.java, r950)
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replaced
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trunk/src/proteinstructure/PdbfileFormatError.java
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deleted
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trunk/src/proteinstructure/PdbfilePdb.java
(Copied from trunk/proteinstructure/PdbfilePdb.java, r950)
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replaced
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trunk/src/proteinstructure/PirFileFormatError.java
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deleted
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trunk/src/proteinstructure/PolyposeRunner.java
(Copied from trunk/proteinstructure/PolyposeRunner.java, r950)
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replaced
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trunk/src/proteinstructure/RIGEnsemble.java
(Copied from trunk/proteinstructure/RIGEnsemble.java, r950)
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replaced
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