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Author: duarte
Date: Fri Jan 29 16:12:34 2010 UTC (9 years, 8 months ago)
Log Message: 
Reorganised the project with a src folder for java source files.
Added a jars dir with all jars needed for the project.
Added .project and .classpath pointing to relative path of jars. 
The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.

Changed paths

Only 100 changes shown, display 46 more changes...
Path Details
Directorytrunk/.classpath added
Directorytrunk/.project added
Directorytrunk/actionTools/ deleted
Directorytrunk/addSeq2Mcma.java deleted
Directorytrunk/alignSeq.java deleted
Directorytrunk/analyseHistone.java deleted
Directorytrunk/averageGraph.java deleted
Directorytrunk/benchmarkGraphAlgorithm.java deleted
Directorytrunk/calculateGridDensity.java deleted
Directorytrunk/compareAlignments.java deleted
Directorytrunk/compareCMs.java deleted
Directorytrunk/computeEnergies.java deleted
Directorytrunk/deltaRank/ deleted
Directorytrunk/dumppdb.java deleted
Directorytrunk/dumpseq.java deleted
Directorytrunk/embed/ deleted
Directorytrunk/features/ deleted
Directorytrunk/genDbGraph.java deleted
Directorytrunk/genGraph.java deleted
Directorytrunk/graphAveraging/ deleted
Directorytrunk/jars/ added
Directorytrunk/jars/JRclient-RE817.jar added
Directorytrunk/jars/Jama-1.0.2.jar added
Directorytrunk/jars/collections-generic-4.01.jar added
Directorytrunk/jars/commons-codec-1.3.jar added
Directorytrunk/jars/drmaa.jar added
Directorytrunk/jars/jaligner.jar added
Directorytrunk/jars/java-getopt-1.0.13.jar added
Directorytrunk/jars/jung-algorithms-2.0-beta1.jar added
Directorytrunk/jars/jung-api-2.0-beta1.jar added
Directorytrunk/jars/jung-graph-impl-2.0-beta1.jar added
Directorytrunk/jars/mysql-connector-java-5.0.5-bin.jar added
Directorytrunk/jars/vecmath.jar added
Directorytrunk/jars/ws-commons-util-1.0.2.jar added
Directorytrunk/jars/xmlrpc-client-3.1.jar added
Directorytrunk/jars/xmlrpc-common-3.1.jar added
Directorytrunk/litNet/ deleted
Directorytrunk/mapMutations.java deleted
Directorytrunk/mirrorIt.java deleted
Directorytrunk/pairwiseSeqId.java deleted
Directorytrunk/ppi/ deleted
Directorytrunk/proteinstructure/ deleted
Directorytrunk/reconstruct.java deleted
Directorytrunk/runMD.java deleted
Directorytrunk/sadp/ deleted
Directorytrunk/scoreDecoys.java deleted
Directorytrunk/sequence/ deleted
Directorytrunk/src/ added
Directorytrunk/src/actionTools/
(Copied from trunk/actionTools, r949) 		added
Directorytrunk/src/addSeq2Mcma.java
(Copied from trunk/addSeq2Mcma.java, r949) 		added
Directorytrunk/src/alignSeq.java
(Copied from trunk/alignSeq.java, r950) 		added
Directorytrunk/src/analyseHistone.java
(Copied from trunk/analyseHistone.java, r949) 		added
Directorytrunk/src/averageGraph.java
(Copied from trunk/averageGraph.java, r950) 		added
Directorytrunk/src/benchmarkGraphAlgorithm.java
(Copied from trunk/benchmarkGraphAlgorithm.java, r950) 		added
Directorytrunk/src/calculateGridDensity.java
(Copied from trunk/calculateGridDensity.java, r949) 		added
Directorytrunk/src/compareAlignments.java
(Copied from trunk/compareAlignments.java, r949) 		added
Directorytrunk/src/compareCMs.java
(Copied from trunk/compareCMs.java, r950) 		added
Directorytrunk/src/computeEnergies.java
(Copied from trunk/computeEnergies.java, r949) 		added
Directorytrunk/src/deltaRank/
(Copied from trunk/deltaRank, r949) 		added
Directorytrunk/src/dumppdb.java
(Copied from trunk/dumppdb.java, r950) 		added
Directorytrunk/src/dumpseq.java
(Copied from trunk/dumpseq.java, r949) 		added
Directorytrunk/src/embed/
(Copied from trunk/embed, r949) 		added
Directorytrunk/src/embed/Distiller.java
(Copied from trunk/embed/Distiller.java, r950) 		replaced
Directorytrunk/src/embed/Embedder.java
(Copied from trunk/embed/Embedder.java, r950) 		replaced
Directorytrunk/src/embed/Reconstructer.java
(Copied from trunk/embed/Reconstructer.java, r950) 		replaced
Directorytrunk/src/embed/Scorer.java
(Copied from trunk/embed/Scorer.java, r950) 		replaced
Directorytrunk/src/embed/contactmaps/CMGrabber.java
(Copied from trunk/embed/contactmaps/CMGrabber.java, r950) 		replaced
Directorytrunk/src/embed/contactmaps/CompareIndis.java
(Copied from trunk/embed/contactmaps/CompareIndis.java, r950) 		replaced
Directorytrunk/src/embed/contactmaps/CorrelationFunction.java
(Copied from trunk/embed/contactmaps/CorrelationFunction.java, r950) 		replaced
Directorytrunk/src/embed/contactmaps/Demes.java
(Copied from trunk/embed/contactmaps/Demes.java, r950) 		replaced
Directorytrunk/src/embed/contactmaps/Individuals.java
(Copied from trunk/embed/contactmaps/Individuals.java, r950) 		replaced
Directorytrunk/src/embed/contactmaps/Stripper.java
(Copied from trunk/embed/contactmaps/Stripper.java, r950) 		replaced
Directorytrunk/src/features/
(Copied from trunk/features, r949) 		added
Directorytrunk/src/genDbGraph.java
(Copied from trunk/genDbGraph.java, r950) 		added
Directorytrunk/src/genGraph.java
(Copied from trunk/genGraph.java, r950) 		added
Directorytrunk/src/graphAveraging/
(Copied from trunk/graphAveraging, r949) 		added
Directorytrunk/src/litNet/
(Copied from trunk/litNet, r949) 		added
Directorytrunk/src/mapMutations.java
(Copied from trunk/mapMutations.java, r950) 		added
Directorytrunk/src/mirrorIt.java
(Copied from trunk/mirrorIt.java, r950) 		added
Directorytrunk/src/pairwiseSeqId.java
(Copied from trunk/pairwiseSeqId.java, r949) 		added
Directorytrunk/src/ppi/
(Copied from trunk/ppi, r949) 		added
Directorytrunk/src/proteinstructure/
(Copied from trunk/proteinstructure, r949) 		added
Directorytrunk/src/proteinstructure/Alignment.java
(Copied from trunk/proteinstructure/Alignment.java, r950) 		replaced
Directorytrunk/src/proteinstructure/CaspRRFileRIGraph.java
(Copied from trunk/proteinstructure/CaspRRFileRIGraph.java, r950) 		replaced
Directorytrunk/src/proteinstructure/CiffileFormatError.java deleted
Directorytrunk/src/proteinstructure/CiffilePdb.java
(Copied from trunk/proteinstructure/CiffilePdb.java, r950) 		replaced
Directorytrunk/src/proteinstructure/DaliRunner.java
(Copied from trunk/proteinstructure/DaliRunner.java, r950) 		replaced
Directorytrunk/src/proteinstructure/DecoyScoring/ deleted
Directorytrunk/src/proteinstructure/FastaFileFormatError.java deleted
Directorytrunk/src/proteinstructure/FileFormatError.java
(Copied from trunk/proteinstructure/FileFormatError.java, r950) 		replaced
Directorytrunk/src/proteinstructure/FileRIGraph.java
(Copied from trunk/proteinstructure/FileRIGraph.java, r950) 		replaced
Directorytrunk/src/proteinstructure/GraphFileFormatError.java deleted
Directorytrunk/src/proteinstructure/GraphIOGDLFile.java
(Copied from trunk/proteinstructure/GraphIOGDLFile.java, r950) 		replaced
Directorytrunk/src/proteinstructure/PaulStructAligner.java
(Copied from trunk/proteinstructure/PaulStructAligner.java, r950) 		replaced
Directorytrunk/src/proteinstructure/Pdb.java
(Copied from trunk/proteinstructure/Pdb.java, r950) 		replaced
Directorytrunk/src/proteinstructure/PdbfileFormatError.java deleted
Directorytrunk/src/proteinstructure/PdbfilePdb.java
(Copied from trunk/proteinstructure/PdbfilePdb.java, r950) 		replaced
Directorytrunk/src/proteinstructure/PirFileFormatError.java deleted
Directorytrunk/src/proteinstructure/PolyposeRunner.java
(Copied from trunk/proteinstructure/PolyposeRunner.java, r950) 		replaced
Directorytrunk/src/proteinstructure/RIGEnsemble.java
(Copied from trunk/proteinstructure/RIGEnsemble.java, r950) 		replaced