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r423
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actionTools/ 419 (11 years ago) by duarte: Re-branching for JUNG2 development
proteinstructure/ 423 (11 years ago) by duarte: New methods in RIGraph copy() and compare(other) Basic testing of copy introduced on testJUNGframework
sadp/ 420 (11 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
tinker/ 420 (11 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
tools/ 419 (11 years ago) by duarte: Re-branching for JUNG2 development
Manifest.txt 419 (11 years ago) by duarte: Re-branching for JUNG2 development
benchmarkGraphAlgorithm.java 420 (11 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
calculateGridDensity.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
cnCoarseNbhood.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
cnEvalTargetNbhood.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
cnHashIterNbhood.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
cnex1.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
compareCMs.java 423 (11 years ago) by duarte: New methods in RIGraph copy() and compare(other) Basic testing of copy introduced on testJUNGframework
createGraphDb.sh 419 (11 years ago) by duarte: Re-branching for JUNG2 development
genDbGraph.java 420 (11 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
genGraph.java 420 (11 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
hashIterNbhood.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
iterEvalNbhood.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
iterateNbhood.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
iterateNbs.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
iterateUpperNbhood.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
iterateUpperNbs.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
listInfoGain.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
listInfoLoss.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
makeNbhTbl.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
maxInfoGain.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
minInfoGain.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
reconstruct.java 420 (11 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
rewriteNBHood.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
rewriteNBHood_parallel.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
runGenDbGraph.sh 419 (11 years ago) by duarte: Re-branching for JUNG2 development
scoreTargetMoves.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testClusterConnection.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testDeltaDistanceMap.java 420 (11 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
testGraph2Pml.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testGraphAverager.java 420 (11 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
testGraphClustering.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testJUNGframework.java 423 (11 years ago) by duarte: New methods in RIGraph copy() and compare(other) Basic testing of copy introduced on testJUNGframework
testMySQLConnection.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testPdb.java 420 (11 years ago) by duarte: First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there. NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
testPyMol.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testPymolServer.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testResidueSelectionString.java 422 (11 years ago) by duarte: Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.
writeTargetMoves.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
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