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tools/ 419 (11 years ago) by duarte: Re-branching for JUNG2 development
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)
sadp/ 426 (11 years ago) by duarte: Now PairWiseAlignmentConverter and PairwiseAlignmentGraphConverter work in the new JUNG framework. New class IntPairComparator Now sorting output in RIGraph.write_graph_to_file
proteinstructure/ 433 (11 years ago) by duarte: Added more comments
actionTools/ 419 (11 years ago) by duarte: Re-branching for JUNG2 development
writeTargetMoves.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.
testPymolServer.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testPyMol.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testPdb.java 424 (11 years ago) by duarte: Added last i/o method from old Graph (write to file in Ioannis network format) Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods Fixed the write_graph_to_file method name in executables in default package
testMySQLConnection.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testJUNGframework.java 430 (11 years ago) by duarte: Fixed tester after changes in getAllCommonNnhSizes
testGraphClustering.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testGraphAverager.java 424 (11 years ago) by duarte: Added last i/o method from old Graph (write to file in Ioannis network format) Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods Fixed the write_graph_to_file method name in executables in default package
testGraph2Pml.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)
testClusterConnection.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
scoreTargetMoves.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
rewriteNBHood_parallel.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
rewriteNBHood.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)
minInfoGain.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
makeNbhTbl.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
listInfoGain.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
iterateUpperNbhood.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
iterateNbhood.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
hashIterNbhood.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
genGraph.java 431 (11 years ago) by duarte: Fixed bug: was not working with crossed contacts (with "/") because the "/" was not allowed in file names. Now replacing / with :
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)
createGraphDb.sh 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
cnex1.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
cnEvalTargetNbhood.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
calculateGridDensity.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
benchmarkGraphAlgorithm.java 424 (11 years ago) by duarte: Added last i/o method from old Graph (write to file in Ioannis network format) Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods Fixed the write_graph_to_file method name in executables in default package
Manifest.txt 419 (11 years ago) by duarte: Re-branching for JUNG2 development
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