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tools/ 419 (11 years ago) by duarte: Re-branching for JUNG2 development
tinker/ 474 (11 years ago) by duarte: Moved max cluster methods from SimilarityGraph to MaxClusterRunner. Removed SimilarityGraph Now MaxClusterRunner can do all modes of maxcluster: ranking, matrix, and pairwise Changed default for DEFAULT_FORCE_CONSTANT in TinkerRunner to 10.0
sadp/ 450 (11 years ago) by lpetzo: ... some more comments
proteinstructure/ 477 (11 years ago) by duarte: Adapted IO methods in NodesAndEdges to JUNG framework: added 2 classes: - GraphIODb: does reading and writing a Graph<V,E> from/to database - GraphIOGDLFile: does writing of a Graph<V,E> to GDL file for aiSee exporting
graphAveraging/ 459 (11 years ago) by stehr: moved GraphAverager to subpackage, added removeVertex function to RIGraph and AIGraph, added getEdgeFromSerials and containsEdgeIJ functions to ProtStructGraph
actionTools/ 447 (11 years ago) by lpetzo: class Getter: - function get() is now throwing GetterError exception class GetterError: - wrapper exception for all type of exceptions thrown in the get() function of class Getter
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 441 (11 years ago) by duarte: Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial) New methods getChains() and getModels() in all Pdb classes New Exception PdbLoadError New tester for getChains and getModels: testGetChains Changed all calls to Pdb construction accordingly (includes changing excpetions)
testMySQLConnection.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testJUNGframework.java 441 (11 years ago) by duarte: Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial) New methods getChains() and getModels() in all Pdb classes New Exception PdbLoadError New tester for getChains and getModels: testGetChains Changed all calls to Pdb construction accordingly (includes changing excpetions)
testGraphAverager.java 474 (11 years ago) by duarte: Moved max cluster methods from SimilarityGraph to MaxClusterRunner. Removed SimilarityGraph Now MaxClusterRunner can do all modes of maxcluster: ranking, matrix, and pairwise Changed default for DEFAULT_FORCE_CONSTANT in TinkerRunner to 10.0
testGraph2Pml.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
testGetChains.java 451 (11 years ago) by duarte: Fixed for new exceptions thrown by Pdb.load()
testDeltaDistanceMap.java 441 (11 years ago) by duarte: Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial) New methods getChains() and getModels() in all Pdb classes New Exception PdbLoadError New tester for getChains and getModels: testGetChains Changed all calls to Pdb construction accordingly (includes changing excpetions)
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
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 471 (11 years ago) by duarte: Added option for min range and max range filtering (-m, -M) Fixed output of an exception
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 441 (11 years ago) by duarte: Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial) New methods getChains() and getModels() in all Pdb classes New Exception PdbLoadError New tester for getChains and getModels: testGetChains Changed all calls to Pdb construction accordingly (includes changing excpetions)
genDbGraph.java 453 (11 years ago) by duarte: Fixed bug: -r option was not being set by default
dumpseq.java 457 (11 years ago) by duarte: Initial commit: script to dump sequences of pdb entries
createGraphDb.sh 419 (11 years ago) by duarte: Re-branching for JUNG2 development
compareCMs.java 441 (11 years ago) by duarte: Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial) New methods getChains() and getModels() in all Pdb classes New Exception PdbLoadError New tester for getChains and getModels: testGetChains Changed all calls to Pdb construction accordingly (includes changing excpetions)
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 441 (11 years ago) by duarte: Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial) New methods getChains() and getModels() in all Pdb classes New Exception PdbLoadError New tester for getChains and getModels: testGetChains Changed all calls to Pdb construction accordingly (includes changing excpetions)
benchmarkGraphAlgorithm.java 441 (11 years ago) by duarte: Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial) New methods getChains() and getModels() in all Pdb classes New Exception PdbLoadError New tester for getChains and getModels: testGetChains Changed all calls to Pdb construction accordingly (includes changing excpetions)
Manifest.txt 419 (11 years ago) by duarte: Re-branching for JUNG2 development
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