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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/ 434 (11 years ago) by duarte: Changed behaviour of observed/unobserved nodes in RIGraph: now unobserved RIGnodes are also in the RIGraph, tagged with observed=false. Thus getObsLength() in ProtStructGraph (which by the way was not working for AIGraphs) is now only in RIGraph and adapted to the new way of tagging unobserved nodes. New method hasSequence() in ProtStrucGraph and Pdb: it is important to know that from now only if hasSequence()==true we put the unobserved nodes in RIGraph, otherwise we don't put them (as before)
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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