 ../
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tools/
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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actionTools/
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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tinker/
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420
(16 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)
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sadp/
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420
(16 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)
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proteinstructure/
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422
(16 years ago)
by duarte:
Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.
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scoreTargetMoves.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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runGenDbGraph.sh
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateUpperNbs.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testClusterConnection.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testMySQLConnection.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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writeTargetMoves.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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Manifest.txt
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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hashIterNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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createGraphDb.sh
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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rewriteNBHood_parallel.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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cnCoarseNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testPymolServer.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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listInfoGain.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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cnHashIterNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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makeNbhTbl.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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cnEvalTargetNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testGraph2Pml.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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cnex1.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testGraphClustering.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateUpperNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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listInfoLoss.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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rewriteNBHood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testPyMol.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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maxInfoGain.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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minInfoGain.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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iterEvalNbhood.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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calculateGridDensity.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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compareCMs.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateNbs.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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reconstruct.java
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420
(16 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)
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genGraph.java
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420
(16 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)
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benchmarkGraphAlgorithm.java
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420
(16 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)
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testPdb.java
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420
(16 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)
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genDbGraph.java
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420
(16 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)
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testDeltaDistanceMap.java
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420
(16 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)
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testGraphAverager.java
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420
(16 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)
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testJUNGframework.java
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421
(16 years ago)
by duarte:
Now graph generation in Pdb also works when we pass a crossed contact type with overlapping atom sets, e.g. ALL/BB (changes were: added a couple of new conditions in Box and in Pdb's AIGraph getGraph(ct,cutoff))
Loads of better comments
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testResidueSelectionString.java
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422
(16 years ago)
by duarte:
Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.
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