 ../
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actionTools/
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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proteinstructure/
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428
(16 years ago)
by duarte:
Fixed bug: was missing last sequence element when adding gap nodes
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sadp/
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426
(16 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
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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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tools/
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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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benchmarkGraphAlgorithm.java
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424
(16 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
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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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cnCoarseNbhood.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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cnHashIterNbhood.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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compareCMs.java
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423
(16 years ago)
by duarte:
New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework
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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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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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genGraph.java
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424
(16 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
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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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iterEvalNbhood.java
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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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iterateNbs.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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iterateUpperNbs.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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listInfoLoss.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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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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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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rewriteNBHood.java
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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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runGenDbGraph.sh
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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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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testClusterConnection.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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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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testGraph2Pml.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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testGraphAverager.java
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424
(16 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
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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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testJUNGframework.java
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424
(16 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
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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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testPdb.java
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424
(16 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
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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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testPymolServer.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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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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writeTargetMoves.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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