 ../
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actionTools/
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447
(14 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
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sadp/
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450
(14 years ago)
by lpetzo:
... some more comments
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graphAveraging/
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459
(14 years ago)
by stehr:
moved GraphAverager to subpackage, added removeVertex function to RIGraph and AIGraph, added getEdgeFromSerials and containsEdgeIJ functions to ProtStructGraph
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tinker/
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474
(14 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
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tools/
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479
(14 years ago)
by duarte:
Submission of commands is now async
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proteinstructure/
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482
(14 years ago)
by stehr:
added missing class for RR file i/o
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scoreTargetMoves.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateNbhood.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateUpperNbs.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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testClusterConnection.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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testMySQLConnection.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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writeTargetMoves.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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Manifest.txt
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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testGraph2Pml.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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hashIterNbhood.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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createGraphDb.sh
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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rewriteNBHood_parallel.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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cnCoarseNbhood.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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testPymolServer.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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listInfoGain.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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cnHashIterNbhood.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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cnEvalTargetNbhood.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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cnex1.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateUpperNbhood.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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listInfoLoss.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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rewriteNBHood.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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testPyMol.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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maxInfoGain.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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minInfoGain.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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makeNbhTbl.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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iterateNbs.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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iterEvalNbhood.java
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419
(14 years ago)
by duarte:
Re-branching for JUNG2 development
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testResidueSelectionString.java
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422
(14 years ago)
by duarte:
Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.
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genGraph.java
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441
(14 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)
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benchmarkGraphAlgorithm.java
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441
(14 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)
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testPdb.java
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441
(14 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)
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testJUNGframework.java
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441
(14 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)
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calculateGridDensity.java
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441
(14 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)
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compareCMs.java
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441
(14 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)
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testDeltaDistanceMap.java
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441
(14 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)
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testGetChains.java
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451
(14 years ago)
by duarte:
Fixed for new exceptions thrown by Pdb.load()
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genDbGraph.java
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453
(14 years ago)
by duarte:
Fixed bug: -r option was not being set by default
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dumpseq.java
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457
(14 years ago)
by duarte:
Initial commit: script to dump sequences of pdb entries
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reconstruct.java
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471
(14 years ago)
by duarte:
Added option for min range and max range filtering (-m, -M)
Fixed output of an exception
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testGraphAverager.java
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474
(14 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
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