 ../
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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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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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graphAveraging/
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483
(14 years ago)
by stehr:
added methods to calculate and filter by consensus scores
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proteinstructure/
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487
(14 years ago)
by stehr:
added new classes RIGEnsemble and FileTypeGuesser (used by Casp Consensus Contact prediction)
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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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testGraphAverager.java
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484
(14 years ago)
by stehr:
changed call to graphAverager.doAveraging() into getConsensusGraph() after refactoring
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reconstruct.java
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485
(14 years ago)
by duarte:
Now exiting upon distgeom error
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