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root/owl/branches/aglappe-jung/proteinstructure
r427
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AAinfo.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
AIGEdge.java 420 (12 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)
AIGNode.java 420 (12 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)
AIGraph.java 421 (12 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
Alignment.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
AlignmentConstructionError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
Box.java 421 (12 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
CatalSiteSet.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
CatalyticSite.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
CiffileFormatError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
CiffilePdb.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
ConformationsNotSameSizeError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
ContactType.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
DbRIGraph.java 421 (12 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
EC.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
ECRegion.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
FastaFileFormatError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
FileFormatError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
FileRIGraph.java 421 (12 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
GraphAverager.java 421 (12 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
GraphFileFormatError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
GraphIdNotFoundError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
IntPairComparator.java 426 (12 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
IntPairSet.java 427 (12 years ago) by duarte: Fixed bug in PairwiseAlignmentGraphConverter: was not adding the nodes for gaps, also some other minor bugs fixed in copying of objects Fixed bug in getAllCommonNbhSizes, 1) now returning a HashMap on Pair<Integer>, not Pair<RIGNode> 2) was filling cells when size=0 Added method getIncidentNodes to IntPairSet as a temporary fix
Interval.java 426 (12 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
IntervalSet.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
MaxClusterRunner.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
MsdsdInconsistentResidueNumbersError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
MsdsdPdb.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
NbhProbDistribution.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
NodesAndEdges.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
PairwiseAlignmentConverter.java 426 (12 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
PairwiseAlignmentGraphConverter.java 427 (12 years ago) by duarte: Fixed bug in PairwiseAlignmentGraphConverter: was not adding the nodes for gaps, also some other minor bugs fixed in copying of objects Fixed bug in getAllCommonNbhSizes, 1) now returning a HashMap on Pair<Integer>, not Pair<RIGNode> 2) was filling cells when size=0 Added method getIncidentNodes to IntPairSet as a temporary fix
PairwiseSequenceAlignment.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
Pdb.java 421 (12 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
PdbChainCodeNotFoundError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
PdbCodeNotFoundError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
PdbaseInconsistencyError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
PdbasePdb.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
PdbfileFormatError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
PdbfilePdb.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
PirFileFormatError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
PredEval.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
ProtStructGraph.java 423 (12 years ago) by duarte: New methods in RIGraph copy() and compare(other) Basic testing of copy introduced on testJUNGframework
RIGCommonNbhood.java 420 (12 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)
RIGEdge.java 423 (12 years ago) by duarte: New methods in RIGraph copy() and compare(other) Basic testing of copy introduced on testJUNGframework
RIGNbhood.java 421 (12 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
RIGNode.java 423 (12 years ago) by duarte: New methods in RIGraph copy() and compare(other) Basic testing of copy introduced on testJUNGframework
RIGraph.java 427 (12 years ago) by duarte: Fixed bug in PairwiseAlignmentGraphConverter: was not adding the nodes for gaps, also some other minor bugs fixed in copying of objects Fixed bug in getAllCommonNbhSizes, 1) now returning a HashMap on Pair<Integer>, not Pair<RIGNode> 2) was filling cells when size=0 Added method getIncidentNodes to IntPairSet as a temporary fix
Scop.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
ScopRegion.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
SecStrucElement.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
SecondaryStructure.java 423 (12 years ago) by duarte: New methods in RIGraph copy() and compare(other) Basic testing of copy introduced on testJUNGframework
SimilarityGraph.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
aapairsBounds.dat 419 (12 years ago) by duarte: Re-branching for JUNG2 development
contactTypes.dat 419 (12 years ago) by duarte: Re-branching for JUNG2 development
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