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root/owl/branches/aglappe-jung/proteinstructure
r426
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contactTypes.dat 419 (12 years ago) by duarte: Re-branching for JUNG2 development
aapairsBounds.dat 419 (12 years ago) by duarte: Re-branching for JUNG2 development
SimilarityGraph.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
SecStrucElement.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
Scop.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
RIGraph.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
RIGNode.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
RIGEdge.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)
ProtStructGraph.java 423 (12 years ago) by duarte: New methods in RIGraph copy() and compare(other) Basic testing of copy introduced on testJUNGframework
PredEval.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
PdbfilePdb.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
PdbasePdb.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
PdbCodeNotFoundError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
PdbChainCodeNotFoundError.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
PairwiseSequenceAlignment.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
PairwiseAlignmentGraphConverter.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
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
NodesAndEdges.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
MsdsdPdb.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
MaxClusterRunner.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
IntervalSet.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
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
IntPairSet.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)
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
GraphIdNotFoundError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
GraphFileFormatError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
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
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
FileFormatError.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
ECRegion.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
EC.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
ContactType.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
CiffilePdb.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
CatalyticSite.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
CatalSiteSet.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
AlignmentConstructionError.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
Alignment.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
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
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)
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)
AAinfo.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
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