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root/owl/branches/aglappe-jung/proteinstructure
r434
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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 434 (12 years ago) by duarte: Changed behaviour of observed/unobserved nodes in RIGraph: now unobserved RIGnodes are also in the RIGraph, tagged with observed=false. Thus getObsLength() in ProtStructGraph (which by the way was not working for AIGraphs) is now only in RIGraph and adapted to the new way of tagging unobserved nodes. New method hasSequence() in ProtStrucGraph and Pdb: it is important to know that from now only if hasSequence()==true we put the unobserved nodes in RIGraph, otherwise we don't put them (as before)
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 433 (12 years ago) by duarte: Added more 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 428 (12 years ago) by duarte: Fixed bug: was missing last sequence element when adding gap nodes
PairwiseSequenceAlignment.java 419 (12 years ago) by duarte: Re-branching for JUNG2 development
Pdb.java 434 (12 years ago) by duarte: Changed behaviour of observed/unobserved nodes in RIGraph: now unobserved RIGnodes are also in the RIGraph, tagged with observed=false. Thus getObsLength() in ProtStructGraph (which by the way was not working for AIGraphs) is now only in RIGraph and adapted to the new way of tagging unobserved nodes. New method hasSequence() in ProtStrucGraph and Pdb: it is important to know that from now only if hasSequence()==true we put the unobserved nodes in RIGraph, otherwise we don't put them (as before)
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 434 (12 years ago) by duarte: Changed behaviour of observed/unobserved nodes in RIGraph: now unobserved RIGnodes are also in the RIGraph, tagged with observed=false. Thus getObsLength() in ProtStructGraph (which by the way was not working for AIGraphs) is now only in RIGraph and adapted to the new way of tagging unobserved nodes. New method hasSequence() in ProtStrucGraph and Pdb: it is important to know that from now only if hasSequence()==true we put the unobserved nodes in RIGraph, otherwise we don't put them (as before)
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 434 (12 years ago) by duarte: Changed behaviour of observed/unobserved nodes in RIGraph: now unobserved RIGnodes are also in the RIGraph, tagged with observed=false. Thus getObsLength() in ProtStructGraph (which by the way was not working for AIGraphs) is now only in RIGraph and adapted to the new way of tagging unobserved nodes. New method hasSequence() in ProtStrucGraph and Pdb: it is important to know that from now only if hasSequence()==true we put the unobserved nodes in RIGraph, otherwise we don't put them (as before)
RIGraph.java 434 (12 years ago) by duarte: Changed behaviour of observed/unobserved nodes in RIGraph: now unobserved RIGnodes are also in the RIGraph, tagged with observed=false. Thus getObsLength() in ProtStructGraph (which by the way was not working for AIGraphs) is now only in RIGraph and adapted to the new way of tagging unobserved nodes. New method hasSequence() in ProtStrucGraph and Pdb: it is important to know that from now only if hasSequence()==true we put the unobserved nodes in RIGraph, otherwise we don't put them (as before)
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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