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r438
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contactTypes.dat 419 (11 years ago) by duarte: Re-branching for JUNG2 development
aapairsBounds.dat 419 (11 years ago) by duarte: Re-branching for JUNG2 development
SimilarityGraph.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
SecondaryStructure.java 423 (11 years ago) by duarte: New methods in RIGraph copy() and compare(other) Basic testing of copy introduced on testJUNGframework
SecStrucElement.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
ScopRegion.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
Scop.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
RIGraph.java 438 (11 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
RIGNode.java 438 (11 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
RIGNbhood.java 421 (11 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 438 (11 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
RIGCommonNbhood.java 420 (11 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 438 (11 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
PredEval.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
PirFileFormatError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
PdbfilePdb.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
PdbfileFormatError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
PdbasePdb.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
PdbaseInconsistencyError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
PdbCodeNotFoundError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
PdbChainCodeNotFoundError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
Pdb.java 438 (11 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
PairwiseSequenceAlignment.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
PairwiseAlignmentGraphConverter.java 428 (11 years ago) by duarte: Fixed bug: was missing last sequence element when adding gap nodes
PairwiseAlignmentConverter.java 426 (11 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 (11 years ago) by duarte: Re-branching for JUNG2 development
NbhProbDistribution.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
MsdsdPdb.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
MsdsdInconsistentResidueNumbersError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
MaxClusterRunner.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
IntervalSet.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
Interval.java 426 (11 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 (11 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
IntPairComparator.java 426 (11 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 (11 years ago) by duarte: Re-branching for JUNG2 development
GraphFileFormatError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
GraphAverager.java 421 (11 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 (11 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 (11 years ago) by duarte: Re-branching for JUNG2 development
FastaFileFormatError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
ECRegion.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
EC.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
DbRIGraph.java 438 (11 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
ContactType.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
ConformationsNotSameSizeError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
CiffilePdb.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
CiffileFormatError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
CatalyticSite.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
CatalSiteSet.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
Box.java 438 (11 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
AlignmentConstructionError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
Alignment.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
AIGraph.java 438 (11 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
AIGNode.java 438 (11 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
AIGEdge.java 438 (11 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
AAinfo.java 438 (11 years ago) by filippis: AAInfo -isValidContactType, isValidSingleAtomContactType, isValidMultipleAtomContactType takes into account the directionality, the overlapping atoms and the "+" -isOverlapping method has been added AIGEdge -copy method added AIGNode -equals and copy methods has been added AIGraph -getRIGraph now takes argument directed and directionality doesn't depend anymore on isCrossed -distances are now set for RIGNodes in getRIGraph -for undirected, crossed graphs we take care not to add parallel RIGedges in getRIGraph -we set now the secondaryStructure object of RIGraph in getRIGraph -addGraph has been added Box -we throw away wrong check in getDistancesWithinBox - read the comment DbRIGraph -constructors now take argument directed and directionality doesn't depend anymore on isCrossed -distances are read also from db and set for RIGEdges Pdb -get_graph now takes as argument directed and directionality doesn't depend anymore on isCrossed -there is check for forbidden cts in get_graph -cts with + are taken into account in get_graph RIGEdge -setAtomWeight and setDistance methods have been added RIGNode -equals method has been added RIGraph -getObsLength has been deleted -we take care now of the new cts (+,undirected crossed), of null secondary structure case and of distances in write_graph_to_db and write_graph_to_db_fast genDbGraph -argument for directionality is now added
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