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r472
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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 455 (11 years ago) by duarte: Minor change : fixed comments
ScopRegion.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
Scop.java 465 (11 years ago) by duarte: New feature: now Pdb objects can be restricted to SCOP domains New member field sid in Pdb and ProtStructGraph if Pdb/ProtStructGraph is restricted to SCOP domain
RIGraph.java 463 (11 years ago) by duarte: Minor change: comments
RIGNode.java 452 (11 years ago) by duarte: New class NbhoodBackgrnd representing a set of neighbourhoods loaded from a set of graphs of a non redundant pdb structures set. Rewrote RIGNbhood so that the TreeMap now contains also the central residue. Added methods equals() and match(). Adapted RIGraph.getNbhood to the new constructor in RIGNbhood
RIGNbhood.java 454 (11 years ago) by duarte: Fixed bug: getCommaSeparatedResSerials was failing when there was 0 neighbors
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 465 (11 years ago) by duarte: New feature: now Pdb objects can be restricted to SCOP domains New member field sid in Pdb and ProtStructGraph if Pdb/ProtStructGraph is restricted to SCOP domain
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 470 (11 years ago) by stehr: Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
PdbfileFormatError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
PdbasePdb.java 470 (11 years ago) by stehr: Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
PdbaseInconsistencyError.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
PdbLoadError.java 441 (11 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)
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 470 (11 years ago) by stehr: Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
PairwiseSequenceAlignment.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
PairwiseAlignmentGraphConverter.java 441 (11 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)
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
NbhoodBackgrnd.java 468 (11 years ago) by duarte: Fixed bug: now assigning frequency 0 to case where countTotal=0 (no observations)
NbhProbDistribution.java 419 (11 years ago) by duarte: Re-branching for JUNG2 development
MsdsdPdb.java 470 (11 years ago) by stehr: Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
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 465 (11 years ago) by duarte: New feature: now Pdb objects can be restricted to SCOP domains New member field sid in Pdb and ProtStructGraph if Pdb/ProtStructGraph is restricted to SCOP domain
Interval.java 472 (11 years ago) by lpetzo: new function: createSelectionString(TreeSet<Integer>)
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
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 469 (11 years ago) by duarte: Fixed potentially dangerous bug: was constructing edges wrongly!: with i residue number as the weight!
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 470 (11 years ago) by stehr: Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
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 465 (11 years ago) by duarte: New feature: now Pdb objects can be restricted to SCOP domains New member field sid in Pdb and ProtStructGraph if Pdb/ProtStructGraph is restricted to SCOP domain
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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