 ../
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AAinfo.java
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438
(12 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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AIGEdge.java
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438
(12 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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AIGNode.java
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438
(12 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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AIGraph.java
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465
(12 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
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Alignment.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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AlignmentConstructionError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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Box.java
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438
(12 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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CatalSiteSet.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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CatalyticSite.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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CiffileFormatError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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CiffilePdb.java
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470
(12 years ago)
by stehr:
Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
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ConformationsNotSameSizeError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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ContactType.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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DbRIGraph.java
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469
(12 years ago)
by duarte:
Fixed potentially dangerous bug: was constructing edges wrongly!: with i residue number as the weight!
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EC.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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ECRegion.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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FastaFileFormatError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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FileFormatError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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FileRIGraph.java
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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
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GraphFileFormatError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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GraphIODb.java
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477
(12 years ago)
by duarte:
Adapted IO methods in NodesAndEdges to JUNG framework:
added 2 classes:
- GraphIODb: does reading and writing a Graph<V,E> from/to database
- GraphIOGDLFile: does writing of a Graph<V,E> to GDL file for aiSee exporting
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GraphIOGDLFile.java
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477
(12 years ago)
by duarte:
Adapted IO methods in NodesAndEdges to JUNG framework:
added 2 classes:
- GraphIODb: does reading and writing a Graph<V,E> from/to database
- GraphIOGDLFile: does writing of a Graph<V,E> to GDL file for aiSee exporting
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GraphIdNotFoundError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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IntPairComparator.java
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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
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IntPairSet.java
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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
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Interval.java
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472
(12 years ago)
by lpetzo:
new function: createSelectionString(TreeSet<Integer>)
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IntervalSet.java
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465
(12 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
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MaxClusterRunner.java
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475
(12 years ago)
by duarte:
Now maxcluster ranking works in all cases.
Fixed some bugs and tested for both rmsd and gdt
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MsdsdInconsistentResidueNumbersError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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MsdsdPdb.java
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470
(12 years ago)
by stehr:
Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
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NbhProbDistribution.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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NbhoodBackgrnd.java
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468
(12 years ago)
by duarte:
Fixed bug: now assigning frequency 0 to case where countTotal=0 (no observations)
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PairwiseAlignmentConverter.java
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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
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PairwiseAlignmentGraphConverter.java
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441
(12 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)
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PairwiseSequenceAlignment.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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Pdb.java
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470
(12 years ago)
by stehr:
Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
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PdbChainCodeNotFoundError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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PdbCodeNotFoundError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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PdbLoadError.java
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441
(12 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)
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PdbaseInconsistencyError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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PdbasePdb.java
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470
(12 years ago)
by stehr:
Pdb objects now return strictly PdbLoadErrors (before, GetterErrors were thrown)
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PdbfileFormatError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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PdbfilePdb.java
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478
(12 years ago)
by lpetzo:
if the pdb file contains SEQRES records we do not allow the sequence length to be shorter than the full-length of the graph. otherwise a PdbfileFormatError is thrown in function read_data_from_file()
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PirFileFormatError.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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PredEval.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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ProtStructGraph.java
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465
(12 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
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RIGCommonNbhood.java
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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)
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RIGEdge.java
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438
(12 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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RIGNbhood.java
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454
(12 years ago)
by duarte:
Fixed bug: getCommaSeparatedResSerials was failing when there was 0 neighbors
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RIGNode.java
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452
(12 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
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RIGraph.java
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463
(12 years ago)
by duarte:
Minor change: comments
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Scop.java
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465
(12 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
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ScopRegion.java
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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SecStrucElement.java
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455
(12 years ago)
by duarte:
Minor change : fixed comments
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SecondaryStructure.java
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423
(12 years ago)
by duarte:
New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework
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aapairsBounds.dat
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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contactTypes.dat
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419
(12 years ago)
by duarte:
Re-branching for JUNG2 development
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