 ../
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AAinfo.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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AIGEdge.java
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420
(16 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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AIGNode.java
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420
(16 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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AIGraph.java
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421
(16 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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Alignment.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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AlignmentConstructionError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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Box.java
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421
(16 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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CatalSiteSet.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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CatalyticSite.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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CiffileFormatError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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CiffilePdb.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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ConformationsNotSameSizeError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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ContactType.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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DbRIGraph.java
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421
(16 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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EC.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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ECRegion.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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FastaFileFormatError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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FileFormatError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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FileRIGraph.java
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421
(16 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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GraphAverager.java
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421
(16 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
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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GraphIdNotFoundError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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IntPairComparator.java
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426
(16 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
(16 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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426
(16 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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IntervalSet.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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MaxClusterRunner.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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MsdsdInconsistentResidueNumbersError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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MsdsdPdb.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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NbhProbDistribution.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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NodesAndEdges.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
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PairwiseAlignmentConverter.java
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426
(16 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
|
428
(16 years ago)
by duarte:
Fixed bug: was missing last sequence element when adding gap nodes
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PairwiseSequenceAlignment.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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Pdb.java
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421
(16 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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PdbChainCodeNotFoundError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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PdbCodeNotFoundError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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PdbaseInconsistencyError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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PdbasePdb.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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PdbfileFormatError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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PdbfilePdb.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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PirFileFormatError.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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PredEval.java
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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ProtStructGraph.java
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423
(16 years ago)
by duarte:
New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework
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RIGCommonNbhood.java
|
420
(16 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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423
(16 years ago)
by duarte:
New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework
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RIGNbhood.java
|
421
(16 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
|
423
(16 years ago)
by duarte:
New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework
|
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RIGraph.java
|
427
(16 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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Scop.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
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ScopRegion.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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SecStrucElement.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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SecondaryStructure.java
|
423
(16 years ago)
by duarte:
New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework
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SimilarityGraph.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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aapairsBounds.dat
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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contactTypes.dat
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419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
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