 ../
|
actionTools/
|
437
(16 years ago)
by lpetzo:
an abstract getter
|
|
proteinstructure/
|
438
(16 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
|
|
sadp/
|
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
|
|
tinker/
|
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)
|
|
tools/
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
Manifest.txt
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
benchmarkGraphAlgorithm.java
|
424
(16 years ago)
by duarte:
Added last i/o method from old Graph (write to file in Ioannis network format)
Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods
Fixed the write_graph_to_file method name in executables in default package
|
|
calculateGridDensity.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
cnCoarseNbhood.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
cnEvalTargetNbhood.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
cnHashIterNbhood.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
cnex1.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
compareCMs.java
|
423
(16 years ago)
by duarte:
New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework
|
|
createGraphDb.sh
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
genDbGraph.java
|
438
(16 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
|
|
genGraph.java
|
431
(16 years ago)
by duarte:
Fixed bug: was not working with crossed contacts (with "/") because the "/" was not allowed in file names. Now replacing / with :
|
|
hashIterNbhood.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
iterEvalNbhood.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
iterateNbhood.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
iterateNbs.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
iterateUpperNbhood.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
iterateUpperNbs.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
listInfoGain.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
listInfoLoss.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
makeNbhTbl.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
maxInfoGain.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
minInfoGain.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
reconstruct.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)
|
|
rewriteNBHood.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
rewriteNBHood_parallel.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
runGenDbGraph.sh
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
scoreTargetMoves.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
testClusterConnection.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
testDeltaDistanceMap.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)
|
|
testGraph2Pml.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
testGraphAverager.java
|
424
(16 years ago)
by duarte:
Added last i/o method from old Graph (write to file in Ioannis network format)
Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods
Fixed the write_graph_to_file method name in executables in default package
|
|
testGraphClustering.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
testJUNGframework.java
|
430
(16 years ago)
by duarte:
Fixed tester after changes in getAllCommonNnhSizes
|
|
testMySQLConnection.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
testPdb.java
|
424
(16 years ago)
by duarte:
Added last i/o method from old Graph (write to file in Ioannis network format)
Using now the more correct degree, indegree, outdegree methods instead of count neighbor methods
Fixed the write_graph_to_file method name in executables in default package
|
|
testPyMol.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
testPymolServer.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
|
testResidueSelectionString.java
|
422
(16 years ago)
by duarte:
Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.
|
|
writeTargetMoves.java
|
419
(16 years ago)
by duarte:
Re-branching for JUNG2 development
|
