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Revision 437 - Directory Listing
Modified Wed Nov 28 15:43:52 2007 UTC (12 years, 7 months ago) by lpetzo
an abstract getter
Revision 435 - Directory Listing
Modified Wed Nov 28 12:11:11 2007 UTC (12 years, 7 months ago) by duarte
Reverted to unobserved RIGNodes not present in the RIGraph
Revision 434 - Directory Listing
Modified Wed Nov 28 09:34:44 2007 UTC (12 years, 7 months ago) by duarte
Changed behaviour of observed/unobserved nodes in RIGraph: now unobserved RIGnodes are also in the RIGraph, tagged with observed=false.
Thus getObsLength() in ProtStructGraph (which by the way was not working for AIGraphs) is now only in RIGraph and adapted to the new way of tagging unobserved nodes.
New method hasSequence() in ProtStrucGraph and Pdb: it is important to know that from now only if hasSequence()==true we put the unobserved nodes in RIGraph, otherwise we don't put them (as before)
Revision 433 - Directory Listing
Modified Tue Nov 27 17:58:26 2007 UTC (12 years, 7 months ago) by duarte
Added more comments

Revision 431 - Directory Listing
Modified Tue Nov 27 08:48:28 2007 UTC (12 years, 7 months ago) by duarte
Fixed bug: was not working with crossed contacts (with "/") because the "/" was not allowed in file names. Now replacing / with :
Revision 430 - Directory Listing
Modified Mon Nov 26 18:20:04 2007 UTC (12 years, 7 months ago) by duarte
Fixed tester after changes in getAllCommonNnhSizes
Revision 428 - Directory Listing
Modified Mon Nov 26 16:01:11 2007 UTC (12 years, 7 months ago) by duarte
Fixed bug: was missing last sequence element when adding gap nodes
Revision 427 - Directory Listing
Modified Mon Nov 26 15:57:37 2007 UTC (12 years, 7 months 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

Revision 426 - Directory Listing
Modified Fri Nov 23 18:04:15 2007 UTC (12 years, 7 months 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
Revision 424 - Directory Listing
Modified Fri Nov 23 14:21:33 2007 UTC (12 years, 7 months 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

Revision 423 - Directory Listing
Modified Fri Nov 23 13:37:17 2007 UTC (12 years, 7 months ago) by duarte
New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework
Revision 422 - Directory Listing
Modified Fri Nov 23 10:08:40 2007 UTC (12 years, 7 months ago) by duarte
Now selection string stuff working: transfered methods from old NodeSet to Interval as static methods.
Revision 421 - Directory Listing
Modified Thu Nov 22 19:42:11 2007 UTC (12 years, 7 months 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
Revision 420 - Directory Listing
Modified Thu Nov 22 17:27:44 2007 UTC (12 years, 7 months 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)
Revision 419 - Directory Listing
Modified Thu Nov 22 14:09:18 2007 UTC (12 years, 7 months ago) by duarte
Re-branching for JUNG2 development
Revision 418 - Directory Listing
Modified Thu Nov 22 13:59:33 2007 UTC (12 years, 7 months ago) by duarte
Deleted the branch, we are going to branch from a newer revision
Revision 415 - Directory Listing
Modified Thu Nov 22 10:19:16 2007 UTC (12 years, 7 months ago) by duarte
Branching for development of new graph framework using JUNG2
Revision 1 - Directory Listing
Added Wed Jan 18 17:48:52 2006 UTC (14 years, 5 months ago) by filippis
Initial import of tools