ViewVC Help
View Directory | Revision Log | Download Tarball | View Changeset | Root Listing
root/owl/branches
Sticky Revision:
Sort logs by:
Revision 430 - Directory Listing
Modified Mon Nov 26 18:20:04 2007 UTC (11 years, 10 months ago) by duarte
Fixed tester after changes in getAllCommonNnhSizes
Revision 428 - Directory Listing
Modified Mon Nov 26 16:01:11 2007 UTC (11 years, 10 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 (11 years, 10 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 (11 years, 11 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 (11 years, 11 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 (11 years, 11 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 (11 years, 11 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 (11 years, 11 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 (11 years, 11 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 (11 years, 11 months ago) by duarte
Re-branching for JUNG2 development
Revision 418 - Directory Listing
Modified Thu Nov 22 13:59:33 2007 UTC (11 years, 11 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 (11 years, 11 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 (13 years, 9 months ago) by filippis
Initial import of tools