Revision 424 - Directory Listing
Modified Fri Nov 23 14:21:33 2007 UTC (14 years, 8 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 (14 years, 8 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 (14 years, 8 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 (14 years, 8 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 (14 years, 8 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 (14 years, 8 months ago) by duarte

Re-branching for JUNG2 development

Revision 418 - Directory Listing
Modified Thu Nov 22 13:59:33 2007 UTC (14 years, 8 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 (14 years, 8 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 (16 years, 6 months ago) by filippis

Initial import of tools