Revision 424 - (view) (annotate) - [select for diffs]
Modified Fri Nov 23 14:21:33 2007 UTC (16 years, 10 months ago) by duarte
File length: 32650 byte(s)
Diff to previous 423

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 - (view) (annotate) - [select for diffs]
Modified Fri Nov 23 13:37:17 2007 UTC (16 years, 10 months ago) by duarte
File length: 31209 byte(s)
Diff to previous 421

New methods in RIGraph copy() and compare(other)
Basic testing of copy introduced on testJUNGframework

Revision 421 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 19:42:11 2007 UTC (16 years, 10 months ago) by duarte
File length: 27285 byte(s)
Diff to previous 420

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 - (view) (annotate) - [select for diffs]
Added Thu Nov 22 17:27:44 2007 UTC (16 years, 10 months ago) by duarte
File length: 26842 byte(s)

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)