Revision 431 - (view) (annotate) - [select for diffs]
Modified Tue Nov 27 08:48:28 2007 UTC (16 years, 10 months ago) by duarte
File length: 6909 byte(s)
Diff to previous 424

Fixed bug: was not working with crossed contacts (with "/") because the "/" was not allowed in file names. Now replacing / with :

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: 6774 byte(s)
Diff to previous 420

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 420 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 17:27:44 2007 UTC (16 years, 10 months ago) by duarte
File length: 6758 byte(s)
Diff to previous 419

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 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 14:09:18 2007 UTC (16 years, 10 months ago) by duarte
File length: 6769 byte(s)
Diff to previous 396

Re-branching for JUNG2 development

Revision 396 - (view) (annotate) - [select for diffs]
Modified Thu Nov 8 15:01:04 2007 UTC (16 years, 10 months ago) by filippis
Original Path: trunk/genGraph.java
File length: 6769 byte(s)
Diff to previous 285

Added mode option in genDbGraph whether to find and store info for the residues (SCOP,NACCESS,EC,CSA,...)

Revision 285 - (view) (annotate) - [select for diffs]
Modified Thu Aug 16 15:10:11 2007 UTC (17 years, 1 month ago) by duarte
Original Path: trunk/genGraph.java
File length: 6642 byte(s)
Diff to previous 277

Fixed a few bugs in reading of list file
Better output and error messages

Revision 277 - (view) (annotate) - [select for diffs]
Added Tue Aug 14 10:54:24 2007 UTC (17 years, 1 month ago) by duarte
Original Path: trunk/genGraph.java
File length: 6413 byte(s)

New script genGraph (generates graph to files)
Better error messages in both