Revision 492 - (view) (annotate) - [select for diffs]
Modified Wed Jan 2 13:18:57 2008 UTC (16 years, 8 months ago) by duarte
File length: 6617 byte(s)
Copied from: branches/aglappe-jung/genGraph.java revision 491
Diff to previous 441

Copied the aglappe-jung branch into trunk.

Revision 441 - (view) (annotate) - [select for diffs]
Modified Thu Nov 29 15:19:37 2007 UTC (16 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/genGraph.java
File length: 6617 byte(s)
Diff to previous 431

Now Pdb constructors don't load data but rather intialise the pdbCode, loading occurs upon call of load(pdbChainCode,modelSerial)
New methods getChains() and getModels() in all Pdb classes
New Exception PdbLoadError
New tester for getChains and getModels: testGetChains
Changed all calls to Pdb construction accordingly (includes changing excpetions)

Revision 431 - (view) (annotate) - [select for diffs]
Modified Tue Nov 27 08:48:28 2007 UTC (16 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/genGraph.java
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
Original Path: branches/aglappe-jung/genGraph.java
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
Original Path: branches/aglappe-jung/genGraph.java
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
Original Path: branches/aglappe-jung/genGraph.java
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
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
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
File length: 6413 byte(s)

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