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: 6767 byte(s)
Copied from: branches/aglappe-jung/testJUNGframework.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/testJUNGframework.java
File length: 6767 byte(s)
Diff to previous 430

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 430 - (view) (annotate) - [select for diffs]
Modified Mon Nov 26 18:20:04 2007 UTC (16 years, 10 months ago) by duarte
Original Path: branches/aglappe-jung/testJUNGframework.java
File length: 6852 byte(s)
Diff to previous 424

Fixed tester after changes in getAllCommonNnhSizes

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/testJUNGframework.java
File length: 6693 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
Original Path: branches/aglappe-jung/testJUNGframework.java
File length: 6280 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
Original Path: branches/aglappe-jung/testJUNGframework.java
File length: 5478 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
Original Path: branches/aglappe-jung/testJUNGframework.java
File length: 5390 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)