Revision 517 - (view) (annotate) - [select for diffs]
Modified Tue Jan 15 13:19:36 2008 UTC (16 years, 10 months ago) by duarte
File length: 2437 byte(s)
Diff to previous 492

Changed Alignment class so that both alignment and sequence indexing are starting at 1 (before alignment indices were starting at 0). Also mapping is now done through arrays not maps.
Changed all other classes using Alignment to accommodate this. 
NOTE: graph averaging hasn't been tested after the change

Revision 492 - (view) (annotate) - [selected]
Modified Wed Jan 2 13:18:57 2008 UTC (16 years, 10 months ago) by duarte
File length: 2168 byte(s)
Copied from: branches/aglappe-jung/testDeltaDistanceMap.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, 11 months ago) by duarte
Original Path: branches/aglappe-jung/testDeltaDistanceMap.java
File length: 2168 byte(s)
Diff to previous 420 , to selected 492

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 420 - (view) (annotate) - [select for diffs]
Modified Thu Nov 22 17:27:44 2007 UTC (16 years, 11 months ago) by duarte
Original Path: branches/aglappe-jung/testDeltaDistanceMap.java
File length: 2140 byte(s)
Diff to previous 419 , to selected 492

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, 11 months ago) by duarte
Original Path: branches/aglappe-jung/testDeltaDistanceMap.java
File length: 2044 byte(s)
Diff to previous 327 , to selected 492

Re-branching for JUNG2 development

Revision 327 - (view) (annotate) - [select for diffs]
Modified Mon Oct 1 08:23:57 2007 UTC (17 years, 1 month ago) by stehr
File length: 2044 byte(s)
Diff to previous 321 , to selected 492

fixed missing references to constants in class AA

Revision 321 - (view) (annotate) - [select for diffs]
Added Tue Sep 18 08:44:30 2007 UTC (17 years, 2 months ago) by stehr
File length: 2120 byte(s)
Diff to selected 492

added test program for difference distance maps, updated Manifest to v0.8.5