Revision 537 - Directory Listing
Modified Wed Feb 13 18:29:05 2008 UTC (16 years, 7 months ago) by duarte

Fixed another bug in GraphAverager. Was still not working correctly: was putting edges twice in the final graph. 
Also now handling correctly graph averaging for directed or undirected graphs.

Revision 536 - Directory Listing
Modified Wed Feb 13 17:44:40 2008 UTC (16 years, 7 months ago) by duarte

Fixed GraphAverager: wasn't working since we introduced JUNG. 
Also added some better output in checkSequences() when sequence don't match between alignment/graphs. Now we take the 2 sequences calculate a pairwise alignment (using jaligner) and output it. This is useful for picking up unobserves and similars.

Revision 517 - Directory Listing
Modified Tue Jan 15 13:19:36 2008 UTC (16 years, 8 months ago) by duarte

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 - Directory Listing
Modified Wed Jan 2 13:18:57 2008 UTC (16 years, 8 months ago) by duarte
Copied from: branches/aglappe-jung/graphAveraging revision 491

Copied the aglappe-jung branch into trunk.

Revision 483 - Directory Listing
Modified Wed Dec 19 14:25:30 2007 UTC (16 years, 9 months ago) by stehr
Original Path: branches/aglappe-jung/graphAveraging

added methods to calculate and filter by consensus scores

Revision 459 - Directory Listing
Added Thu Dec 6 15:05:43 2007 UTC (16 years, 9 months ago) by stehr
Original Path: branches/aglappe-jung/graphAveraging

moved GraphAverager to subpackage, added removeVertex function to RIGraph and AIGraph, added getEdgeFromSerials and containsEdgeIJ functions to ProtStructGraph