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Revision 613 - Directory Listing
Modified Mon May 5 14:05:06 2008 UTC (11 years, 4 months ago) by stehr
Changed behaviour of graphAverager: Now evaluating consensus threshold based only on edges that could really exist (i.e. both ends map to non-gaps) rather than simple count of templates. The old behaviour can be restored (for comparison) by setting legacyMode=true in getAverageGraph() and getConsensusGraph().
Revision 611 - Directory Listing
Modified Wed Apr 30 17:45:06 2008 UTC (11 years, 4 months ago) by duarte
Added some more error output
Revision 546 - Directory Listing
Modified Wed Feb 20 15:53:51 2008 UTC (11 years, 6 months ago) by duarte
New feature in GraphAverager: method to write the voters together with the edges; new constructor taking a RIGEnsemble
Fixed bug in RIGEnsemble: was not working for cif files.
Added a graph averaging output to main() in RIGEnsemble

Revision 537 - Directory Listing
Modified Wed Feb 13 18:29:05 2008 UTC (11 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 (11 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 (11 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 (11 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 (11 years, 8 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 (11 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