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Revision 651 - Directory Listing
Modified Wed May 21 18:11:02 2008 UTC (11 years, 10 months ago) by duarte
New class PhiPsiAverager to get consensus of phi/psi angles from a TemplateList and an Alignment. Tested with a few examples and seems to work. The wrapping of angles at 180/-180 is not yet taking into account, i.e. if an interval falls in the region just below 180 and just above -180, no consensus will be found.
Pdb: added some checks to methods getPhi/Psi so that it doesn't fail when there's no coordinates.
Changed yet again the design of TemplateList/Template. Now loading of PDB data happens upon call of the loadPDBdata method. Changed dependencies accordingly.
Revision 641 - Directory Listing
Modified Fri May 16 15:48:55 2008 UTC (11 years, 10 months ago) by stehr
added option to GraphAverager and averageGraph to create dummy sequence with length of alignment to view the overlaid graphs without mapping to a target sequence
Revision 613 - Directory Listing
Modified Mon May 5 14:05:06 2008 UTC (11 years, 11 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, 11 months ago) by duarte
Added some more error output
Revision 546 - Directory Listing
Modified Wed Feb 20 15:53:51 2008 UTC (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 1 month 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 (12 years, 2 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 (12 years, 3 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 (12 years, 3 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 (12 years, 4 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