Revision 652 - Directory Listing
Modified Thu May 22 08:26:29 2008 UTC (14 years ago) by duarte

Fixed bug: recenterInterval was not working: was not taking min/max correctly.
New method to get the consensus mapped onto a target sequence.

Revision 651 - Directory Listing
Modified Wed May 21 18:11:02 2008 UTC (14 years 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 (14 years 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 (14 years 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 (14 years ago) by duarte

Added some more error output

Revision 546 - Directory Listing
Modified Wed Feb 20 15:53:51 2008 UTC (14 years, 3 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 (14 years, 3 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 (14 years, 3 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 (14 years, 4 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 (14 years, 4 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 (14 years, 5 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 (14 years, 5 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