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Revision 811 - Directory Listing
Modified Thu Nov 27 15:11:53 2008 UTC (10 years, 9 months ago) by duarte
New options -e and -i in reconstruct (for forcing angle constraints)
Revision 810 - Directory Listing
Modified Thu Nov 27 13:50:14 2008 UTC (10 years, 9 months ago) by duarte
Two new statics: to get phi/psi constraints for intervals of one given structure.
Revision 788 - Directory Listing
Modified Mon Nov 3 15:13:59 2008 UTC (10 years, 10 months ago) by filippis
white TO talyn
Revision 760 - Directory Listing
Modified Wed Sep 24 18:18:53 2008 UTC (11 years ago) by duarte
Rewrote the secondary structure handling in Alignment. Also changed first parameter in writeFasta to be a PrintStream not an OutputStream
Revision 759 - Directory Listing
Modified Wed Sep 24 15:59:30 2008 UTC (11 years ago) by duarte
Added printing of pairwise alignment when checkSequnces fail for target sequence
Revision 758 - Directory Listing
Modified Wed Sep 24 15:27:48 2008 UTC (11 years ago) by duarte
GraphAverager: got rid of redundant code in countVotes. Changed signature of one of the constructors: now requires target sequence.
averageGraph: adapted accordingly
Alignment: new method removeSequence (untested), fixed some docs
Revision 708 - Directory Listing
Modified Thu Jul 31 09:44:35 2008 UTC (11 years, 1 month ago) by stehr
added a comment line
Revision 698 - Directory Listing
Modified Tue Jul 15 10:11:23 2008 UTC (11 years, 2 months ago) by duarte
Fixed bug: now PhiPsiAverager behaves like GraphAverager:  consensus is on templates agreeing out of potential templates (non-gaps) instead of out of total number of templates.
Revision 697 - Directory Listing
Modified Fri Jul 11 16:34:22 2008 UTC (11 years, 2 months ago) by duarte
Made voteThreshold and angleInterval global.
Improved comments
Revision 690 - Directory Listing
Modified Fri Jun 20 17:22:31 2008 UTC (11 years, 3 months ago) by duarte
Changed the type used for the set of template graphs/pdbs from arrays to TemplateList. Now the loading of pdb data and getting the graphs is done by TemplateList.
Revision 688 - Directory Listing
Modified Fri Jun 20 14:13:16 2008 UTC (11 years, 3 months ago) by duarte
Fixed bugs in averageGraph:
- output of benchmark statistics and pairwise comparison was overlapping
- benchmark mode was broken after introduction of align mode (when no sequence file given we were always creating dummy sequence in both align or benchmark modes)

Improved:
- better handling of modes through mode variable that takes 1 of 3 states
- better input check
- in align mode now calling another GraphAverager constructor instead of creating dummy seq/tag within averageGraph
- changed constructor in GraphAverager: now sequence not a parameter, instead taken from alignment. Check for input moved down to averageGraph
- now allowing alignments that contain other sequences than the target and the templates
- new exception GraphAveragerError thrown in GraphAverager constructor when sequences of alignment and templates don't match
Revision 683 - Directory Listing
Modified Fri May 30 13:49:33 2008 UTC (11 years, 3 months ago) by duarte
Fixed bug: PhiPsiAverager was not working at all for single template case. 
Fixed bug: in ConsensusInterval changed MARGIN value to 2, for cases where max=min to make sure we pass an Interval bigger than 0 to tinker.
Revision 677 - Directory Listing
Modified Wed May 28 13:29:07 2008 UTC (11 years, 3 months ago) by stehr
added boolean parameter 'showSequence' to Alignment.writeSecStructMatching()
Revision 673 - Directory Listing
Modified Mon May 26 18:13:29 2008 UTC (11 years, 4 months ago) by duarte
Important change: now final interval taken for restraints is not anymore of size angleInterval, but simply goes from min to max.
Revision 671 - Directory Listing
Modified Mon May 26 13:43:24 2008 UTC (11 years, 4 months ago) by duarte
Introduced some more useful debugging output in the main method: phi/psi of target (if one is avalable from a reconstruction) is also printed.
Revision 667 - Directory Listing
Modified Fri May 23 16:04:48 2008 UTC (11 years, 4 months ago) by duarte
Fixed (hopefuly) the issue of wrapping angles (at -180,180). Tested minimally and seems fine.
Revision 662 - Directory Listing
Modified Thu May 22 16:55:39 2008 UTC (11 years, 4 months ago) by duarte
Fixed bug: algorithm to find consensus was not working correctly. We weren't taking in account the 2-dimensionality of the problem. Changed the approach completely, new algorithm.
Made the ConsensusInterval class a separate class and added new class ConsensusSquare to represent a phi/psi angle consensus region.
Revision 659 - Directory Listing
Modified Thu May 22 13:00:05 2008 UTC (11 years, 4 months ago) by stehr
Also adding caspParents member to graph classes, value will be kept from Pdb if present; adding method to GraphAverager to retrieve the most frequently used parents specified in the templates
Revision 654 - Directory Listing
Modified Thu May 22 10:22:59 2008 UTC (11 years, 4 months ago) by stehr
added new mode of averaging without consensus threshold but specifiying the number of contacts to be predicted and picking starting from highest consensus down
Revision 653 - Directory Listing
Modified Thu May 22 10:02:53 2008 UTC (11 years, 4 months ago) by duarte
IntervalCandidate not Comparable anymore, finding max is now done with a specific Comparator. Additionally it now extends Interval so we can use the Interval type for the final public output.
Revision 652 - Directory Listing
Modified Thu May 22 08:26:29 2008 UTC (11 years, 4 months 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 (11 years, 4 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, 4 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, 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, 7 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, 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 (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