Revision
811 -
Directory Listing
Modified
Thu Nov 27 15:11:53 2008 UTC
(12 years, 1 month 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
(12 years, 1 month 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
(12 years, 2 months ago)
by
filippis
white TO talyn
Revision
760 -
Directory Listing
Modified
Wed Sep 24 18:18:53 2008 UTC
(12 years, 3 months 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
(12 years, 3 months 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
(12 years, 3 months 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
(12 years, 5 months ago)
by
stehr
added a comment line
Revision
698 -
Directory Listing
Modified
Tue Jul 15 10:11:23 2008 UTC
(12 years, 6 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
(12 years, 6 months ago)
by
duarte
Made voteThreshold and angleInterval global.
Improved comments
Revision
690 -
Directory Listing
Modified
Fri Jun 20 17:22:31 2008 UTC
(12 years, 7 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
(12 years, 7 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
(12 years, 7 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
(12 years, 7 months ago)
by
stehr
added boolean parameter 'showSequence' to Alignment.writeSecStructMatching()
Revision
673 -
Directory Listing
Modified
Mon May 26 18:13:29 2008 UTC
(12 years, 7 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
(12 years, 7 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
(12 years, 7 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
(12 years, 8 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
(12 years, 8 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
(12 years, 8 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
(12 years, 8 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
(12 years, 8 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
(12 years, 8 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
(12 years, 8 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
(12 years, 8 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
(12 years, 8 months ago)
by
duarte
Added some more error output
Revision
546 -
Directory Listing
Modified
Wed Feb 20 15:53:51 2008 UTC
(12 years, 11 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
(12 years, 11 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
(12 years, 11 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
(13 years 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
459 -
Directory Listing
Added
Thu Dec 6 15:05:43 2007 UTC
(13 years, 1 month 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