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Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (9 years ago) by jmduarteg
Renaming all xxxxError named exceptions to xxxxException. Long overdue thing (was historical because it came from python). Learnt just recently that java does have a concept of Error too.
Revision 1170 - Directory Listing
Modified Wed Aug 4 10:43:52 2010 UTC (9 years, 5 months ago) by hstehr
adding secondary structure functions to RIGEnsemble and GraphAverager: GraphAverager can now use DSSP to get consensus secondary structure from underlying structures.
Revision 1066 - Directory Listing
Modified Wed May 12 12:00:11 2010 UTC (9 years, 8 months ago) by hstehr
new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()
Revision 1064 - Directory Listing
Modified Tue May 11 14:57:20 2010 UTC (9 years, 8 months ago) by hstehr
fixed a bug in GraphAverager.getGraphWithTopContacts() which caused a null pointer exception in jung.SparseGraph.addEdge(), this may even be a bug in jung
Revision 1063 - Directory Listing
Modified Mon May 10 10:23:03 2010 UTC (9 years, 8 months ago) by stehr
Creating constructor which was apparently lost during some previous refactoring but which was needed by class cccp.testGraphAverager
Revision 1047 - Directory Listing
Modified Mon Apr 26 16:13:36 2010 UTC (9 years, 9 months ago) by jmduarteg
SecondaryStructure now implements Iterable after refactoring of getIterator
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (9 years, 9 months ago) by hstehr
refactoring: moved many many classes to more appropriate packages; created new packages owl.core.sequence.alignment, owl.core.structure.alignment, owl.core.structure.features
Revision 1007 - Directory Listing
Modified Wed Mar 31 13:27:18 2010 UTC (9 years, 9 months ago) by hstehr
Copied from: trunk/src/graphAveraging revision 1005
refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
Revision 1005 - Directory Listing
Modified Wed Mar 31 12:29:26 2010 UTC (9 years, 9 months ago) by hstehr
Original Path: trunk/src/graphAveraging
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Revision 1000 - Directory Listing
Modified Mon Mar 29 10:20:38 2010 UTC (9 years, 10 months ago) by jmduarteg
Original Path: trunk/src/graphAveraging
Now DsspRunner is purely static (makes more sense)
Revision 988 - Directory Listing
Modified Thu Mar 18 12:02:13 2010 UTC (9 years, 10 months ago) by jmduarteg
Original Path: trunk/src/graphAveraging
Moved dssp runner out of Pdb to its own class. New test for runDssp in PdbTest.

Revision 968 - Directory Listing
Modified Mon Feb 22 16:03:45 2010 UTC (9 years, 11 months ago) by duarte
Original Path: trunk/src/graphAveraging
Updated make-aglappe script (and renamed to make-owl).
Changed aglappe strings to OWL (following new name of library)
Revision 958 - Directory Listing
Modified Fri Feb 12 15:22:36 2010 UTC (9 years, 11 months ago) by duarte
Original Path: trunk/src/graphAveraging
Moved Interval* and IntPair* classes to tools package
Revision 951 - Directory Listing
Modified Fri Jan 29 16:12:34 2010 UTC (9 years, 11 months ago) by duarte
Original Path: trunk/src/graphAveraging
Copied from: trunk/graphAveraging revision 949
Reorganised the project with a src folder for java source files.
Added a jars dir with all jars needed for the project.
Added .project and .classpath pointing to relative path of jars. 
The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.
Revision 811 - Directory Listing
Modified Thu Nov 27 15:11:53 2008 UTC (11 years, 2 months ago) by duarte
Original Path: trunk/graphAveraging
New options -e and -i in reconstruct (for forcing angle constraints)
Revision 810 - Directory Listing
Modified Thu Nov 27 13:50:14 2008 UTC (11 years, 2 months ago) by duarte
Original Path: trunk/graphAveraging
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 (11 years, 2 months ago) by filippis
Original Path: trunk/graphAveraging
white TO talyn
Revision 760 - Directory Listing
Modified Wed Sep 24 18:18:53 2008 UTC (11 years, 4 months ago) by duarte
Original Path: trunk/graphAveraging
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, 4 months ago) by duarte
Original Path: trunk/graphAveraging
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, 4 months ago) by duarte
Original Path: trunk/graphAveraging
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, 5 months ago) by stehr
Original Path: trunk/graphAveraging
added a comment line
Revision 698 - Directory Listing
Modified Tue Jul 15 10:11:23 2008 UTC (11 years, 6 months ago) by duarte
Original Path: trunk/graphAveraging
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, 6 months ago) by duarte
Original Path: trunk/graphAveraging
Made voteThreshold and angleInterval global.
Improved comments
Revision 690 - Directory Listing
Modified Fri Jun 20 17:22:31 2008 UTC (11 years, 7 months ago) by duarte
Original Path: trunk/graphAveraging
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, 7 months ago) by duarte
Original Path: trunk/graphAveraging
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, 7 months ago) by duarte
Original Path: trunk/graphAveraging
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, 8 months ago) by stehr
Original Path: trunk/graphAveraging
added boolean parameter 'showSequence' to Alignment.writeSecStructMatching()
Revision 673 - Directory Listing
Modified Mon May 26 18:13:29 2008 UTC (11 years, 8 months ago) by duarte
Original Path: trunk/graphAveraging
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, 8 months ago) by duarte
Original Path: trunk/graphAveraging
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, 8 months ago) by duarte
Original Path: trunk/graphAveraging
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, 8 months ago) by duarte
Original Path: trunk/graphAveraging
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, 8 months ago) by stehr
Original Path: trunk/graphAveraging
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, 8 months ago) by stehr
Original Path: trunk/graphAveraging
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, 8 months ago) by duarte
Original Path: trunk/graphAveraging
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, 8 months ago) by duarte
Original Path: trunk/graphAveraging
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, 8 months ago) by duarte
Original Path: trunk/graphAveraging
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, 8 months ago) by stehr
Original Path: trunk/graphAveraging
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, 8 months ago) by stehr
Original Path: trunk/graphAveraging
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, 8 months ago) by duarte
Original Path: trunk/graphAveraging
Added some more error output
Revision 546 - Directory Listing
Modified Wed Feb 20 15:53:51 2008 UTC (11 years, 11 months ago) by duarte
Original Path: trunk/graphAveraging
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, 11 months ago) by duarte
Original Path: trunk/graphAveraging
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, 11 months ago) by duarte
Original Path: trunk/graphAveraging
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 ago) by duarte
Original Path: trunk/graphAveraging
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 ago) by duarte
Original Path: trunk/graphAveraging
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, 1 month 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, 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