Revision
546 -
Directory Listing
Modified
Wed Feb 20 15:53:51 2008 UTC
(16 years, 8 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
(16 years, 9 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
(16 years, 9 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
(16 years, 10 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
459 -
Directory Listing
Added
Thu Dec 6 15:05:43 2007 UTC
(16 years, 11 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
