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Revision 449 - Directory Listing
Modified Tue Dec 4 15:20:15 2007 UTC (11 years, 10 months ago) by lpetzo
Johannes provided us we the debugged version of noncrossing(), kept the old version for sentimental reason as noncrossing_()
Revision 426 - Directory Listing
Modified Fri Nov 23 18:04:15 2007 UTC (11 years, 11 months ago) by duarte
Now PairWiseAlignmentConverter and PairwiseAlignmentGraphConverter work in the new JUNG framework.
New class IntPairComparator
Now sorting output in RIGraph.write_graph_to_file
Revision 420 - Directory Listing
Modified Thu Nov 22 17:27:44 2007 UTC (11 years, 11 months ago) by duarte
First implementation of the new graph framework using JUNG2. Still a few classes to fix, but all basic functionality is there.
NOTE: at the moment ProtStructGraph is a SparseGraph which doesn't guarantee that the graph has no parallel or loop edges (I thought that would be solved by using the SimpleGraph interface but it doesn't, that's only a marker interface)
Revision 419 - Directory Listing
Modified Thu Nov 22 14:09:18 2007 UTC (11 years, 11 months ago) by duarte
Re-branching for JUNG2 development
Revision 416 - Directory Listing
Modified Thu Nov 22 11:18:28 2007 UTC (11 years, 11 months ago) by lpetzo
Original Path: trunk/sadp
- changed the identation mode
- added some comments
Revision 386 - Directory Listing
Modified Wed Nov 7 17:35:26 2007 UTC (11 years, 11 months ago) by lpetzo
Original Path: trunk/sadp
MODIFICATIONS
-------------

class SADP:
- added exception handling stuff for exceptions thrown by class Alignment
Revision 371 - Directory Listing
Modified Thu Oct 25 15:33:49 2007 UTC (12 years ago) by lpetzo
Original Path: trunk/sadp
Class ContactMap:
- Exception ContactMapConstructionError is thrown if the construction of a contact map from a Graph object fails.
- changed method to determine the number of nodes of a graph object.
- changed method to iterate through the set of edges of the graph (though the previous version seemed to be much more efficient ...)

Class SADP:
- added some new members controlling to input order of the contact maps (preservedInputOrder)
- the progress status of the run() method is send to a Retriever object
- added getters and setter for all data member.
- implemented methods to compute the sequence alignment and the node matching
- a couple of changes in method main
Revision 370 - Directory Listing
Modified Thu Oct 25 15:19:22 2007 UTC (12 years ago) by lpetzo
Original Path: trunk/sadp
to be thrown if the construction of a contact map from a proteinstructure.Graph instance fails
Revision 316 - Directory Listing
Added Thu Sep 13 08:47:55 2007 UTC (12 years, 1 month ago) by lpetzo
Original Path: trunk/sadp
initial version of sadp