Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (9 years, 1 month 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 1084 - Directory Listing
Modified Mon May 31 13:38:56 2010 UTC (9 years, 9 months ago) by matt4077

renamed  conflicting ContactMap class.

Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (9 years, 11 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, 11 months ago) by hstehr
Copied from: trunk/src/sadp 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, 11 months ago) by hstehr
Original Path: trunk/src/sadp

refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core

Revision 958 - Directory Listing
Modified Fri Feb 12 15:22:36 2010 UTC (10 years ago) by duarte
Original Path: trunk/src/sadp

Moved Interval* and IntPair* classes to tools package

Revision 951 - Directory Listing
Modified Fri Jan 29 16:12:34 2010 UTC (10 years, 1 month ago) by duarte
Original Path: trunk/src/sadp
Copied from: trunk/sadp 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 501 - Directory Listing
Modified Tue Jan 8 10:04:46 2008 UTC (12 years, 1 month ago) by duarte
Original Path: trunk/sadp

Changed implementation of Alignment: now based on indices rather than tags. Interface remains mostly the same

Revision 492 - Directory Listing
Modified Wed Jan 2 13:18:57 2008 UTC (12 years, 1 month ago) by duarte
Original Path: trunk/sadp
Copied from: branches/aglappe-jung/sadp revision 491

Copied the aglappe-jung branch into trunk.

Revision 450 - Directory Listing
Modified Tue Dec 4 15:21:35 2007 UTC (12 years, 2 months ago) by lpetzo
Original Path: branches/aglappe-jung/sadp

... some more comments

Revision 449 - Directory Listing
Modified Tue Dec 4 15:20:15 2007 UTC (12 years, 2 months ago) by lpetzo
Original Path: branches/aglappe-jung/sadp

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 (12 years, 3 months ago) by duarte
Original Path: branches/aglappe-jung/sadp

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 (12 years, 3 months ago) by duarte
Original Path: branches/aglappe-jung/sadp

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 (12 years, 3 months ago) by duarte
Original Path: branches/aglappe-jung/sadp

Re-branching for JUNG2 development

Revision 416 - Directory Listing
Modified Thu Nov 22 11:18:28 2007 UTC (12 years, 3 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 (12 years, 3 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, 4 months 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, 4 months 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, 5 months ago) by lpetzo
Original Path: trunk/sadp

initial version of sadp