Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (10 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 1084 - Directory Listing
Modified Mon May 31 13:38:56 2010 UTC (10 years, 7 months ago) by matt4077

renamed  conflicting ContactMap class.

Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (10 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 (10 years, 9 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 (10 years, 9 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, 11 months 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, 11 months 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 (13 years 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 (13 years 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 (13 years, 1 month 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 (13 years, 1 month 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 (13 years, 2 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 (13 years, 2 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 (13 years, 2 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 (13 years, 2 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 (13 years, 2 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 (13 years, 3 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 (13 years, 3 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 (13 years, 4 months ago) by lpetzo
Original Path: trunk/sadp

initial version of sadp