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
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
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