Revision
1084 -
Directory Listing
Modified
Mon May 31 13:38:56 2010 UTC
(12 years, 1 month ago)
by
matt4077
renamed conflicting ContactMap class.
Revision
1009 -
Directory Listing
Modified
Wed Mar 31 15:50:04 2010 UTC
(12 years, 3 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
(12 years, 3 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
(12 years, 3 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
(12 years, 4 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
(12 years, 5 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
(14 years, 5 months 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
(14 years, 6 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
(14 years, 7 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
(14 years, 7 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
(14 years, 7 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
(14 years, 7 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
(14 years, 8 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
(14 years, 8 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
(14 years, 9 months ago)
by
lpetzo
Original Path:
trunk/sadp
initial version of sadp
