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Revision 1399 - Directory Listing
Modified Tue May 24 09:06:15 2011 UTC (8 years, 6 months ago) by jmduarteg
Improved PDB file writing: now writing SEQRES lines and fixed some formatting issues with long atom names (i.e. CL, NA,...)
Revision 1392 - Directory Listing
Modified Thu May 19 14:27:50 2011 UTC (8 years, 6 months ago) by jmduarteg
MAJOR CHANGE: now able to read and treat properly HETATMS and nucleotides from PDB entries. All tests pass. Anyway surely there will be some bugs to iron out still.
Revision 1372 - Directory Listing
Modified Wed Mar 30 09:55:49 2011 UTC (8 years, 8 months ago) by jmduarteg
MAJOR INTERFACE CHANGE: the main PDB data loading interface has changed. Now all loading of data occurs through PdbAsymUnit. Refactoring of some classes: Pdb is now PdbChain.
Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (8 years, 9 months ago) by jmduarteg
Renamed xxxxError classes to xxxxException as they should be.
Revision 1316 - Directory Listing
Modified Wed Feb 9 15:55:49 2011 UTC (8 years, 9 months ago) by jmduarteg
Got rid (finally!) of AAinfo. Its functionality is now in ContactType and AminoAcid.
Revision 1314 - Directory Listing
Modified Wed Feb 9 11:36:04 2011 UTC (8 years, 9 months ago) by jmduarteg
Finally got rid of all duplicated amino acid methods in AAinfo. Now everything unified in AminoAcid enum.
Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (8 years, 10 months 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 1245 - Directory Listing
Modified Thu Sep 30 10:44:38 2010 UTC (9 years, 2 months ago) by gmueller
does most of the job SparseMatrix did before
Revision 1243 - Directory Listing
Modified Thu Sep 30 08:34:46 2010 UTC (9 years, 2 months ago) by gmueller
some methods removed and added to a new class, other simplified
Revision 1240 - Directory Listing
Modified Tue Sep 21 12:12:07 2010 UTC (9 years, 2 months ago) by hstehr
suppressing two warnings
Revision 1239 - Directory Listing
Modified Tue Sep 21 12:01:35 2010 UTC (9 years, 2 months ago) by gmueller
sparse matrix exception
Revision 1227 - Directory Listing
Modified Tue Sep 7 09:47:02 2010 UTC (9 years, 3 months ago) by gmueller
new methods added
-method, takes care of row and column index maps (refreshMatrix())
-methods, adding or removing entries, without refreshing index mapping
-norm methods(norm1(), norm2(), normInf()) as well as a special innerProduct() method

Revision 1220 - Directory Listing
Modified Wed Sep 1 14:20:44 2010 UTC (9 years, 3 months ago) by hstehr
deleting two classes which were making problems
Revision 1202 - Directory Listing
Modified Thu Aug 19 10:21:08 2010 UTC (9 years, 3 months ago) by hstehr
suppress "method not used" warning
Revision 1018 - Directory Listing
Modified Fri Apr 9 10:40:29 2010 UTC (9 years, 7 months ago) by hstehr
removing a warning in owl.embed.contactmaps.Demes
Revision 1016 - Directory Listing
Modified Fri Apr 9 09:18:35 2010 UTC (9 years, 7 months ago) by jmduarteg
Added a supresswarnings tag (it's simply unused code)
Revision 1015 - Directory Listing
Modified Fri Apr 9 09:16:04 2010 UTC (9 years, 7 months ago) by jmduarteg
Fixed import (was a compile error)
Revision 1014 - Directory Listing
Modified Thu Apr 8 16:34:26 2010 UTC (9 years, 8 months ago) by gmueller
cone peeling algorithm as implemented in sathyas classes, does not contain any public constructors, must use public statics
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (9 years, 8 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
Added Wed Mar 31 13:27:18 2010 UTC (9 years, 8 months ago) by hstehr
refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl