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Revision 1040 - Directory Listing
Modified Wed Apr 21 10:44:19 2010 UTC (9 years, 4 months ago) by jmduarteg
New UniprotConnection taken from Henning's structural impact project (lots of new jar dependencies with that). New EmblWSDBFetchConnection class to get sequences from EMBL web services.
Revision 1039 - Directory Listing
Modified Tue Apr 20 10:19:32 2010 UTC (9 years, 4 months ago) by cvehlow
New class gmbp for handling (saving) angle (theta-phi) ranges for certain contacts (iNum-jNum combinations);
Revision 1038 - Directory Listing
Modified Tue Apr 20 10:08:47 2010 UTC (9 years, 4 months ago) by matt4077
revert. wasn't the best idea.
Revision 1037 - Directory Listing
Modified Tue Apr 20 09:53:00 2010 UTC (9 years, 4 months ago) by matt4077
adding phi/psi constraints to edges
Revision 1036 - Directory Listing
Modified Mon Apr 19 14:27:11 2010 UTC (9 years, 4 months ago) by jmduarteg
Changed return type of addFeature to boolean to match the java Collection interface
Revision 1035 - Directory Listing
Modified Mon Apr 19 13:10:39 2010 UTC (9 years, 4 months ago) by jmduarteg
Extracted the EC data parsing code to its own connection class.
Revision 1034 - Directory Listing
Modified Mon Apr 19 12:42:21 2010 UTC (9 years, 4 months ago) by jmduarteg
Extracted Scop parsing code to its own connection class.
Revision 1033 - Directory Listing
Modified Mon Apr 19 12:26:22 2010 UTC (9 years, 4 months ago) by jmduarteg
Extracted the CSA parsing code to its own connection class.
Revision 1032 - Directory Listing
Modified Mon Apr 19 10:13:10 2010 UTC (9 years, 4 months ago) by jmduarteg
Extracted the calc-vol and calc-surf runner code to its own Runner class.
Revision 1031 - Directory Listing
Modified Mon Apr 19 10:00:34 2010 UTC (9 years, 4 months ago) by jmduarteg
Removed the PISA/PQS oligomeric state code because: a) was not used, b) PQS is obsolete, c) I'm going to redo the PISA stuff soon. Oligomeric state should be implemented as some kind of feature.
Revision 1030 - Directory Listing
Modified Mon Apr 19 09:39:07 2010 UTC (9 years, 4 months ago) by jmduarteg
Extracted constants to owl_test_paths.dat and added CASP7 fasta files to resources dir. Now BlastParsersTest should be able to run anywhere.
Revision 1029 - Directory Listing
Modified Mon Apr 19 09:01:51 2010 UTC (9 years, 4 months ago) by jmduarteg
Fixed hard-coded resources paths broken since major restructuring of project.
Revision 1028 - Directory Listing
Modified Fri Apr 16 13:21:40 2010 UTC (9 years, 5 months ago) by cvehlow
Faster SQL queries
Revision 1027 - Directory Listing
Modified Fri Apr 16 10:03:57 2010 UTC (9 years, 5 months ago) by jmduarteg
Fixed some docs and indentation
Revision 1026 - Directory Listing
Modified Thu Apr 15 15:28:29 2010 UTC (9 years, 5 months ago) by cvehlow
changes
Revision 1025 - Directory Listing
Modified Thu Apr 15 09:28:23 2010 UTC (9 years, 5 months ago) by jmduarteg
Remove hard-coded MySQL parameters. Please use always .my.cnf files for MySQL parameters!
Revision 1024 - Directory Listing
Modified Wed Apr 14 15:59:13 2010 UTC (9 years, 5 months ago) by cvehlow

Revision 1023 - Directory Listing
Modified Tue Apr 13 17:14:22 2010 UTC (9 years, 5 months ago) by cvehlow
FloatPairSet first commit
Revision 1022 - Directory Listing
Modified Sun Apr 11 17:37:12 2010 UTC (9 years, 5 months ago) by stehr
new methods in RIGEnsemble: loadFromMultiModelFile(File file, String chain), getAverageGraph(), getConsensusGraph(double weightCutoff)
Revision 1021 - Directory Listing
Modified Fri Apr 9 15:30:15 2010 UTC (9 years, 5 months ago) by hstehr
adding some methods to RIGraph which are needed by CMView: discretizeByWeightCutoff(double), discretizeByNumContacts(int), getFullLength()
Revision 1020 - Directory Listing
Modified Fri Apr 9 15:22:20 2010 UTC (9 years, 5 months ago) by cvehlow
Classes for sphoxel and nbhstraces handling. csv handling
Revision 1019 - Directory Listing
Modified Fri Apr 9 13:16:07 2010 UTC (9 years, 5 months ago) by cvehlow
First version of class for sphoxel computation.
Revision 1018 - Directory Listing
Modified Fri Apr 9 10:40:29 2010 UTC (9 years, 5 months ago) by hstehr
removing a warning in owl.embed.contactmaps.Demes
Revision 1017 - Directory Listing
Modified Fri Apr 9 09:42:32 2010 UTC (9 years, 5 months ago) by jmduarteg
New methods for random sampling a RIGraph and randomly adding noise. The code was already somewhere in the embed package but here seems more convenient.
Revision 1016 - Directory Listing
Modified Fri Apr 9 09:18:35 2010 UTC (9 years, 5 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, 5 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, 5 months ago) by gmueller
cone peeling algorithm as implemented in sathyas classes, does not contain any public constructors, must use public statics
Revision 1013 - Directory Listing
Modified Thu Apr 1 10:49:30 2010 UTC (9 years, 5 months ago) by matt4077
resolving conflicts
Revision 1012 - Directory Listing
Modified Thu Apr 1 08:41:01 2010 UTC (9 years, 5 months ago) by hstehr
bugfix: hard-coded paths to files aapairsBounds.dat and contactTypes.dat had to be updated following the refactoring (this was already fixed by previous commit); introduced proper error messags if files are not found
Revision 1011 - Directory Listing
Modified Wed Mar 31 20:21:01 2010 UTC (9 years, 5 months ago) by jmduarteg
Fixed bug introduced in refactoring: the resource path for the contact data files is hard coded in the AAinfo class. 
Revision 1010 - Directory Listing
Modified Wed Mar 31 16:05:52 2010 UTC (9 years, 5 months ago) by hstehr
refactoring: removed a warning in MultipleSequenceAlignment and deleted obsolete directory src/tests
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (9 years, 5 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 1008 - Directory Listing
Modified Wed Mar 31 14:03:27 2010 UTC (9 years, 5 months ago) by hstehr
refactoring: adapting test packages to match new package structure
Revision 1007 - Directory Listing
Modified Wed Mar 31 13:27:18 2010 UTC (9 years, 5 months ago) by hstehr
refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl
Revision 1006 - Directory Listing
Modified Wed Mar 31 13:00:35 2010 UTC (9 years, 5 months ago) by hstehr
refactoring: created packages runners.blast, runners.gromacs, structure.graphs, moved actionTools to util, structure.decoyScoring to owl.decoyScoring, tinker to runners.tinker
Revision 1005 - Directory Listing
Modified Wed Mar 31 12:29:26 2010 UTC (9 years, 5 months ago) by hstehr
refactoring: renaming proteinstructure to structure and tools to util; moving connections,features,runners,sequence,structure,util to owl.core
Revision 1004 - Directory Listing
Added Wed Mar 31 11:59:33 2010 UTC (9 years, 5 months ago) by hstehr
starting refactoring: first creating packages owl and owl.core