Revision 1022 - Directory Listing
Modified Sun Apr 11 17:37:12 2010 UTC (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 months ago) by cvehlow

First version of class for sphoxel computation.

Revision 1018 - Directory Listing
Modified Fri Apr 9 10:40:29 2010 UTC (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 months ago) by jmduarteg

Fixed import (was a compile error)

Revision 1014 - Directory Listing
Modified Thu Apr 8 16:34:26 2010 UTC (12 years, 2 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 (12 years, 2 months ago) by matt4077

resolving conflicts

Revision 1012 - Directory Listing
Modified Thu Apr 1 08:41:01 2010 UTC (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 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 (12 years, 2 months ago) by hstehr

starting refactoring: first creating packages owl and owl.core