Revision 1066 - Directory Listing
Modified Wed May 12 12:00:11 2010 UTC (12 years, 3 months ago) by hstehr

new methods needed for CCCP: RIGraph.addEdgeIJ(i,j,weight), RIGEnsembl.loadFromDirectory(), GraphAverager.addZeroEdges(), SecondaryStructure.print()

Revision 1062 - Directory Listing
Modified Sun May 9 21:54:40 2010 UTC (12 years, 3 months ago) by stehr

fixed a minor bug in JPredConnection; new method SecondaryStructure.getConsensusSecondaryStructure(); changed visibility of RIGEnsemble.addFile() to public

Revision 1052 - Directory Listing
Modified Tue Apr 27 16:07:48 2010 UTC (12 years, 3 months ago) by hstehr

Fixing bad bug in JPredConnection which would always load the results from my test example instead of the real one; some minor edits in RIGraph

Revision 1038 - Directory Listing
Modified Tue Apr 20 10:08:47 2010 UTC (12 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 (12 years, 4 months ago) by matt4077

adding phi/psi constraints to edges

Revision 1022 - Directory Listing
Modified Sun Apr 11 17:37:12 2010 UTC (12 years, 4 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, 4 months ago) by hstehr

adding some methods to RIGraph which are needed by CMView: discretizeByWeightCutoff(double), discretizeByNumContacts(int), getFullLength()

Revision 1017 - Directory Listing
Modified Fri Apr 9 09:42:32 2010 UTC (12 years, 4 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 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (12 years, 4 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 1006 - Directory Listing
Added Wed Mar 31 13:00:35 2010 UTC (12 years, 4 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