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Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (8 years, 10 months ago) by jmduarteg
Renamed xxxxError classes to xxxxException as they should be.
Revision 1305 - Directory Listing
Modified Fri Jan 21 10:11:16 2011 UTC (9 years 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 1304 - Directory Listing
Modified Sun Jan 16 16:06:09 2011 UTC (9 years ago) by jmduarteg
Fixed important bug: we didn't model the blast data properly. A hit is composed of several hsps. Now our classes following that data model properly (before we treated a hit as an hsp).
Revision 1223 - Directory Listing
Modified Wed Sep 1 14:26:00 2010 UTC (9 years, 4 months ago) by hstehr
updated classes for evaluating our CASP predictions
Revision 1222 - Directory Listing
Modified Wed Sep 1 14:23:40 2010 UTC (9 years, 4 months ago) by hstehr
please don't check in Mac specific constants
Revision 1221 - Directory Listing
Modified Wed Sep 1 14:21:58 2010 UTC (9 years, 4 months ago) by hstehr
updating annotations to get rid of warnings
Revision 1208 - Directory Listing
Modified Mon Aug 23 12:09:34 2010 UTC (9 years, 5 months ago) by cvehlow
Scoring:KendallsTau-method added to  Statistics
Revision 1203 - Directory Listing
Modified Thu Aug 19 10:52:46 2010 UTC (9 years, 5 months ago) by hstehr
renamed class benchmarkAll to createResultWebPages
Revision 1200 - Directory Listing
Modified Thu Aug 19 10:16:06 2010 UTC (9 years, 5 months ago) by hstehr
removed some bad characters
Revision 1196 - Directory Listing
Modified Thu Aug 19 10:06:15 2010 UTC (9 years, 5 months ago) by hstehr
new class for scoring all casp7/casp8/casp9 server models in terms of GDT_TS and Acc/Cov of the contact map
Revision 1187 - Directory Listing
Modified Wed Aug 11 14:46:34 2010 UTC (9 years, 5 months ago) by cvehlow
Implementation of class for Check for Correctness of Casp server model files
Revision 1186 - Directory Listing
Modified Wed Aug 11 14:28:33 2010 UTC (9 years, 5 months ago) by cvehlow
max Cluster Path two possibilities (Mac Unix)
Revision 1185 - Directory Listing
Modified Wed Aug 11 13:34:13 2010 UTC (9 years, 5 months ago) by cvehlow
Method added which returns complete result in TreeMap
Revision 1173 - Directory Listing
Modified Wed Aug 4 15:27:40 2010 UTC (9 years, 5 months ago) by hstehr
minor modifications to casp benchmarking script
Revision 1171 - Directory Listing
Modified Wed Aug 4 10:47:28 2010 UTC (9 years, 5 months ago) by hstehr
small update for compatibility with Casp9 data (changing baker group name string)
Revision 1169 - Directory Listing
Modified Mon Aug 2 17:29:07 2010 UTC (9 years, 5 months ago) by hstehr
some more fixes for doing benchmarking on Casp9 targets
Revision 1167 - Directory Listing
Modified Mon Aug 2 14:42:36 2010 UTC (9 years, 5 months ago) by hstehr
updated casp benchmarking classes for Casp9, still missing: update group suffix
Revision 1070 - Directory Listing
Modified Wed May 19 16:20:42 2010 UTC (9 years, 8 months ago) by jmduarteg
Fixed bug in TcoffeeRunner. The t_coffee process was hanging after spawning. This didn't happen before, it can be related to the version of t_coffee (I'm using 8.14). Basically t_coffee seems to be doing something weird with stderr and stdout, java doesn't like it and makes the process hang (as usual java has a lot of problems in this area, see StreamGobbler class). The way to solve it is use the -quiet switch of t_coffee that can be used to redirect output to a file or have a complete quiet terminal.
Revision 1009 - Directory Listing
Modified Wed Mar 31 15:50:04 2010 UTC (9 years, 9 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, 9 months ago) by hstehr
refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl