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Revision 1335 - Directory Listing
Modified Wed Mar 9 08:38:35 2011 UTC (8 years, 7 months ago) by jmduarteg
Now throwing InterruptedException. Refactor BlastErro to BlastException
Revision 1334 - Directory Listing
Modified Wed Mar 9 08:13:04 2011 UTC (8 years, 7 months ago) by jmduarteg
Refactoring xxxError to xxxException
Revision 1326 - Directory Listing
Modified Thu Mar 3 13:21:18 2011 UTC (8 years, 7 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 (8 years, 8 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 1304 - Directory Listing
Modified Sun Jan 16 16:06:09 2011 UTC (8 years, 9 months 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, 1 month 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, 1 month 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, 1 month 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, 1 month ago) by cvehlow
Scoring:KendallsTau-method added to  Statistics
Revision 1203 - Directory Listing
Modified Thu Aug 19 10:52:46 2010 UTC (9 years, 1 month ago) by hstehr
renamed class benchmarkAll to createResultWebPages
Revision 1200 - Directory Listing
Modified Thu Aug 19 10:16:06 2010 UTC (9 years, 1 month ago) by hstehr
removed some bad characters
Revision 1196 - Directory Listing
Modified Thu Aug 19 10:06:15 2010 UTC (9 years, 1 month 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, 2 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, 2 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, 2 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, 2 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, 2 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, 2 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, 2 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, 4 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, 6 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, 6 months ago) by hstehr
refactoring: moved casp, deltaRank, embed, graphAveraging, ppi, sadp to owl