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Revision 1693 - Directory Listing
Modified Wed Nov 27 09:02:57 2013 UTC (5 years, 10 months ago) by jmduarteg
Tagging for eppic release 2.0.3
- more PDB metadata parsing: biounit assembly and release date
- improved rmsd calculation: new OptimalSuperposition class introduced
- improvements in interface calculation: now going to 12th cell
- introduced chain clusters and interface clusters
- some more checks in cif file parsing: now won't crash on phenix files
Revision 1647 - Directory Listing
Modified Thu Jul 4 08:39:06 2013 UTC (6 years, 3 months ago) by jmduarteg
Original Path: trunk/jars
Fixing bug in jaligner: the NeedlemanWunschGotoh method used by owl.core.sequence.PairwiseSequenceAlignment had a bug causing infinite hanging when using very long sequences. The issue would happen when either of the 2 sequences to align was longer than 32768 (16 bit) and the other sequence would match it after the 32768 region, a test case is included in this commit to demonstrate it. The problem was an overflow: an array used for the traceback procedure was declared as short[] (16 bit), changing it to int[] (32 bit) the issue disappears. 
As the development in jaligner seems to be stopped I've simply downloaded the source, fixed the issue there (plus removing the loggers) and repackaged in a jar (jaligner-bugfixed.jar) that includes the sources.
Revision 1597 - Directory Listing
Modified Wed Nov 7 08:58:43 2012 UTC (6 years, 11 months ago) by jmduarteg
Original Path: trunk/jars
Several changes related to blast:
- now supporting blast+ blastp. 
- blast xml parser can now ignore the DTD url, avoiding unnecessary network access if desired
- refactoring: legacy blast related stuff is now refactored to contain "legacy", runBlastp refers to blast+
Also updated uniprot jar.
Revision 1546 - Directory Listing
Modified Thu Mar 15 15:07:38 2012 UTC (7 years, 7 months ago) by jmduarteg
Original Path: trunk/jars
Removing unused class and thus JRclient dependency
Revision 1518 - Directory Listing
Modified Mon Jan 30 09:33:28 2012 UTC (7 years, 8 months ago) by jmduarteg
Original Path: trunk/jars
Updating uniprot japi
Revision 1490 - Directory Listing
Modified Thu Nov 17 14:51:43 2011 UTC (7 years, 11 months ago) by jmduarteg
Original Path: trunk/jars
Updated uniprot japi jar to november's one
Revision 1481 - Directory Listing
Modified Mon Oct 24 08:54:36 2011 UTC (8 years ago) by jmduarteg
Original Path: trunk/jars
Updated uniprot japi jars
Revision 1463 - Directory Listing
Modified Wed Aug 31 09:06:39 2011 UTC (8 years, 1 month ago) by jmduarteg
Original Path: trunk/jars
Updating common-maths jar to latest stable release 2.2 (from 1.2)
Revision 1437 - Directory Listing
Modified Wed Aug 17 10:07:33 2011 UTC (8 years, 2 months ago) by jmduarteg
Original Path: trunk/jars
Removed not needed jar (only cmview needs this one)
Revision 1408 - Directory Listing
Modified Fri Jun 3 08:22:56 2011 UTC (8 years, 4 months ago) by jmduarteg
Original Path: trunk/jars
Updated uniprot jar
Revision 1385 - Directory Listing
Modified Thu Apr 7 14:55:45 2011 UTC (8 years, 6 months ago) by jmduarteg
Original Path: trunk/jars
New uniprot japi version
Revision 1366 - Directory Listing
Modified Mon Mar 28 17:46:49 2011 UTC (8 years, 6 months ago) by hstehr
Original Path: trunk/jars
preparing for adding 'mutanom' package: adding dependencies to jars dir
Revision 1309 - Directory Listing
Modified Mon Jan 31 11:46:02 2011 UTC (8 years, 8 months ago) by jmduarteg
Original Path: trunk/jars
New jar for uniprot JAPI
Revision 1288 - Directory Listing
Modified Fri Dec 10 15:23:40 2010 UTC (8 years, 10 months ago) by matt4077
Original Path: trunk/jars
adding java help to jars collection which is not really needed for building OWL but for building CMView
Revision 1275 - Directory Listing
Modified Wed Nov 3 14:17:53 2010 UTC (8 years, 11 months ago) by jmduarteg
Original Path: trunk/jars
New uniprot japi 2010_11
Revision 1257 - Directory Listing
Modified Thu Oct 7 18:34:46 2010 UTC (9 years ago) by hstehr
Original Path: trunk/jars
updating jars for Uniprot release 2010_10
Revision 1160 - Directory Listing
Modified Fri Jul 23 15:11:40 2010 UTC (9 years, 3 months ago) by jmduarteg
Original Path: trunk/jars
Updating to latest uniprot 2010_08
Revision 1113 - Directory Listing
Modified Wed Jun 16 10:26:00 2010 UTC (9 years, 4 months ago) by jmduarteg
Original Path: trunk/jars
Replacing uniprot japi jar after new uniprot release 2010_07
Revision 1040 - Directory Listing
Modified Wed Apr 21 10:44:19 2010 UTC (9 years, 6 months ago) by jmduarteg
Original Path: trunk/jars
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 993 - Directory Listing
Modified Mon Mar 22 14:14:10 2010 UTC (9 years, 7 months ago) by jmduarteg
Original Path: trunk/jars
Removing the svn:executable properties from jars that didn't need it
Revision 967 - Directory Listing
Modified Thu Feb 18 15:53:18 2010 UTC (9 years, 8 months ago) by duarte
Original Path: trunk/jars
Forgot to really add the libraries in the last commit!
Revision 966 - Directory Listing
Modified Thu Feb 18 15:51:56 2010 UTC (9 years, 8 months ago) by duarte
Original Path: trunk/jars
Updated jung jars to version 2.0.1 (finally the release version, not alpha or beta!)
Revision 951 - Directory Listing
Added Fri Jan 29 16:12:34 2010 UTC (9 years, 8 months ago) by duarte
Original Path: trunk/jars
Reorganised the project with a src folder for java source files.
Added a jars dir with all jars needed for the project.
Added .project and .classpath pointing to relative path of jars. 
The project should now work out of the box after a check-out with eclipse. No need to setup external jars or anything.