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Revision 1647 - Directory Listing
Modified Thu Jul 4 08:39:06 2013 UTC (6 years, 3 months ago) by jmduarteg
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
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
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
Updating uniprot japi
Revision 1490 - Directory Listing
Modified Thu Nov 17 14:51:43 2011 UTC (7 years, 10 months ago) by jmduarteg
Updated uniprot japi jar to november's one
Revision 1481 - Directory Listing
Modified Mon Oct 24 08:54:36 2011 UTC (7 years, 11 months ago) by jmduarteg
Updated uniprot japi jars
Revision 1463 - Directory Listing
Modified Wed Aug 31 09:06:39 2011 UTC (8 years, 1 month ago) by jmduarteg
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, 1 month ago) by jmduarteg
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
Updated uniprot jar
Revision 1385 - Directory Listing
Modified Thu Apr 7 14:55:45 2011 UTC (8 years, 6 months ago) by jmduarteg
New uniprot japi version
Revision 1366 - Directory Listing
Modified Mon Mar 28 17:46:49 2011 UTC (8 years, 6 months ago) by hstehr
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
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
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
New uniprot japi 2010_11
Revision 1257 - Directory Listing
Modified Thu Oct 7 18:34:46 2010 UTC (9 years ago) by hstehr
updating jars for Uniprot release 2010_10
Revision 1160 - Directory Listing
Modified Fri Jul 23 15:11:40 2010 UTC (9 years, 2 months ago) by jmduarteg
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
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, 5 months ago) by jmduarteg
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, 6 months ago) by jmduarteg
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, 7 months ago) by duarte
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, 7 months ago) by duarte
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
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.