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Revision 1647 - (view) (annotate) - [select for diffs]
Modified Thu Jul 4 08:39:06 2013 UTC (5 years, 9 months ago) by jmduarteg
File length: 2815 byte(s)
Diff to previous 1546
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 1546 - (view) (annotate) - [select for diffs]
Modified Thu Mar 15 15:07:38 2012 UTC (7 years, 1 month ago) by jmduarteg
File length: 2822 byte(s)
Diff to previous 1481
Removing unused class and thus JRclient dependency
Revision 1481 - (view) (annotate) - [select for diffs]
Modified Mon Oct 24 08:54:36 2011 UTC (7 years, 5 months ago) by jmduarteg
File length: 2931 byte(s)
Diff to previous 1463
Updated uniprot japi jars
Revision 1463 - (view) (annotate) - [select for diffs]
Modified Wed Aug 31 09:06:39 2011 UTC (7 years, 7 months ago) by jmduarteg
File length: 2867 byte(s)
Diff to previous 1366
Updating common-maths jar to latest stable release 2.2 (from 1.2)
Revision 1366 - (view) (annotate) - [select for diffs]
Modified Mon Mar 28 17:46:49 2011 UTC (8 years ago) by hstehr
File length: 2684 byte(s)
Diff to previous 1291
preparing for adding 'mutanom' package: adding dependencies to jars dir
Revision 1291 - (view) (annotate) - [select for diffs]
Modified Fri Dec 17 16:38:25 2010 UTC (8 years, 4 months ago) by cvehlow
File length: 2111 byte(s)
Diff to previous 1065
Control database access! for CGAP
Revision 1065 - (view) (annotate) - [select for diffs]
Modified Tue May 11 15:14:45 2010 UTC (8 years, 11 months ago) by hstehr
File length: 1855 byte(s)
Diff to previous 1064
reverting changes to .project and .classpath which were accidentally committed
Revision 1064 - (view) (annotate) - [select for diffs]
Modified Tue May 11 14:57:20 2010 UTC (8 years, 11 months ago) by hstehr
File length: 1962 byte(s)
Diff to previous 1040
fixed a bug in GraphAverager.getGraphWithTopContacts() which caused a null pointer exception in jung.SparseGraph.addEdge(), this may even be a bug in jung
Revision 1040 - (view) (annotate) - [select for diffs]
Modified Wed Apr 21 10:44:19 2010 UTC (9 years ago) by jmduarteg
File length: 1855 byte(s)
Diff to previous 966
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 966 - (view) (annotate) - [select for diffs]
Modified Thu Feb 18 15:51:56 2010 UTC (9 years, 2 months ago) by duarte
File length: 1252 byte(s)
Diff to previous 951
Updated jung jars to version 2.0.1 (finally the release version, not alpha or beta!)
Revision 951 - (view) (annotate) - [select for diffs]
Added Fri Jan 29 16:12:34 2010 UTC (9 years, 2 months ago) by duarte
File length: 1264 byte(s)
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.

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