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r1647
File Last Change
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batik/ 1366 (8 years ago) by hstehr: preparing for adding 'mutanom' package: adding dependencies to jars dir
uniprot/ 1597 (6 years 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.
ws-commons-util-1.0.2.jar 951 (9 years 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.
collections-generic-4.01.jar 951 (9 years 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.
xmlrpc-common-3.1.jar 951 (9 years 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.
drmaa.jar 951 (9 years 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.
mysql-connector-java-5.0.5-bin.jar 951 (9 years 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.
Jama-1.0.2.jar 951 (9 years 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.
java-getopt-1.0.13.jar 951 (9 years 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.
xmlrpc-client-3.1.jar 951 (9 years 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.
jung-graph-impl-2.0.1.jar 967 (9 years ago) by duarte: Forgot to really add the libraries in the last commit!
jung-algorithms-2.0.1.jar 967 (9 years ago) by duarte: Forgot to really add the libraries in the last commit!
jung-api-2.0.1.jar 967 (9 years ago) by duarte: Forgot to really add the libraries in the last commit!
vecmath.jar 993 (9 years ago) by jmduarteg: Removing the svn:executable properties from jars that didn't need it
commons-codec-1.3.jar 993 (9 years ago) by jmduarteg: Removing the svn:executable properties from jars that didn't need it
commons-lang-2.5.jar 1366 (8 years ago) by hstehr: preparing for adding 'mutanom' package: adding dependencies to jars dir
commons-math-2.2.jar 1463 (8 years ago) by jmduarteg: Updating common-maths jar to latest stable release 2.2 (from 1.2)
jaligner-bugfixed.jar 1647 (6 years 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.
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