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root/owl/tags/owl-for-eppic-2.0.4/.classpath
Revision: 1647
Committed: Thu Jul 4 08:39:06 2013 UTC (6 years, 2 months ago) by jmduarteg
Original Path: trunk/.classpath
File size: 2815 byte(s)
Log Message:
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.
Line File contents
1 <?xml version="1.0" encoding="UTF-8"?>
2 <classpath>
3 <classpathentry kind="src" path="src"/>
4 <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
5 <classpathentry exported="true" kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
6 <classpathentry exported="true" kind="lib" path="jars/collections-generic-4.01.jar"/>
7 <classpathentry exported="true" kind="lib" path="jars/commons-codec-1.3.jar"/>
8 <classpathentry exported="true" kind="lib" path="jars/drmaa.jar"/>
9 <classpathentry exported="true" kind="lib" path="jars/Jama-1.0.2.jar"/>
10 <classpathentry exported="true" kind="lib" path="jars/java-getopt-1.0.13.jar"/>
11 <classpathentry exported="true" kind="lib" path="jars/mysql-connector-java-5.0.5-bin.jar"/>
12 <classpathentry exported="true" kind="lib" path="jars/vecmath.jar"/>
13 <classpathentry exported="true" kind="lib" path="jars/jung-algorithms-2.0.1.jar"/>
14 <classpathentry exported="true" kind="lib" path="jars/jung-api-2.0.1.jar" sourcepath="/afs/psi.ch/project/bioinfo/software/jars/jung2-src/jung-api-2.0-beta1-sources.jar"/>
15 <classpathentry exported="true" kind="lib" path="jars/jung-graph-impl-2.0.1.jar" sourcepath="/afs/psi.ch/project/bioinfo/software/jars/jung2-src/jung-graph-impl-2.0-beta1-sources.jar"/>
16 <classpathentry kind="lib" path="jars/uniprot/uniprotjapi.jar"/>
17 <classpathentry kind="lib" path="jars/uniprot/commons-logging.jar"/>
18 <classpathentry kind="lib" path="jars/uniprot/aopalliance.jar"/>
19 <classpathentry kind="lib" path="jars/uniprot/commons-httpclient.jar"/>
20 <classpathentry kind="lib" path="jars/uniprot/log4j.jar"/>
21 <classpathentry kind="lib" path="jars/commons-lang-2.5.jar"/>
22 <classpathentry kind="lib" path="jars/batik/batik-awt-util.jar"/>
23 <classpathentry kind="lib" path="jars/batik/batik-dom.jar"/>
24 <classpathentry kind="lib" path="jars/batik/batik-ext.jar"/>
25 <classpathentry kind="lib" path="jars/batik/batik-svg-dom.jar"/>
26 <classpathentry kind="lib" path="jars/batik/batik-svggen.jar"/>
27 <classpathentry kind="lib" path="jars/batik/batik-util.jar"/>
28 <classpathentry kind="lib" path="jars/batik/batik-xml.jar"/>
29 <classpathentry kind="lib" path="jars/commons-math-2.2.jar"/>
30 <classpathentry kind="lib" path="jars/uniprot/spring.aop.jar"/>
31 <classpathentry kind="lib" path="jars/uniprot/spring.beans.jar"/>
32 <classpathentry kind="lib" path="jars/uniprot/spring.context.jar"/>
33 <classpathentry kind="lib" path="jars/uniprot/spring.core.jar"/>
34 <classpathentry kind="lib" path="jars/uniprot/spring.web.jar"/>
35 <classpathentry kind="lib" path="jars/ws-commons-util-1.0.2.jar"/>
36 <classpathentry kind="lib" path="jars/xmlrpc-client-3.1.jar"/>
37 <classpathentry kind="lib" path="jars/xmlrpc-common-3.1.jar"/>
38 <classpathentry kind="lib" path="jars/jaligner-bugfixed.jar"/>
39 <classpathentry kind="output" path="bin"/>
40 </classpath>