Dear All,

I got this exception when I ran the unit test for :
org.biojavax.ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver. Here is my environment specification:

IDE: Eclipse 3.2
JRE: java-1.5.0-gcj-1.5.0.0
OS: Ubuntu 8.04 (Hardy Heron)

Does any one ever run Biojava in Linux environment ? I suspect that this
error is because of the JRE. Has anyone been successful in running
biojava in ubuntu before ? If yes may I know your eclipse JRE setting ? 

Thank you.

Regards,
Zainul Franciscus


Stack trace:

org.biojava.bio.BioError: Unable to initialize DNATools
   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117)
   at java.lang.Class.initializeClass(libgcj.so.81)
   at
org.biojavax.ga.functions.SimpleCrossOverFunctionTest.testPerformCrossOver(SimpleCrossOverFunctionTest.java:56)
   at java.lang.reflect.Method.invoke(libgcj.so.81)
   at junit.framework.TestCase.runTest(TestCase.java:168)
   at junit.framework.TestCase.runBare(TestCase.java:134)
   at junit.framework.TestResult$1.protect(TestResult.java:110)
   at junit.framework.TestResult.runProtected(TestResult.java:128)
   at junit.framework.TestResult.run(TestResult.java:113)
   at junit.framework.TestCase.run(TestCase.java:124)
   at junit.framework.TestSuite.runTest(TestSuite.java:232)
   at junit.framework.TestSuite.run(TestSuite.java:227)
   at
org.junit.internal.runners.JUnit38ClassRunner.run(JUnit38ClassRunner.java:81)
   at
org.eclipse.jdt.internal.junit4.runner.JUnit4TestReference.run(JUnit4TestReference.java:38)
   at
org.eclipse.jdt.internal.junit.runner.TestExecution.run(TestExecution.java:38)
   at
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:460)
   at
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.runTests(RemoteTestRunner.java:673)
   at
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.run(RemoteTestRunner.java:386)
   at
org.eclipse.jdt.internal.junit.runner.RemoteTestRunner.main(RemoteTestRunner.java:196)
Caused by: org.biojava.bio.BioError: Couldn't locate
AlphabetManager.xml.  This probably means that your biojava.jar file is
corrupt or incorrectly built.
   at
org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:150)
   at java.lang.Class.initializeClass(libgcj.so.81)
   at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:79)
   ...18 more