Hi Udana, sounds like forester.jar is missing from your classpath....
Andreas On Thu, Feb 10, 2011 at 9:01 AM, udana chathuranga <[email protected]> wrote: > hi all, > > When I was going through the biojava cookbook as I was interested in this > project. I tried the example in the page > http://biojava.org/wiki/BioJava:CookBook3:MSA and I got a classnotfound > exception for the line "Profile<ProteinSequence, AminoAcidCompound> profile > = Alignments.getMultipleSequenceAlignment(lst);". > > Error Message: > > Exception in thread "main" java.lang.NoClassDefFoundError: > org/forester/phylogenyinference/DistanceMatrix > at > org.biojava3.alignment.Alignments.getMultipleSequenceAlignment(Alignments.java:176) > at CookbookMSA.multipleSequenceAlignment(CookbookMSA.java:29) > at CookbookMSA.main(CookbookMSA.java:18) > Caused by: java.lang.ClassNotFoundException: > org.forester.phylogenyinference.DistanceMatrix > at java.net.URLClassLoader$1.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(Unknown Source) > at java.lang.ClassLoader.loadClass(Unknown Source) > at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) > at java.lang.ClassLoader.loadClass(Unknown Source) > at java.lang.ClassLoader.loadClassInternal(Unknown Source) > > Is this a know issue or Am I doing something wrong with the code? > Help me on this I have attached the java source file that I have tried. > > Thanks > Regards > udana. > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
