[Biojava-l] Problem with MultipleSequenceAlignment

[Scooter Willis]

You are probably missing a reference to the forester jar file located
in the biojava3-phylo module.

On Fri, Feb 11, 2011 at 10:15 AM, udana chathuranga
<uchathuranga at gmail.com> 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?
>
> Thanks
> Regards
> udana.
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>