[Biojava-l] I search for java.jar

[Matthew Pocock]

Hi,

Firstly, I think you will need to put biojava.jar into
your classpath rather than java.jar.

Seccondly, you are running the class
PdbToXMLConverter. Did you compile this yourself? If
you did, I think you may have a package statement on
the first non-comment, non-empty line that says:

package org.biojava.bio.program;

To make the program run, you eiter need the .class
file from compiling this to be in a directory
org/biojava/bio/program (relative to your classpath)
and type java
org.biojava.bio.program.PdbToXMLConverter 1FS1.pdb, or
you need to remove the package line from the file. If
you did not compile the application yourself, you will
probably find that putting biojava.jar into your path
and typing the new command-line works.

If you have any more trouble, drop us a line.

Matthew


 --- jon portuondo murguiondo
<jon.portuondo01@campus.upf.es> wrote: > Hello,
> I have a problem when I try to execute the program
> PdbToXML. I think the problem is I don't have the
> java.jar library, but where I can find it? (I have
> linux). I would be very pleased you could help me.
> The errors are the following (if you think the
> problem is not the java.jar library, tell me
> please!):
> [jon@diana ~]$ java PdbToXMLConverter 1FS1.pdb 
> Exception in thread "main"
> java.lang.NoClassDefFoundError: PdbToXMLConverter
> (wrong name:
> org/biojava/bio/program/PdbToXMLConverter)
>         at java.lang.ClassLoader.defineClass0(Native
> Method)
>         at
>
java.lang.ClassLoader.defineClass(ClassLoader.java:502)
>         at
>
java.security.SecureClassLoader.defineClass(SecureClassLoader.java:123)
>         at
>
java.net.URLClassLoader.defineClass(URLClassLoader.java:250)
>         at
>
java.net.URLClassLoader.access$100(URLClassLoader.java:54)
>         at
>
java.net.URLClassLoader$1.run(URLClassLoader.java:193)
>         at
> java.security.AccessController.doPrivileged(Native
> Method)
>         at
>
java.net.URLClassLoader.findClass(URLClassLoader.java:186)
>         at
>
java.lang.ClassLoader.loadClass(ClassLoader.java:299)
>         at
>
sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:265)
>         at
>
java.lang.ClassLoader.loadClass(ClassLoader.java:255)
>         at
>
java.lang.ClassLoader.loadClassInternal(ClassLoader.java:315)
> 
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