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I downloaded TreeView-1.1.1-win.zip and installed on my Windows XP.
Upon running the software, I get this error message on my command prompt;
Exception in thread "main" java.lang.NoClassDefFoundError: net/n3/nanoxml/XMLException
at edu.stanford.genetics.treeview.TreeViewApp.<init>(Unknown Source)
at edu.stanford.genetics.treeview.app.LinkedViewApp.<init>(Unknown Source)
at edu.stanford.genetics.treeview.app.LinkedViewApp.main(Unknown Source)
at LinkedView.main(Unknown Source)
Is there something I can do with it?
The class net/n3/nanoxml/XMLException should be found in the following jar file:
In other words, there should be a "lib" subdirectory relative to the Treeview.jar file that is in the classpath of the Treeview.jar file. Is this not the case?
You can also try specifying the classpath explicitly on the command line, like
java -cp TreeView.jar:lib/nanoxml-2.2.2.jar LinkedView
Upon installing with setup.exe, installation puts everything in the base directory. There was no "lib" subdirectory. Is it so because there is something wrong in setup.exe?
Having read your posting, I created lib subdirectory, moved nanoxml-2.2.2.jar in it, and ran TreeView. This time it started OK but, when I open a cdt file, TreeView displays "No plugins loaded" message.
Should I create a "plugins" subdirectory also and move some files there? If so, which ones should they be? In my current installation, the base directory contains the following;
Yes, please create a subdirectory named "plugins" and put the following jar files in it:
These are the plugin jars. Most likely, you only care about the Dendrogram.jar plugin. The others are less frequently used. You should also make an "images" subdirectory and put the following images there:
Also, depending on your java setup you may need to make a META-INF subdirectory and put the following in it:
Finally, if you use karyoscope, make a "coordinates" directory and put the following in it:
All that should be left is
I am not sure why the installer does not work for you, as it worked for me just now on windows XP.
Thank you very much for your help.