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swhwang10
2007-10-04
2013-05-15
  • swhwang10
    swhwang10
    2007-10-04

    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?

     
    • Alok Saldanha
      Alok Saldanha
      2007-10-04

      The class net/n3/nanoxml/XMLException should be found in the following jar file:

      lib/nanoxml-2.2.2.jar

      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

       
    • swhwang10
      swhwang10
      2007-10-04

      Thanks.

      (Q1)
      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?

      (Q2)
      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;

      Dendrogram.jar
      gpl.txt
      ImageCoordinates.pcl
      karyoscope.gif
      Karyoscope.jar
      Makefile
      MANIFEST.MF
      nanoxml-2.2.2.jar
      plot.gif
      resources.h
      resources.rc
      Scatterplot.jar
      setup.c
      setup.ico
      tree.gif
      Treeanno.jar
      treeview.gif
      treeview.ico
      TreeView.jar
      treeviewIcon.bmp
      treeviewIcon.icns
      treeviewIconSmall.bmp
      win32TreeView.bat
      YeastCoordinates.pcl

       
      • Alok Saldanha
        Alok Saldanha
        2007-10-04

        Yes, please create a subdirectory named "plugins" and put the following jar files in it:

        Dendrogram.jar
        Karyoscope.jar
        Scatterplot.jar
        Treeanno.jar

        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:

        karyoscope.gif
        plot.gif
        tree.gif
        treeview.gif
        treeviewIcon.icns

        Also, depending on your java setup you may need to make a META-INF subdirectory and put the following in it:

        MANIFEST.MF

        Finally, if you use karyoscope, make a "coordinates" directory and put the following in it:

        ImageCoordinates.pcl
        YeastCoordinates.pcl

        All that should be left is

        gpl.txt
        treeview.ico
        TreeView.jar
        win32TreeView.bat

        I am not sure why the installer does not work for you, as it worked for me just now on windows XP.

         
    • swhwang10
      swhwang10
      2007-10-05

      Thank you very much for your help.