java models


Cvapp is for editing and converting morphology files. There are currently two versions available which are due to be merged but have not yet been combined. The original version, cvapp1.0, is identical to the one included in the morphology archive. The usage notes for that version apply to both.

It is available as

There is another version modified by Steve van Hooser to handle remeshing of structures for Genesis. Remeshing is done internally by neuron, so this version is of no benefit there. Indeed, the Neuron output appears to be brocken, so unless you need the remeshing facilities, stick to the original version above.

Steve's version is available as

In either case, the first two files are equivalent, and when uncompressed produce a directory containing the source and class files. The .jar file contains just the class files and doesn't need unpacking. To run cvapp from the jar file, first install the full java development kit (JDK) or the Java Runtime Environment - JRE and then one of the following should work:

  jre -jar cvapp100.jar cvapp
  jre -cp cvapp100.jar cvapp
  java -jar cvapp100.jar cvapp
  setenv CLASSPATH ./cvapp100.jar; java cvapp
  CLASSPATH="./cvapp100.jar"; export CLASSPATH; java cvapp

Under windows you should type these from a dos box. Exactly which one to use depends on the version of java and the shell you are using. If you haven't put the java or jre executable in your path you will have to type the full path as in for example
  C:\jdk1.1.8\bin\java -jar cvapp100.jar cvapp

Information on how to use cvapp can be found in the usage notes.

Dieter Jaeger has written detailed instructions for converting and remeshing structures for Genesis using Steves 1.4.3 version, describing the new features and how to run it.