Below is a list of things that we are using or could use to Embed NetLogo

There is also Improvements to NetLogo Embedding which discusses things the NetLogo group could do to make the embedding work better.

Embedding as an Applet

We currently embed NetLogo using its applet class. This is done by this class:
org.concord.otrunknl4.OTNLogoModelView

The nlogo class being used is:
org.nlogo.window.LiteApplet

General Documenation

This is the web based documentation for NetLogo http://ccl.northwestern.edu/netlogo/docs/
This include information about controlling and logging NetLogo

Controlling NetLogo with NetLogo scripts

This page: http://ccl.northwestern.edu/netlogo/docs/controlling.html

Shows how the
org.nlogo.app.App
class has a static field "app" which can be used to run scripts in the current NetLogo application. For example:

App.app.command("set density 62");

Getting Log data from NetLogo

This page: http://ccl.northwestern.edu/netlogo/docs/logging.html

Describes how log data can be retrieve from NetLogo. It is using the Log4J library to do the logging.
I think a custom log handler could be installed
so the log messages generated by NetLogo could be caught directly instead of having them sent to an xml file first.

This seems like the interface that needs to be used to handle the log messages: http://logging.apache.org/log4j/1.2/apidocs/org/apache/log4j/Appender.html

This page: http://logging.apache.org/log4j/1.2/manual.html
Has info about appenders, and adding them to loggers