Which part exactly? The compilation command?
java -DPROLOGDIR=%PROLOGDIR%
-classpath %MYCLASSPATH% flogicbasicsExample
The API expects two Java properties, PROLOGDIR and FLORADIR. These can be set either on command line, as shown above with -D, or using setProperty in your Java program. In the latter case, no need for the -D parameters.
If you do set them on command line, you need to supply -DPROLOGDIR=path-to-prolog-bindir and -DFLORADIR=path-to-flora-dir, where you have to replace the italics with the actual stuff. The above command does the same with the help of cmd variables, which can be set using the shell script flora_settings.bat.
This has a concrete runnable example with all the concrete compilation/run commands that you need, including the classpath parameter.