These commands are executed in the background when you compile your code in your IDE like Netbeans/Eclipse/IntelliJ
You can also compile your code manually without the need of an IDE. That is what is described in the book.
Oracle Java SE6 Certified Programmer
Oracle Java EE5 Certified Web Component Developer
Pivotal Certified Spring Professional
If you are just starting out, most folks around here would recommended not using and IDE like Netbeans/Eclipse/IntelliJ. There is enough to learn just with Java that adding in a behemoth like those make it that much harder - and often you end up fighting with the tool rather than the language.
Get a simple text editor (I use ConText, but search around and you will find plenty of recommendations for others) and compile your code by hand on the command line.
There are only two hard things in computer science: cache invalidation, naming things, and off-by-one errors