I am afraid such a "complete" e-book simply does not exist. Honestly, I think it is not necessary at all. If you know the basic Java syntax, you will find JavaCard quite easy to learn (although annoying to use). All the usual difficult stuff (threading, GUI, IO, annotations, templates, databases, ...) is just missing in Javacard and the standard libraries are so limited you will be able to learn them in a few days.
There are a few nice tutorials out there:
http://www.oracle.com/technetwork/java/embedded/javacard/overview/index.html
http://javacard.vetilles.com/tutorial/
and a very good SO question:
How to get started with Java Cards?
To answer your question: JavaCard is just a language for writing smartcard applications called applets. It handles all the application logic, but it does not specify the APDU format. That is because JavaCard is not the only smartcard technology. APDU format is specifed in ISO7816 standard, which I really recommend you to read through. It is not free to download, but you can find the most important parts here:
http://www.cardwerk.com/smartcards/smartcard_standard_ISO7816-4_5_basic_organizations.aspx
You would find there, that your APDU command consists of a header:
00A404000E
and a data part:
63616C63756C61746F722E617070.
The header specifies what function should be called:
00 - class byte (CLA, 00 means "inter-industry command sent to logical channel 0")
A4 - instruction byte (INS, A4 means "SELECT applet command")
04 - parameter 1 (P1)
00 - parameter 2 (P2)
0E - length of the data part (Lc)
and the data part contains the identifier of the applet which should be selected for future usage (in your case it is an ASCII encoded string "calculator.app" btw).
