how does mavlink or any other over-the-air protocol come in play with software?

Question

I'm trying to understand how one software such as Mission Planner or APM2 or QGroundControl works from beginning to end.
So, each application/software source code does not directly execute passing mavlink protocols, correct?
Are the mavlink protocols embedded in the library packages, which are being used in the program?
If so, I still can't find any mavlink protocol on each command, such as isArmed() or isConnected(), in the library source code.
Essentially, I want to create my own java library with mavlink so that I can create my own ground control station software which is not tracked by a company, such as DJI.
Thank you.

Answer 1

Perhaps you'll find dronefleet/mavlink useful. It allows reading/writing mavlink messages and provides an abstraction layer from the low-level stuff.

Disclaimer: I am the author of this library.