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they are generated from python scripts (which read the c++ headers). have a look at https://github.com/opencv/opencv/tree/master/modules/java/generator , and https://docs.opencv.org/master/da/d49/tutorial_py_bindings_basics.html (same idea for python and matlab).
if you run cmake / make locally, to build the opencv libs, those generated jni / java files will be in opencv/build/modules/java_bindings_generator/gen
