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"but I'm guessing this is valid for c++, not java."

unfortunately, yes.

the problem here is, that there are no public setters, and the wrapper mechanism ignores public member vars. ( same problem applies to python, too )

a simple :

CV_WRAP void setTransitionMatrix( const Mat & trans ) {
    transitionMatrix = trans;

in the Kalman class would solve the problem ( the CV_WRAP tag would make the wrappers bind it )

on the other hand, i doubt, that setting KF.statePre makes any sense, that'll be overwritten in the predict method anyway. and the eye-matrix you're using for the transition is the default value already.