http://java.sun.com/javafx/1.2/docs/api/javafx.util/javafx.util.Math.html

See the atan2 method description:
public atan2(x: Double, y: Double) : Double

However it really calculates atan2 method for the (y, x) instead of (x,y)

The javadoc of java Math class has right (y,x) order:
See http://java.sun.com/j2se/1.5.0/docs/api/java/lang/Math.html
atan2(double y, double x)
          Converts rectangular coordinates (x, y) to polar (r, theta).