We do not currently have Java APIs for all buses available in the INDIGO Firmware on STM32F746GDISCO. We only allow to manipulate GPIOs [1].
However you can easily use the buses you described by evaluating the MicroEJ SDK [2] that allows to create your own custom platform. You can extends a platform by using two methods SNI [3] or Shielded Plug [4], using that you can interact with the BSP safely.
Hope it helps.
Gaëtan
[1] https://developer.microej.com/javadoc/microej_5.x/foundation/ej/hal/gpio/GPIO.html
[2] https://developer.microej.com/getting-started-sdk-stm-5.html
[3] https://github.com/MicroEJ/How-To/tree/master/SNI-LED
[4] https://github.com/MicroEJ/Example-Standalone-Java-C-Interface/tree/master/ProducerConsumerUsingShieldedPlug