Stm32 Encoder interface

You need to elaborate more on what exactly it is you want?

Firstly what sort of encoder are you using? what sort of motor controller? and what sort of motor?

Typically if you know your motor controller configuration you will know what will make it go forwards and backwards so that should never be an issue.

you can use hall interface with timer2 , timer3 or timer4 interrupt handler with xored inputs. this means every xored transition of hall sensor generates interrupt and this interrupt triggers timer1 com (commutation) event. according to this com event you can generate various type of signals such as pwm-on, on-pwm, pwm-pwm for upper and lower mosfet gate signals.you can find sufficient information at 

http://www.google.com.tr/url?sa=t&source=web&cd=1&ved=0CCQQ_hIwAA&url=http://open-bldc.org/&ei=GOZMTqCJKq3c4QTtj6CzBw&usg=AFQjCNGnDAi_NKzkoVYseutFBiSP_MAEZw