Communicating betweeen Android device and Arduino (sketch uploading)

I'm working over sketch uploading from Android device to Arduino board and it works for Duemilanove (FTDI-based) and Uno (ATMega-based) when testing for pc/arduino using rxtx (pure java).
But it does not work if using usb-android lib (GitHub - mik3y/usb-serial-for-android: Android USB host serial driver library for CDC, FTDI, Arduino and other devices.) as setDTR/setRTS methods are not implemented yet.
FTDI android drivers (http://www.ftdichip.com/Android.htm) allow to send setDTR/setRTS signals but fail to send/read data after it.

So the problem is in USB API and i can't figure out what's wrong..

Does anybody know what happens for FTDI-based arduino boards after DTR/RTS are toggled?
I belive that device is reset and wait for bootloader commands (stk500) for ~50-250 ms. Am i right?

Solved myself:

Check out this: http://arduinocommander.blogspot.com/2013/03/upload-sketch.html