Arduino due, is there any way to program it outside the IDE?

Official Hardware Mega Due
1

is it possible to program the arduino due while using the Native USB port (not programing), and to set one of the pins to logical "HIGH"/"LOW"?

or the arduino is read only while on the native USB port is being used?

2

Huh? Yes, it is possible to program the Due through the native USB port and you do not need the IDE to do this. Bossac is a command line program you can use to program the Due. If you want official tools there is also SAM-BA. Or, you can use JTAG but that's not through the native USB port. But, I don't know what you mean by setting one of the pins to logical high/low. What does that have to do with programming the Due? You mean you want to upload a sketch that does that? Without the Arduino core files?

3

I successfully managed to programm my DUE via Atmel Studio 7 following along this guide for Atmel Studio 6 http://codetron.net/arduino-due-in-atmel-studio-using-c-led-blinking/

Programming port though.

4

Perhaps OP means drive the pins directly, in real-time, without programming - using the native USB port as a direct command port?

If that is so, one could, of course, write code to read data from the native USB port and set output pins accordingly..

I dunno, just a wild guess.