In my app I start a nanoTime in this way:
long startTime = System.nanoTime();
now I want that at a specific value of 'startTime' (ex: 1000000) is called a method "myMethod"
private void myMethod(){
//all operations
}
what's the best way to do it?
No, you aren't starting anything, just taking the current time.
https://docs.oracle.com/javase/1.5.0/docs/api/java/lang/System.html#nanoTime()
If you want to start a Runnable at a certain time, use Handler.postAtTime()
http://developer.android.com/reference/android/os/Handler.html#postAtTime(java.lang.Runnable, long)
For example