This code asserts and then clears DTR, I would try changing the second bit to assert RTS (so it matches the setup your java snippet performs) on a pc at the moment but i think thats means TIOCCDTR->TIOCSRTS
if (ioctl(fileDescriptor, TIOCSDTR) == kMyErrReturn)
// Assert Data Terminal Ready (DTR)
{
printf("Error asserting DTR %s - %s(%d).\n",
deviceFilePath, strerror(errno), errno);
}
if (ioctl(fileDescriptor, TIOCCDTR) == kMyErrReturn)
// Clear Data Terminal Ready (DTR)
{
printf("Error clearing DTR %s - %s(%d).\n",
deviceFilePath, strerror(errno), errno);
}