size_t readBaseband(int fd, void *buffer, unsigned short size) {
LOG(LOGLEVEL_STATUS, "Reading %u bytes from flash...\n", size);
writePacket(fd, 0x803, &size, sizeof(size));
void *temp = malloc(PACKET_SIZE(size));
size_t length = readPacket(fd, DEFAULT_TIMEOUT, temp, PACKET_SIZE(size));
void *ret = verifyPacket(temp, length);
if (ret) {
CmdPacket *packet = (CmdPacket *) temp;
LOG(LOGLEVEL_DEBUG, "Read returns %d bytes:\n", packet->dataSize);
LOGDO(LOGLEVEL_DEBUG, printBuffer(ret, packet->dataSize));
if (packet->dataSize <= size) {
memcpy(buffer, ret, packet->dataSize);
} else {
LOG(LOGLEVEL_WARN, "Warning: The returned data does not fit into the buffer!\n");
memcpy(buffer, ret, size);
}
free(temp);
return packet->dataSize;
} else {
LOG(LOGLEVEL_DEBUG, "Read returns: ERROR!\n");
free(temp);
return 0;
}
}
void computePijHom::fillPij(const tree& et, const stochasticProcess& sp, int derivationOrder, bool isReversible) {
_V.resize(et.getNodesNum());
treeIterTopDownConst tIt(et);
tree::nodeP myNode = tIt.first();
{// skipping the root, but allocating place for the root pij even if they are not use
// to maintain that all arrays have the same size.
_V[myNode->id()].resize(sp.alphabetSize());
}
LOGDO(50,et.output(myLog::LogFile(),tree::ANCESTOR));
LOGDO(50,et.output(myLog::LogFile(),tree::PHYLIP));
for (; myNode != tIt.end(); myNode = tIt.next()) {
if (!(myNode->isRoot()))
_V[myNode->id()].fillPij(myNode->dis2father()*sp.getGlobalRate(),sp,derivationOrder,isReversible);
// else
// myLog::LogFile()<<"ROOT IS "<<myNode->name()<<endl;
}
}
void seekBaseband(int fd, unsigned int offset) {
LOG(LOGLEVEL_INFO, "Seeking to 0x%08x...\n", offset);
writePacket(fd, 0x802, &offset, sizeof(offset));
char buffer[PACKET_SIZE(SEEK_REPLY_PACKET_SIZE)];
size_t length = readPacket(fd, DEFAULT_TIMEOUT, buffer, sizeof(buffer));
LOG(LOGLEVEL_DEBUG, "Seek returns:\n");
LOGDO(LOGLEVEL_DEBUG, printBuffer(verifyPacket(buffer, length), SEEK_REPLY_PACKET_SIZE));
}
void prepareFlash(int fd) {
LOG(LOGLEVEL_INFO, "Preparing flash access...\n");
short param = 0;
writePacket(fd, 0x84, ¶m, sizeof(param));
char buffer[PACKET_SIZE(CFI1_PACKET_SIZE)];
size_t length = readPacket(fd, DEFAULT_TIMEOUT, buffer, sizeof(buffer));
LOG(LOGLEVEL_DEBUG, "CFI Stage 1 returns:\n");
LOGDO(LOGLEVEL_DEBUG, printBuffer(verifyPacket(buffer, length), CFI1_PACKET_SIZE));
writePacket(fd, 0x85, NULL, 0);
length = readPacket(fd, DEFAULT_TIMEOUT, buffer, sizeof(buffer));
short *unknown = verifyPacket(buffer, length);
LOG(LOGLEVEL_DEBUG, "CFI Stage 2 returns: %d\n", unknown ? *unknown : 0);
//LOGDO(LOGLEVEL_DEBUG, printBuffer(buffer, length));
}
static void writePacket(int fd, short cmd, void *data, size_t length) {
char *buffer = malloc(PACKET_SIZE(length));
//memset(buffer, 0, PACKET_SIZE(length));
CmdPacket *packet = (CmdPacket *) buffer;
packet->w02 = 2;
packet->cmd = cmd;
packet->dataSize = length;
memcpy(buffer + CMD_PACKET_SIZE, data, length);
CmdPacketEnd *end = (CmdPacketEnd *) (buffer + CMD_PACKET_SIZE + length);
end->checksum = checksum(packet, data);
end->w03 = 3;
LOG(LOGLEVEL_TRACE, "Writing packet:\n");
LOGDO(LOGLEVEL_TRACE, printBuffer(buffer, PACKET_SIZE(length)));
write(fd, buffer, PACKET_SIZE(length));
free(buffer);
}
static size_t readPacket(int fd, int timeout, void *buffer, size_t length) {
fd_set nfd;
FD_ZERO(&nfd);
FD_SET(fd, &nfd);
struct timeval tv = {
.tv_sec = timeout,
.tv_usec = timeout ? 0 : 10000
};
size_t hlen = 0;
//LOG(LOGLEVEL_INFO, "length=%lu hlen=%lu\n", length, hlen);
while (length - hlen > 0 && select(fd + 1, &nfd, 0, 0, &tv) > 0) {
hlen += read(fd, buffer + hlen, length - hlen);
//LOG(LOGLEVEL_INFO, "hlen=%lu\n", hlen);
//LOGDO(LOGLEVEL_DEBUG, printBuffer(buffer, hlen));
}
LOG(LOGLEVEL_TRACE, "Read packet:\n");
LOGDO(LOGLEVEL_TRACE, printBuffer(buffer, hlen));
return hlen;
}
int openBaseband(const char *device) {
LOG(LOGLEVEL_INFO, "Opening %s...\n", device);
int fd = open(device, O_NOCTTY | O_RDWR);
ioctl(fd, TIOCNXCL);
fcntl(fd, F_SETFL, 0);
struct termios options;
tcgetattr(fd, &options);
int tcxonxoff = 0;
ioctl(fd, 0x8004540A, &tcxonxoff);//_IOW('T', 10, int) = TCXONC?
cfsetspeed(&options, DEFAULT_SPEED);
cfmakeraw(&options);
options.c_cc[VMIN] = 0;
options.c_cc[VTIME] = 5;
options.c_iflag = (options.c_iflag | (IGNBRK | IGNPAR)) & ~(ICRNL | IXON | IXOFF | IXANY | INPCK | ISTRIP | BRKINT);
options.c_oflag = options.c_oflag & ~OPOST;
options.c_cflag = (options.c_cflag | (CREAD | CS8 | CLOCAL | HUPCL | CRTSCTS)) & ~PARENB;
options.c_lflag = options.c_lflag & ~(ECHO | ISIG | IEXTEN | ICANON);
tcsetattr(fd, TCSANOW, &options);
ioctl(fd, TIOCSDTR);
ioctl(fd, TIOCCDTR);
int lineBits = TIOCM_DTR | TIOCM_RTS | TIOCM_CTS | TIOCM_DSR;
ioctl(fd, TIOCMSET, &lineBits);
LOG(LOGLEVEL_DEBUG, "Baseband opened.\n");
char buffer[128] = { '`', '\r' };
LOG(LOGLEVEL_INFO, "Waiting for initialization...\n");
size_t length;
do {
if (write(fd, buffer, 2) == -1) {
LOG(LOGLEVEL_ERROR, "Can't write to baseband\n");
close(fd);
return -1;
}
length = readPacket(fd, 0, buffer, sizeof(buffer));
} while (length == 0 || buffer[0] != 0xb);
return fd;
}
