static void process_gpgga_token(void) {
switch (token_nr) {
#if PARSE_GPS_TIME
case 1:
/* time
* HHMMSS(.sssss)
*/
parse_clock(&nmea_wip.gga.clock);
break;
#endif
case 2:
/* latitude
* BBBB.BBBB
*/
parse_coord(&nmea_wip.gga.lat);
break;
case 3:
/* orientation
* N north
* S south
*/
if (token_buffer[0] == 'N') {
nmea_wip.gga.flags |= (1<<NMEA_RMC_FLAGS_LAT_NORTH);
} else {
nmea_wip.gga.flags &= ~(1<<NMEA_RMC_FLAGS_LAT_NORTH);
}
break;
case 4:
/* longitude
* LLLLL.LLLL
*/
parse_coord(&nmea_wip.gga.lon);
break;
case 5:
/* orientation
* E east
* W west
*/
if (token_buffer[0] == 'E') {
nmea_wip.gga.flags |= (1<<NMEA_RMC_FLAGS_LON_EAST);
} else {
nmea_wip.gga.flags &= ~(1<<NMEA_RMC_FLAGS_LON_EAST);
}
break;
case 6:
/* signal quality */
nmea_wip.gga.quality = atoi(token_buffer);
if (nmea_wip.gga.quality) {
nmea_wip.gga.flags |= (1<<NMEA_RMC_FLAGS_STATUS_OK);
} else {
nmea_wip.gga.flags &= ~(1<<NMEA_RMC_FLAGS_STATUS_OK);
}
break;
case 7:
/* number of used satellites */
nmea_wip.gga.sats = atoi(token_buffer);
break;
#if PARSE_GPS_ALTITUDE
case 9:
/* altitude */
parse_altitude(&nmea_wip.gga.alt);
break;
#endif
default:
/* nothing to do */
break;
}
}
void load_cfile_sim()
{
long line_count = 0;
FILE * fp;
/* the following variable is used for checking whether we have a newick
string in the species&tree tag, in the case of 1 species. For species
trees we do not accept a tree, whereas for network we require a newick
string. The program always reads a line. If that line is a tree it is
processed, otherwise this variable is set such that we do not read another
line */
long line_not_processed = 0;
fp = xopen(opt_simulate,"r");
while (line_not_processed || getnextline(fp))
{
int valid = 0;
char * token;
char * value;
long token_len;
line_not_processed = 0;
++line_count;
token_len = get_token(line,&token,&value);
if (!token_len) continue;
if (token_len < 0)
fatal("Invalid syntax when parsing file %s on line %ld",
opt_simulate, line_count);
if (token_len == 4)
{
if (!strncasecmp(token,"seed",4))
{
if (!get_long(value,&opt_seed))
fatal("Option 'seed' expects one integer (line %ld)", line_count);
if (opt_seed == -1)
opt_seed = (long)time(NULL);
valid = 1;
}
else if (!strncasecmp(token,"arch",4))
{
char * temp;
if (!get_string(value,&temp))
fatal("Option %s expects a string (line %ld)", token, line_count);
if (!strcmp(temp,"cpu"))
opt_arch = PLL_ATTRIB_ARCH_CPU;
else if (!strcasecmp(temp,"sse"))
opt_arch = PLL_ATTRIB_ARCH_SSE;
else if (!strcasecmp(temp,"avx"))
opt_arch = PLL_ATTRIB_ARCH_AVX;
else if (!strcasecmp(temp,"avx2"))
opt_arch = PLL_ATTRIB_ARCH_AVX2;
else
fatal("Invalid instruction set (%s) (line %ld)", temp, line_count);
free(temp);
valid = 1;
}
}
else if (token_len == 5)
{
if (!strncasecmp(token,"clock",5))
{
if (!parse_clock(value))
fatal("Option 'clock' expects values '1', '2 a' or '3 a' (line %ld)",
line_count);
valid = 1;
}
else if (!strncasecmp(token,"model",5))
{
if (!get_long(value,&opt_model) || opt_model < 0)
fatal("Option 'model' expects value '%d' or '%d' (line %ld)",
BPP_DNA_MODEL_JC69, BPP_DNA_MODEL_GTR, line_count);
valid = 1;
}
}
else if (token_len == 6)
{
if (!strncasecmp(token,"qrates",6))
{
if (!parse_qrates(value))
fatal("Option 'qrates' expects one switch and 6 values (line %ld)",
line_count);
valid = 1;
}
}
else if (token_len == 7)
{
if (!strncasecmp(token,"seqfile",7))
{
if (!get_string(value, &opt_msafile))
fatal("Option '%s' expects a string (line %ld)", token, line_count);
valid = 1;
}
else if (!strncasecmp(token,"diploid",7))
{
if (!parse_diploid(value))
fatal("Option %s expects values 0 or 1 for each species (line %ld)",
token,line_count);
valid = 1;
}
}
else if (token_len == 8)
{
if (!strncasecmp(token,"treefile",8))
{
if (!get_string(value, &opt_treefile))
fatal("Option 'treefile' expects a string (line %ld)", line_count);
valid = 1;
}
else if (!strncasecmp(token,"imapfile",8))
{
if (!get_string(value, &opt_mapfile))
fatal("Option 'imapfile' expects a string (line %ld)", line_count);
valid = 1;
}
}
else if (token_len == 9)
{
if (!strncasecmp(token,"basefreqs",9))
{
if (!parse_basefreqs(value))
fatal("Option 'basefreqs' expects one switch and 4 values (line %ld)",
line_count);
valid = 1;
}
else if (!strncasecmp(token,"migration",9))
{
if (!get_long(value,&opt_migration))
fatal("Option 'migration' expects one integer (line %ld)", line_count);
parse_migration_matrix(fp, line_count);
valid = 1;
}
}
else if (token_len == 10)
{
if (!strncasecmp(token,"concatfile",10))
{
if (!get_string(value,&opt_concatfile))
fatal("Option 'concatfile' expects a string (line %ld)", line_count);
valid = 1;
}
}
else if (token_len == 11)
{
if (!strncasecmp(token,"loci&length",11))
{
if (!parse_loci_and_lengths(value))
fatal("Option 'loci&length' expects two positive integer values (line %ld)",
line_count);
valid = 1;
}
}
else if (token_len == 12)
{
if (!strncasecmp(token,"species&tree",12))
{
/* TODO: Currently only the old BPP format is allowed. Make it also
accept only the tree in newick format, i.e. one line instead of 3 */
long spcount = 0;
if (!parse_speciesandtree(value,&spcount))
fatal("Erroneous format of 'species&tree' (line %ld)", line_count);
if (!getnextline(fp))
fatal("Incomplete 'species&tree' record (line %ld)", line_count);
++line_count;
if (!readandvalidatecount(line,spcount))
fatal("Erroneous enumeration of species sequences in 'species&tree' "
"tag (line %ld).\nExpected number of species is %ld.\n",
line_count, spcount);
if (spcount > 1)
{
if (!getnextline(fp))
fatal("Incomplete 'species&tree' record (line %ld)", line_count);
++line_count;
if (!get_tree_string_with_thetas(line,&opt_streenewick))
fatal("Expected newick tree string in 'species&tree' (line %ld) ",
"with ending ';' character", line_count);
}
else if (spcount == 1)
{
/* TODO: This is an ugly hack to account for the case where we have 1
species and a network */
int reached_eof = 0;
if (!getnextline(fp))
reached_eof = 1;
++line_count;
line_not_processed = 1;
if (!reached_eof && starts_with_opar(line))
{
if (!get_string(line,&opt_streenewick))
fatal("Expected newick string in 'species&tree' (line %ld)",
line_count);
line_not_processed = 0;
}
else
{
opt_streenewick = (char *)xmalloc((size_t)(strlen(opt_reorder)+2) *
sizeof(char));
strcpy(opt_streenewick, opt_reorder);
opt_streenewick[strlen(opt_reorder)] = ';';
opt_streenewick[strlen(opt_reorder)+1] = '\0';
}
if (reached_eof)
break;
}
valid = 1;
}
}
else if (token_len == 13)
{
if (!strncasecmp(token,"modelparafile",13))
{
if (!get_string(value,&opt_modelparafile))
fatal("Option 'modelparafile' expects a string (line %ld)",
line_count);
valid = 1;
}
}
else if (token_len == 14)
{
if (!strncasecmp(token,"alpha_siterate",14))
{
if (!parse_siterate(value))
fatal("Erroneous format of 'alpha_siterate' (line %ld)", line_count);
valid = 1;
}
}
else if (token_len == 15)
{
if (!strncasecmp(token,"alpha_locusrate",15))
{
if (!get_double(value, &opt_locusrate_alpha))
fatal("Option 'alpha_locusrate' expects one value (line %ld)",
line_count);
if (opt_locusrate_alpha < 0)
fatal("Option 'alpha_locusrate' expects a non-negative value (line %ld)",
line_count);
if (opt_locusrate_alpha == 0)
opt_est_locusrate = 0;
else
opt_est_locusrate = 1;
valid = 1;
}
}
if (!valid)
fatal("Invalid syntax when parsing file %s on line %ld",
opt_simulate, line_count);
}
check_validity();
#if 0
if (opt_diploid)
update_sp_seqcount();
#endif
fclose(fp);
}
static void process_gprmc_token(void) {
switch (token_nr) {
#if !PARSE_GPS_NMEA_GGA /* avoid duplicate parsing code */
#if PARSE_GPS_TIME
case 1:
/* time
* HHMMSS(.sssss)
*/
parse_clock(&nmea_wip.rmc.clock);
break;
#endif
case 2:
/* status
* A OK
* V Warning
*/
if (token_buffer[0] == 'A') {
nmea_wip.rmc.flags |= (1<<NMEA_RMC_FLAGS_STATUS_OK);
} else {
nmea_wip.rmc.flags &= ~(1<<NMEA_RMC_FLAGS_STATUS_OK);
}
break;
case 3:
/* latitude
* BBBB.BBBB
*/
parse_coord(&nmea_wip.rmc.lat);
break;
case 4:
/* orientation
* N north
* S south
*/
if (token_buffer[0] == 'N') {
nmea_wip.rmc.flags |= (1<<NMEA_RMC_FLAGS_LAT_NORTH);
} else {
nmea_wip.rmc.flags &= ~(1<<NMEA_RMC_FLAGS_LAT_NORTH);
}
break;
case 5:
/* longitude
* LLLLL.LLLL
*/
parse_coord(&nmea_wip.rmc.lon);
break;
case 6:
/* orientation
* E east
* W west
*/
if (token_buffer[0] == 'E') {
nmea_wip.rmc.flags |= (1<<NMEA_RMC_FLAGS_LON_EAST);
} else {
nmea_wip.rmc.flags &= ~(1<<NMEA_RMC_FLAGS_LON_EAST);
}
break;
#endif
case 7:
/* speed
* GG.G
*/
break;
case 8:
/* course
* RR.R
*/
break;
#if PARSE_GPS_TIME
case 9:
/* date
* DDMMYY
*/
parse_date(&nmea_wip.rmc.date);
break;
#endif
case 10:
/* magnetic declination
* M.M
*/
break;
case 11:
/* sign of declination
* E east
* W west
*/
break;
case 12:
/* signal integrity
* A autonomous mode
* D differential mode
* E estimated mode
* M manual input mode
* S simulated mode
* N data not valid
*/
break;
}
}
