void inputoptions()
{
/* read the options information */
Char ch;
long i, extranum, cursp, curst;
if (!firstset) {
if (eoln(infile))
scan_eoln(infile);
fscanf(infile, "%ld%ld", &cursp, &curst);
if (cursp != spp) {
printf("\nERROR: INCONSISTENT NUMBER OF SPECIES IN DATA SET %4ld\n",
ith);
exxit(-1);
}
sites = curst;
reallocsites();
}
for (i = 1; i <= sites; i++)
weight[i] = 1;
weightsum = sites;
extranum = 0;
fscanf(infile, "%*[ 0-9]");
readoptions(&extranum, "W");
for (i = 1; i <= extranum; i++) {
matchoptions(&ch, "W");
inputweights2(1, sites+1, &weightsum, weight, &weights, "RESTDIST");
}
} /* inputoptions */
void inputoptions()
{
/* read options information */
long i;
if (!firstset && !justwts) {
samenumsp(&sites, ith);
reallocsites();
}
for (i = 0; i < sites; i++) {
category[i] = 1;
oldweight[i] = 1;
}
if (justwts || weights)
inputweights(sites, oldweight, &weights);
if (printdata)
putc('\n', outfile);
if (jukes && printdata)
fprintf(outfile, " Jukes-Cantor Distance\n");
if (kimura && printdata)
fprintf(outfile, " Kimura 2-parameter Distance\n");
if (f84 && printdata)
fprintf(outfile, " F84 Distance\n");
if (similarity)
fprintf(outfile, " \n Table of similarity between sequences\n");
if (firstset && printdata && (kimura || f84))
fprintf(outfile, "\nTransition/transversion ratio = %10.6f\n", ttratio);
if (ctgry && categs > 1) {
inputcategs(0, sites, category, categs, "DnaDist");
if (printdata)
printcategs(outfile, sites, category, "Site categories");
} else if (printdata && (categs > 1)) {
fprintf(outfile, "\nSite category Rate of change\n\n");
for (i = 1; i <= categs; i++)
fprintf(outfile, "%12ld%13.3f\n", i, rate[i - 1]);
putc('\n', outfile);
printcategories();
}
if ((jukes || kimura || logdet) && freqsfrom) {
printf(" WARNING: CANNOT USE EMPIRICAL BASE FREQUENCIES");
printf(" WITH JUKES-CANTOR, KIMURA, JIN/NEI OR LOGDET DISTANCES\n");
exxit(-1);
}
if (jukes)
ttratio = 0.5000001;
if (weights && printdata)
printweights(outfile, 0, sites, oldweight, "Sites");
} /* inputoptions */
