void inputoptions()
{
/* input the information on the options */
long i;
scan_eoln(infile);
for (i = 0; i < (chars); i++)
weight[i] = 1;
if (ancvar)
inputancestors(anczero0, ancone0);
if (factors)
inputfactors(chars, factor, &factors);
if (weights)
inputweights(chars, weight, &weights);
putchar('\n');
if (weights)
printweights(stdout, 0, chars, weight, "Characters");
if (factors)
printfactors(stdout, chars, factor, "");
for (i = 0; i < (chars); i++) {
if (!ancvar) {
anczero[i] = true;
ancone[i] = false;
} else {
anczero[i] = anczero0[i];
ancone[i] = ancone0[i];
}
}
if (ancvar)
printancestors(stdout, anczero, ancone);
if (!thresh)
threshold = spp;
questions = false;
for (i = 0; i < (chars); i++) {
questions = (questions || (ancone[i] && anczero[i]));
threshwt[i] = threshold * weight[i];
}
} /* inputoptions */
void inputoptions()
{
/* input the information on the options */
long weightsum, maxfactsize, i, j, k, l, m;
if (data == genefreqs) {
k = 0;
l = 0;
for (i = 0; i < (loci); i++) {
m = alleles[i];
k++;
for (j = 1; j <= m; j++) {
l++;
factorr[l - 1] = k;
}
}
} else {
for (i = 1; i <= (sites); i++)
factorr[i - 1] = i;
}
for (i = 0; i < (sites); i++)
oldweight[i] = 1;
if (weights)
inputweightsstr2(phyloweights->Str[0],0, sites, &weightsum, oldweight, &weights, "seqboot");
if (factors && printdata) {
for(i = 0; i < sites; i++)
factor[i] = (char)('0' + (factorr[i]%10));
printfactors(outfile, sites, factor, " (least significant digit)");
}
if (weights && printdata)
printweights(outfile, 0, sites, oldweight, "Sites");
for (i = 0; i < (loci); i++)
how_many[i] = 0;
for (i = 0; i < (loci); i++)
where[i] = 0;
for (i = 1; i <= (sites); i++) {
how_many[factorr[i - 1] - 1]++;
if (where[factorr[i - 1] - 1] == 0)
where[factorr[i - 1] - 1] = i;
}
groups = factorr[sites - 1];
newgroups = 0;
newsites = 0;
maxfactsize = 0;
for(i = 0 ; i < loci ; i++){
if(how_many[i] > maxfactsize){
maxfactsize = how_many[i];
}
}
maxnewsites = groups * maxfactsize;
allocnew();
for (i = 0; i < (groups); i++) {
if (oldweight[where[i] - 1] > 0) {
newgroups++;
newsites += how_many[i];
newwhere[newgroups - 1] = where[i];
newhowmany[newgroups - 1] = how_many[i];
}
}
} /* inputoptions */