void getalleles()
{ /* set up number of alleles at loci */
long i, j, m;
if (!firstset)
samenumsp(&loci, ith);
if (contchars ) {
totalleles = loci;
for (i = 1; i <= loci; i++) {
locus[i - 1] = i;
alleles[i - 1] = 1;
}
df = loci;
} else {
totalleles = 0;
scan_eoln(infile);
if (printdata) {
fprintf(outfile, "\nNumbers of alleles at the loci:\n");
fprintf(outfile, "------- -- ------- -- --- -----\n\n");
}
for (i = 1; i <= loci; i++) {
if (eoln(infile))
scan_eoln(infile);
if (fscanf(infile, "%ld", &alleles[i - 1]) != 1) {
printf("ERROR: Unable to read number of alleles at locus %ld\n", i);
exxit(-1);
}
if (alleles[i - 1] <= 0) {
printf("ERROR: Bad number of alleles: %ld at locus %ld\n", alleles[i-1], i);
exxit(-1);
}
totalleles += alleles[i - 1];
if (printdata)
fprintf(outfile, "%4ld", alleles[i - 1]);
}
locus = (long *)Malloc(totalleles*sizeof(long));
m = 0;
for (i = 1; i <= loci; i++) {
for (j = 0; j < alleles[i - 1]; j++)
locus[m+j] = i;
m += alleles[i - 1];
}
df = totalleles - loci;
}
allocview(&curtree, nonodes2, totalleles);
if (!usertree) {
allocview(&bestree, nonodes2, totalleles);
allocview(&priortree, nonodes2, totalleles);
if (njumble > 1)
allocview(&bestree2, nonodes2, totalleles);
}
for (i = 0; i < spp; i++)
x[i] = (phenotype3)Malloc(totalleles*sizeof(double));
pbar = (double *)Malloc(totalleles*sizeof(double));
if (usertree)
for (i = 0; i < MAXSHIMOTREES; i++)
l0gf[i] = (double *)Malloc(totalleles*sizeof(double));
if (printdata)
putc('\n', outfile);
} /* getalleles */
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 */
void inputoptions()
{
/* input the information on the options */
long i;
if(justwts) {
if(firstset) {
scan_eoln(infile);
if (ancvar) {
inputancestors(anczero0, ancone0);
}
if (mixture) {
inputmixture(wagner0);
}
}
for (i = 0; i < (chars); i++)
weight[i] = 1;
inputweights(chars, weight, &weights);
for (i = 0; i < (words); i++) {
if (mixture)
wagner[i] = wagner0[i];
else if (allsokal)
wagner[i] = 0;
else
wagner[i] = (1L << (bits + 1)) - (1L << 1);
}
}
else {
if (!firstset) {
samenumsp(&chars, ith);
}
scan_eoln(infile);
for (i = 0; i < (chars); i++)
weight[i] = 1;
if (ancvar) {
inputancestors(anczero0, ancone0);
}
if (mixture) {
inputmixture(wagner0);
}
if (weights)
inputweights(chars, weight, &weights);
for (i = 0; i < (words); i++) {
if (mixture)
wagner[i] = wagner0[i];
else if (allsokal)
wagner[i] = 0;
else
wagner[i] = (1L << (bits + 1)) - (1L << 1);
}
}
for (i = 0; i < (chars); i++) {
if (!ancvar) {
anczero[i] = true;
ancone[i] = (((1L << (i % bits + 1)) & wagner[i / bits]) != 0);
} else {
anczero[i] = anczero0[i];
ancone[i] = ancone0[i];
}
}
noroot = true;
questions = false;
for (i = 0; i < (chars); i++) {
if (weight[i] > 0) {
noroot = (noroot && ancone[i] && anczero[i] &&
((((1L << (i % bits + 1)) & wagner[i / bits]) != 0)
|| threshold <= 2.0));
}
questions = (questions || (ancone[i] && anczero[i]));
threshwt[i] = threshold * weight[i];
}
} /* inputoptions */