void seqboot_inputdatafreq(AjPPhyloFreq freq)
{
/* input the names and sequences for each species */
long i, j, k, l, m, n;
double x;
ajint ipos=0;
nodef = (double **)Malloc(spp*sizeof(double *));
for (i = 0; i < (spp); i++)
nodef[i] = (double *)Malloc(sites*sizeof(double));
j = nmlngth + (sites + (sites - 1) / 10) / 2 - 5;
if (j < nmlngth - 1)
j = nmlngth - 1;
if (j > 37)
j = 37;
if (printdata) {
fprintf(outfile, "\nBootstrapping algorithm, version %s\n\n\n",VERSION);
if (bootstrap) {
if (blocksize > 1) {
if (regular)
fprintf(outfile, "Block-bootstrap with block size %ld\n\n", blocksize);
else
fprintf(outfile, "Partial (%2.0f%%) block-bootstrap with block size %ld\n\n",
100*fracsample, blocksize);
} else {
if (regular)
fprintf(outfile, "Bootstrap\n\n");
else
fprintf(outfile, "Partial (%2.0f%%) bootstrap\n\n", 100*fracsample);
}
} else {
if (jackknife) {
if (regular)
fprintf(outfile, "Delete-half Jackknife\n\n");
else
fprintf(outfile, "Delete-%2.0f%% Jackknife\n\n", 100*(1.0-fracsample));
} else {
if (permute) {
fprintf(outfile, "Species order permuted separately for each");
fprintf(outfile, " locus\n\n");
}
else {
if (ild) {
fprintf(outfile, "Locus");
fprintf(outfile, " order permuted\n\n");
} else {
if (lockhart)
fprintf(outfile, "Locus");
fprintf(outfile, " order permuted separately for each species\n\n");
}
}
}
}
fprintf(outfile, "%3ld species, %3ld loci\n\n", spp, loci);
fprintf(outfile, "Name");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "Data\n");
fprintf(outfile, "----");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "----\n\n");
}
for (i = 1; i <= (spp); i++) {
initnamefreq(freq,i - 1);
j = 1;
while (j <= sites) {
x = freq->Data[ipos++];
if ((unsigned)x > 1.0) {
printf("GENE FREQ OUTSIDE [0,1] in species %ld\n", i);
embExitBad();
} else {
nodef[i - 1][j - 1] = x;
j++;
}
}
}
if (!printdata)
return;
m = (sites - 1) / 8 + 1;
for (i = 1; i <= m; i++) {
for (j = 0; j < spp; j++) {
for (k = 0; k < nmlngth; k++)
putc(nayme[j][k], outfile);
fprintf(outfile, " ");
l = i * 8;
if (l > sites)
l = sites;
n = (i - 1) * 8;
for (k = n; k < l; k++) {
fprintf(outfile, "%8.5f", nodef[j][k]);
}
putc('\n', outfile);
}
putc('\n', outfile);
}
putc('\n', outfile);
} /* seqboot_inputdatafreq */
void inputdata()
{ /* read species data */
long i, j, k, l, m, m0, n, p;
double sum;
ajint ipos = 0;
if (printdata) {
fprintf(outfile, "\nName");
if (contchars)
fprintf(outfile, " Phenotypes\n");
else
fprintf(outfile, " Gene Frequencies\n");
fprintf(outfile, "----");
if (contchars)
fprintf(outfile, " ----------\n");
else
fprintf(outfile, " ---- -----------\n");
putc('\n', outfile);
if (!contchars) {
for (j = 1; j <= nmlngth - 8; j++)
putc(' ', outfile);
fprintf(outfile, "locus:");
p = 1;
for (j = 1; j <= loci; j++) {
if (all)
n = alleles[j - 1];
else
n = alleles[j - 1] - 1;
for (k = 1; k <= n; k++) {
fprintf(outfile, "%10ld", j);
if (p % 6 == 0 && (all || p < df)) {
putc('\n', outfile);
for (l = 1; l <= nmlngth - 2; l++)
putc(' ', outfile);
}
p++;
}
}
fprintf(outfile, "\n\n");
}
}
for (i = 0; i < spp; i++) {
initnamefreq(phylofreq, i);
if (printdata)
for (j = 0; j < nmlngth; j++)
putc(nayme[i][j], outfile);
m = 1;
p = 1;
for (j = 1; j <= loci; j++) {
m0 = m;
sum = 0.0;
if (contchars)
n = 1;
else if (all)
n = alleles[j - 1];
else
n = alleles[j - 1] - 1;
for (k = 1; k <= n; k++) {
x[i][m - 1] = phylofreq->Data[ipos++];
sum += x[i][m - 1];
if (!contchars && x[i][m - 1] < 0.0) {
printf("\n\nERROR: locus %ld in species %ld: an allele", j, i+1);
printf(" frequency is negative\n");
exxit(-1);
}
if (printdata) {
fprintf(outfile, "%10.5f", x[i][m - 1]);
if (p % 6 == 0 && (all || p < df)) {
putc('\n', outfile);
for (l = 1; l <= nmlngth; l++)
putc(' ', outfile);
}
}
p++;
m++;
}
if (all && !contchars) {
if (fabs(sum - 1.0) > epsilon2) {
printf(
"\n\nERROR: Locus %ld in species %ld: frequencies do not add up to 1\n",
j, i + 1);
printf("\nFrequencies are:\n");
for (l = m0; l <= m-3; l++)
printf("%f+", x[i][l]);
printf("%f = %f\n\n", x[i][m-2], sum);
exxit(-1);
} else {
for (l = 0; l <= m-2; l++)
x[i][l] /= sum;
}
}
if (!all && !contchars) {
x[i][m-1] = 1.0 - sum;
if (x[i][m-1] < 0.0) {
if (x[i][m-1] > -epsilon2) {
for (l = 0; l <= m-2; l++)
x[i][l] /= sum;
x[i][m-1] = 0.0;
} else {
printf("\n\nERROR: Locus %ld in species %ld: ", j, i + 1);
printf("frequencies add up to more than 1\n");
printf("\nFrequencies are:\n");
for (l = m0-1; l <= m-3; l++)
printf("%f+", x[i][l]);
printf("%f = %f\n\n", x[i][m-2], sum);
exxit(-1);
}
}
m++;
}
}
if (printdata)
putc('\n', outfile);
}
if (printdata)
putc('\n', outfile);
} /* inputdata */
