void seqboot_inputdata()
{
/* input the names and sequences for each species */
long i, j, k, l, m, n, basesread, basesnew=0;
double x;
Char charstate;
boolean allread, done;
nodep = matrix_char_new(spp, sites);
j = nmlngth + (sites + (sites - 1) / 10) / 2 - 5;
if (j < nmlngth - 1)
j = nmlngth - 1;
if (j > 37)
j = 37;
interleaved = (interleaved && ((data == seqs) || (data == restsites)));
basesread = 0;
allread = false;
while (!allread) {
/* eat white space -- if the separator line has spaces on it*/
do {
charstate = gettc(infile);
} while (charstate == ' ' || charstate == '\t');
ungetc(charstate, infile);
if (eoln(infile))
scan_eoln(infile);
i = 1;
while (i <= spp) {
if ((interleaved && basesread == 0) || !interleaved)
initname(i-1);
j = interleaved ? basesread : 0;
done = false;
while (!done && !eoff(infile)) {
if (interleaved)
done = true;
while (j < sites && !(eoln(infile) ||eoff(infile))) {
charstate = gettc(infile);
if (charstate == '\n' || charstate == '\t')
charstate = ' ';
if (charstate == ' ' ||
(data == seqs && charstate >= '0' && charstate <= '9'))
continue;
uppercase(&charstate);
j++;
if (charstate == '.')
charstate = nodep[0][j-1];
nodep[i-1][j-1] = charstate;
}
if (interleaved)
continue;
if (j < sites)
scan_eoln(infile);
else if (j == sites)
done = true;
}
if (interleaved && i == 1)
basesnew = j;
scan_eoln(infile);
if ((interleaved && j != basesnew) || ((!interleaved) && j != sites)) {
printf("\n\nERROR: sequences out of alignment at site %ld", j+1);
printf(" of species %ld\n\n", i);
exxit(-1);
}
i++;
}
if (interleaved) {
basesread = basesnew;
allread = (basesread == sites);
} else
allread = (i > spp);
}
if (!printdata)
return;
} /* seqboot_inputdata */
void restdist_inputdata()
{
/* read the species and sites data */
long i, j, k, l, sitesread = 0, sitesnew = 0;
Char ch;
boolean allread, done;
if (printdata)
putc('\n', outfile);
j = nmlngth + (sites + (sites - 1) / 10) / 2 - 5;
if (j < nmlngth - 1)
j = nmlngth - 1;
if (j > 39)
j = 39;
if (printdata) {
fprintf(outfile, "Name");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "Sites\n");
fprintf(outfile, "----");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "-----\n\n");
}
sitesread = 0;
allread = false;
while (!(allread)) {
allread = true;
if (eoln(infile)) {
fscanf(infile, "%*[^\n]");
getc(infile);
}
i = 1;
while (i <= spp ) {
if ((interleaved && sitesread == 0) || !interleaved)
initname(i - 1);
if (interleaved)
j = sitesread;
else
j = 0;
done = false;
while (!done && !eoff(infile)) {
if (interleaved)
done = true;
while (j < sites && !(eoln(infile) || eoff(infile))) {
ch = getc(infile);
if (ch == '\n')
ch = ' ';
if (ch == ' ')
continue;
uppercase(&ch);
if (ch != '1' && ch != '0' && ch != '+' && ch != '-' && ch != '?') {
printf(" WARNING -- BAD SYMBOL %c",ch);
printf(" AT POSITION %5ld OF SPECIES %3ld\n",j,i);
exxit(-1);
}
if (ch == '1')
ch = '+';
if (ch == '0')
ch = '-';
j++;
y[i - 1][j - 1] = ch;
}
if (interleaved)
continue;
if (j < sites) {
fscanf(infile, "%*[^\n]");
getc(infile);
} else if (j == sites)
done = true;
}
if (interleaved && i == 1)
sitesnew = j;
fscanf(infile, "%*[^\n]");
getc(infile);
if ((interleaved && j != sitesnew ) || ((!interleaved) && j != sites)){
printf("ERROR: SEQUENCES OUT OF ALIGNMENT\n");
exxit(-1);}
i++;
}
if (interleaved) {
sitesread = sitesnew;
allread = (sitesread == sites);
} else
allread = (i > spp);
}
if (printdata) {
for (i = 1; i <= ((sites - 1) / 60 + 1); i++) {
for (j = 0; j < spp; j++) {
for (k = 0; k < nmlngth; k++)
putc(nayme[j][k], outfile);
fprintf(outfile, " ");
l = i * 60;
if (l > sites)
l = sites;
for (k = (i - 1) * 60 + 1; k <= l; k++) {
putc(y[j][k - 1], outfile);
if (k % 10 == 0 && k % 60 != 0)
putc(' ', outfile);
}
putc('\n', outfile);
}
putc('\n', outfile);
}
putc('\n', outfile);
}
} /* restdist_inputdata */
void seqboot_inputdata()
{
/* input the names and sequences for each species */
long i, j, k, l, m, n, basesread, basesnew=0;
double x;
Char charstate;
boolean allread, done;
if (data == genefreqs) {
nodef = matrix_double_new(spp, sites);
} else {
nodep = matrix_char_new(spp, sites);
}
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");
if (data == genefreqs)
fprintf(outfile, " locus\n\n");
if (data == seqs)
fprintf(outfile, " site\n\n");
if (data == morphology)
fprintf(outfile, " character\n\n");
if (data == restsites)
fprintf(outfile, " site\n\n");
}
else {
if (ild) {
if (data == genefreqs)
fprintf(outfile, "Locus");
if (data == seqs)
fprintf(outfile, "Site");
if (data == morphology)
fprintf(outfile, "Character");
if (data == restsites)
fprintf(outfile, "Site");
fprintf(outfile, " order permuted\n\n");
} else {
if (lockhart)
if (data == genefreqs)
fprintf(outfile, "Locus");
if (data == seqs)
fprintf(outfile, "Site");
if (data == morphology)
fprintf(outfile, "Character");
if (data == restsites)
fprintf(outfile, "Site");
fprintf(outfile, " order permuted separately for each species\n\n");
}
}
}
}
if (data == genefreqs)
fprintf(outfile, "%3ld species, %3ld loci\n\n", spp, loci);
else {
fprintf(outfile, "%3ld species, ", spp);
if (data == seqs)
fprintf(outfile, "%3ld sites\n\n", sites);
else if (data == morphology)
fprintf(outfile, "%3ld characters\n\n", sites);
else if (data == restsites)
fprintf(outfile, "%3ld sites\n\n", sites);
}
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");
}
interleaved = (interleaved && ((data == seqs) || (data == restsites)));
if (data == genefreqs) {
for (i = 1; i <= (spp); i++) {
initname(i - 1);
j = 1;
while (j <= sites && !eoff(infile)) {
if (eoln(infile))
scan_eoln(infile);
if ( fscanf(infile, "%lf", &x) != 1) {
printf("ERROR: Invalid value for locus %ld of species %ld\n", j, i);
exxit(-1);
} else if ((unsigned)x > 1.0) {
printf("GENE FREQ OUTSIDE [0,1] in species %ld\n", i);
exxit(-1);
} else {
nodef[i - 1][j - 1] = x;
j++;
}
}
scan_eoln(infile);
}
return;
}
basesread = 0;
allread = false;
while (!allread) {
/* eat white space -- if the separator line has spaces on it*/
do {
charstate = gettc(infile);
} while (charstate == ' ' || charstate == '\t');
ungetc(charstate, infile);
if (eoln(infile))
scan_eoln(infile);
i = 1;
while (i <= spp) {
if ((interleaved && basesread == 0) || !interleaved)
initname(i-1);
j = interleaved ? basesread : 0;
done = false;
while (!done && !eoff(infile)) {
if (interleaved)
done = true;
while (j < sites && !(eoln(infile) ||eoff(infile))) {
charstate = gettc(infile);
if (charstate == '\n' || charstate == '\t')
charstate = ' ';
if (charstate == ' ' ||
(data == seqs && charstate >= '0' && charstate <= '9'))
continue;
uppercase(&charstate);
j++;
if (charstate == '.')
charstate = nodep[0][j-1];
nodep[i-1][j-1] = charstate;
}
if (interleaved)
continue;
if (j < sites)
scan_eoln(infile);
else if (j == sites)
done = true;
}
if (interleaved && i == 1)
basesnew = j;
scan_eoln(infile);
if ((interleaved && j != basesnew) || ((!interleaved) && j != sites)){
printf("\n\nERROR: sequences out of alignment at site %ld", j+1);
printf(" of species %ld\n\n", i);
exxit(-1);}
i++;
}
if (interleaved) {
basesread = basesnew;
allread = (basesread == sites);
} else
allread = (i > spp);
}
if (!printdata)
return;
if (data == genefreqs)
m = (sites - 1) / 8 + 1;
else
m = (sites - 1) / 60 + 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, " ");
if (data == genefreqs)
l = i * 8;
else
l = i * 60;
if (l > sites)
l = sites;
if (data == genefreqs)
n = (i - 1) * 8;
else
n = (i - 1) * 60;
for (k = n; k < l; k++) {
if (data == genefreqs)
fprintf(outfile, "%8.5f", nodef[j][k]);
else {
if (j + 1 > 1 && nodep[j][k] == nodep[0][k])
charstate = '.';
else
charstate = nodep[j][k];
putc(charstate, outfile);
if ((k + 1) % 10 == 0 && (k + 1) % 60 != 0)
putc(' ', outfile);
}
}
putc('\n', outfile);
}
putc('\n', outfile);
}
putc('\n', outfile);
} /* seqboot_inputdata */
void restdist_inputdata()
{
/* read the species and sites data */
long i, j, k, l, sitesread = 0, sitesnew = 0;
Char ch;
boolean allread, done;
if (printdata)
putc('\n', outfile);
j = nmlngth + (sites + (sites - 1) / 10) / 2 - 5;
if (j < nmlngth - 1)
j = nmlngth - 1;
if (j > 39)
j = 39;
if (printdata) {
fprintf(outfile, "Name");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "Sites\n");
fprintf(outfile, "----");
for (i = 1; i <= j; i++)
putc(' ', outfile);
fprintf(outfile, "-----\n\n");
}
sitesread = 0;
allread = false;
while (!(allread)) {
/* eat white space -- if the separator line has spaces on it*/
do {
ch = gettc(infile);
} while (ch == ' ' || ch == '\t');
ungetc(ch, infile);
if (eoln(infile))
scan_eoln(infile);
i = 1;
while (i <= spp ) {
if ((interleaved && sitesread == 0) || !interleaved)
initname(i - 1);
if (interleaved)
j = sitesread;
else
j = 0;
done = false;
while (!done && !eoff(infile)) {
if (interleaved)
done = true;
while (j < sites && !(eoln(infile) || eoff(infile))) {
ch = gettc(infile);
if (ch == '\n' || ch == '\t')
ch = ' ';
if (ch == ' ')
continue;
uppercase(&ch);
if (ch != '1' && ch != '0' && ch != '+' && ch != '-' && ch != '?') {
printf(" ERROR -- Bad symbol %c",ch);
printf(" at position %ld of species %ld\n", j+1, i);
exxit(-1);
}
if (ch == '1')
ch = '+';
if (ch == '0')
ch = '-';
j++;
y[i - 1][j - 1] = ch;
}
if (interleaved)
continue;
if (j < sites)
scan_eoln(infile);
else if (j == sites)
done = true;
}
if (interleaved && i == 1)
sitesnew = j;
scan_eoln(infile);
if ((interleaved && j != sitesnew ) || ((!interleaved) && j != sites)){
printf("ERROR: SEQUENCES OUT OF ALIGNMENT\n");
exxit(-1);}
i++;
}
if (interleaved) {
sitesread = sitesnew;
allread = (sitesread == sites);
} else
allread = (i > spp);
}
if (printdata) {
for (i = 1; i <= ((sites - 1) / 60 + 1); i++) {
for (j = 0; j < spp; j++) {
for (k = 0; k < nmlngth; k++)
putc(nayme[j][k], outfile);
fprintf(outfile, " ");
l = i * 60;
if (l > sites)
l = sites;
for (k = (i - 1) * 60 + 1; k <= l; k++) {
putc(y[j][k - 1], outfile);
if (k % 10 == 0 && k % 60 != 0)
putc(' ', outfile);
}
putc('\n', outfile);
}
putc('\n', outfile);
}
putc('\n', outfile);
}
} /* restdist_inputdata */