void treeout(node *p)
{ /* write out file with representation of final tree */
long i, n, w;
Char c;
double x;
if (p->tip) {
n = 0;
for (i = 1; i <= nmlngth; i++) {
if (nayme[p->index - 1][i - 1] != ' ')
n = i;
}
for (i = 0; i < n; i++) {
c = nayme[p->index - 1][i];
if (c == ' ')
c = '_';
putc(c, outtree);
}
col += n;
} else {
putc('(', outtree);
col++;
treeout(p->next->back);
putc(',', outtree);
col++;
if (col > 55) {
putc('\n', outtree);
col = 0;
}
treeout(p->next->next->back);
if (p == curtree.start) {
putc(',', outtree);
col++;
if (col > 45) {
putc('\n', outtree);
col = 0;
}
treeout(p->back);
}
putc(')', outtree);
col++;
}
x = p->v;
if (x > 0.0)
w = (long)(0.43429448222 * log(x));
else if (x == 0.0)
w = 0;
else
w = (long)(0.43429448222 * log(-x)) + 1;
if (w < 0)
w = 0;
if (p == curtree.start)
fprintf(outtree, ";\n");
else {
fprintf(outtree, ":%*.8f", (int)w + 7, x);
col += w + 8;
}
} /* treeout */
void treeout(node *p, long *col, double m, boolean njoin, node *start)
{
/* write out file with representation of final tree */
/* used in fitch & neighbor */
long i=0, n=0, w=0;
Char c;
double x=0.0;
if (p->tip) {
n = 0;
for (i = 1; i <= nmlngth; i++) {
if (nayme[p->index - 1][i - 1] != ' ')
n = i;
}
for (i = 0; i < n; i++) {
c = nayme[p->index - 1][i];
if (c == ' ')
c = '_';
putc(c, outtree);
}
*col += n;
} else {
putc('(', outtree);
(*col)++;
treeout(p->next->back, col, m, njoin, start);
putc(',', outtree);
(*col)++;
if (*col > 55) {
putc('\n', outtree);
*col = 0;
}
treeout(p->next->next->back, col, m, njoin, start);
if (p == start && njoin) {
putc(',', outtree);
treeout(p->back, col, m, njoin, start);
}
putc(')', outtree);
(*col)++;
}
x = p->v;
if (x > 0.0)
w = (long)(m * log(x));
else if (x == 0.0)
w = 0;
else
w = (long)(m * log(-x)) + 1;
if (w < 0)
w = 0;
if (p == start)
fprintf(outtree, ";\n");
else {
fprintf(outtree, ":%*.5f", (int) w + 7, x);
*col += w + 8;
}
} /* treeout */
void treeout(node *p, long nextree, long *col, node *root)
{
/* write out file with representation of final tree */
/* used in dollop, dolmove, dolpenny, & move */
long i, n;
Char c;
node *q;
if (p->tip) {
n = 0;
for (i = 1; i <= nmlngth; i++) {
if (nayme[p->index - 1][i - 1] != ' ')
n = i;
}
for (i = 0; i < n; i++) {
c = nayme[p->index - 1][i];
if (c == ' ')
c = '_';
putc(c, outtree);
}
*col += n;
} else {
q = p->next;
putc('(', outtree);
(*col)++;
while (q != p) {
treeout(q->back, nextree, col, root);
q = q->next;
if (q == p)
break;
putc(',', outtree);
(*col)++;
if (*col > 65) {
putc('\n', outtree);
*col = 0;
}
}
putc(')', outtree);
(*col)++;
}
if (p != root)
return;
if (nextree > 2)
fprintf(outtree, "[%6.4f];\n", 1.0 / (nextree - 1));
else
fprintf(outtree, ";\n");
} /* treeout */
void maketree()
{
/* construct the tree */
long i ;
inputdata(replicates, printdata, lower, upper, x, reps);
/* if (njoin && (spp < 3)) {
mexPrintf("\nERROR: Neighbor-Joining runs must have at least 3 species\n\n");
exxit(-1);
} */
if (progress)
putchar('\n');
if (ith == 1)
setuptree(&curtree, nonodes2 + 1);
for (i = 1; i <= spp; i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
for (i = 0; i < spp; i++)
cluster[i] = curtree.nodep[i];
jointree();
if (njoin)
curtree.start = curtree.nodep[outgrno - 1]->back;
printree(curtree.start, treeprint, njoin, (boolean)(!njoin));
if (treeprint)
summarize();
if (trout) {
col = 0;
if (njoin)
treeout(curtree.start, &col, 0.43429448222, njoin, curtree.start);
else
curtree.root = curtree.start,
treeoutr(curtree.start,&col,&curtree);
}
if (progress) {
mexPrintf("\nOutput written on file \"%s\"\n\n", outfilename);
if (trout)
mexPrintf("Tree written on file \"%s\"\n\n", outtreename);
}
} /* maketree */
void describe()
{
/* prints ancestors, steps and table of numbers of steps in
each character */
if (treeprint)
fprintf(outfile, "\nrequires a total of %10.3f\n", -like);
if (stepbox) {
putc('\n', outfile);
writesteps(weights, dollo, numsteps);
}
if (questions)
guesstates(guess);
if (ancseq) {
hypstates(fullset, dollo, guess, treenode, root, garbage, zeroanc, oneanc);
putc('\n', outfile);
}
putc('\n', outfile);
if (trout) {
col = 0;
treeout(root, nextree, &col, root);
}
} /* describe */
void summarize(long numtrees)
{
/* print out branch lengths etc. */
long i, j, totalnum;
fprintf(outfile, "\nremember:");
if (outgropt)
fprintf(outfile, " (although rooted by outgroup)");
fprintf(outfile, " this is an unrooted tree!\n\n");
if (!minev)
fprintf(outfile, "Sum of squares = %11.5f\n\n", -curtree.likelihood);
else
fprintf(outfile, "Sum of branch lengths = %11.5f\n\n", -curtree.likelihood);
if ((power == 2.0) && !minev) {
totalnum = 0;
for (i = 1; i <= nums; i++) {
for (j = 1; j <= nums; j++) {
if (i != j)
totalnum += reps[i - 1][j - 1];
}
}
fprintf(outfile, "Average percent standard deviation = ");
fprintf(outfile, "%11.5f\n\n",
100 * sqrt(-curtree.likelihood / (totalnum - 2)));
}
fprintf(outfile, "Between And Length\n");
fprintf(outfile, "------- --- ------\n");
describe(curtree.start->next->back);
describe(curtree.start->next->next->back);
describe(curtree.start->back);
fprintf(outfile, "\n\n");
if (trout) {
col = 0;
treeout(curtree.start, &col, 0.43429445222, true,
curtree.start);
}
} /* summarize */
void maketree()
{
/* construct the tree */
long i ;
inputdata(replicates, printdata, lower, upper, x, reps);
if (progress)
putchar('\n');
if (ith == 1)
setuptree(&curtree, nonodes2 + 1);
for (i = 1; i <= spp; i++)
enterorder[i - 1] = i;
if (jumble)
randumize(seed, enterorder);
for (i = 0; i < spp; i++)
cluster[i] = curtree.nodep[i];
jointree();
if (outgropt)
curtree.start = curtree.nodep[outgrno - 1]->back;
printree(&curtree, curtree.start->next,
treeprint, njoin, !njoin);
if (treeprint)
summarize();
if (trout) {
col = 0;
if (njoin)
treeout(curtree.start, &col, 0.43429448222, njoin, curtree.start);
else
curtree.root = curtree.start,
treeoutr(curtree.start,&col,&curtree);
}
if (progress) {
printf("\nOutput written on output file\n\n");
if (trout)
printf("Tree written on tree file\n\n");
}
} /* maketree */
void summarize(void)
{ /* print out branch lengths etc. */
double chilow,chihigh;
fprintf(outfile, "\nremember: ");
if (outgropt)
fprintf(outfile, "(although rooted by outgroup) ");
fprintf(outfile, "this is an unrooted tree!\n\n");
fprintf(outfile, "Ln Likelihood = %11.5f\n", curtree.likelihood);
if (df == 1) {
chilow = 0.000982;
chihigh = 5.02389;
} else if (df == 2) {
chilow = 0.05064;
chihigh = 7.3777;
} else {
chilow = 1.0 - 2.0 / (df * 9);
chihigh = chilow;
chilow -= 1.95996 * sqrt(2.0 / (df * 9));
chihigh += 1.95996 * sqrt(2.0 / (df * 9));
chilow *= chilow * chilow;
chihigh *= chihigh * chihigh;
}
fprintf(outfile, "\nBetween And Length");
fprintf(outfile, " Approx. Confidence Limits\n");
fprintf(outfile, "------- --- ------");
fprintf(outfile, " ------- ---------- ------\n");
describe(curtree.start->next->back, chilow,chihigh);
describe(curtree.start->next->next->back, chilow,chihigh);
describe(curtree.start->back, chilow, chihigh);
fprintf(outfile, "\n\n");
if (trout) {
col = 0;
treeout(curtree.start);
}
} /* summarize */
